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Chan, Andy Lung Jan. "Education, Experience and Translator Certification as Signaling Mechanisms." FORUM / Revue internationale d’interprétation et de traduction / International Journal of Interpretation and Translation 8, no. 1 (April 1, 2010): 37–54. http://dx.doi.org/10.1075/forum.8.1.02cha.
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Alors que la demande en services de traduction a augmenté à cause de la mondialisation et de l’essor des technologiques de l’information et des communications, le caractère généralisé de l’usage d’Internet a également accru l’incertitude en matière d’embauche et, par conséquent, les coÛts de la recherche de traducteurs compétents. Afin d’examiner les effets indicateurs de la scolarité, de l’expérience et de l’agrément en traduction dans le processus de recrutement, Hong Kong a fait l'objet d'une étude de cas. Parmi les constats dégagés, mentionnons la fragmentation du marché de la traduction; le bas statut professionnel des traducteurs; le caractère généralisé de la traduction dans une deuxième langue; la surdépendance des employeurs envers le niveau de scolarisation comme indicateur de recrutement; une ignorance relative des divers agréments du domaine de la traduction; et l'importance accordée à l'expérience professionnelle et les connaissances en informatique. Même si le corpus de l’étude ne reflète que le marché de la traduction à Hong Kong, il pourrait s’en dégager des situations générales en matière de recrutement de traducteurs dans d'autres pays et régions bilingues.
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Chen, Daniel, and Darrell Duffie. "Market Fragmentation." American Economic Review 111, no. 7 (July 1, 2021): 2247–74. http://dx.doi.org/10.1257/aer.20200829.
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We model a simple market setting in which fragmentation of trade of the same asset across multiple exchanges improves allocative efficiency. Fragmentation reduces the inhibiting effect of price-impact avoidance on order submission. Although fragmentation reduces market depth on each exchange, it also isolates cross-exchange price impacts, leading to more aggressive overall order submission and better rebalancing of unwanted positions across traders. Fragmentation also has implications for the extent to which prices reveal traders’ private information. While a given exchange price is less informative in more fragmented markets, all exchange prices taken together are more informative. (JEL D47, D82, G14)
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van Veelen, P. A., U. R. Tjaden, and J. van der Greef. "Sequence-informative fragmentation in 252Cf-plasma desorption mass-spectrometry." Journal of Controlled Release 21, no. 1-3 (July 1992): 201. http://dx.doi.org/10.1016/0168-3659(92)90023-k.
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Haselmann, K. F., B. A. Budnik, F. Kjeldsen, M. L. Nielsen, J. V. Olsen, and R. A. Zubarev. "Electronic Excitation Gives Informative Fragmentation of Polypeptide Cations and Anions." European Journal of Mass Spectrometry 8, no. 2 (April 2002): 117–21. http://dx.doi.org/10.1255/ejms.479.
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A Fourier transform mass spectrometer is a versatile instrument with a range of available fragmentation techniques. Comparison of polypeptide fragmentation patterns revealed that the techniques involving electronic excitation, such as hot-electron-capture dissociation (HECD) and electron-detachment dissociation (EDD), are even more informative than vibrational excitation (VE) techniques such as collisional activation. For dications of the peptide KIMHASELMANN, 11 eV HECD cleaved all inter-residue links in at least two places, with up to five fragments characterizing each link. For dianions of the same molecule, VE produced only one backbone cleavage whereas EDD gave ten, including five internal cleavage fragments. This is consistent with the general postulate that homogeneous electronic excitation yields more types of cleavage than near-equilibrium processes such as VE.
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Vaidogas, Egidijus Rytas. "Bayesian Processing of Data on Bursts of Pressure Vessels." Information Technology and Control 50, no. 4 (December 16, 2021): 607–26. http://dx.doi.org/10.5755/j01.itc.50.4.29690.
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Two alternative Bayesian approaches are proposed for the prediction of fragmentation of pressure vessels triggered off by accidental explosions (bursts) of these containment structures. It is shown how to carry out this prediction with post-mortem data on fragment numbers counted after past explosion accidents. Results of the prediction are estimates of probabilities of individual fragment numbers. These estimates are expressed by means of Bayesian prior or posterior distributions. It is demonstrated how to elicit the prior distributions from relatively scarce post-mortem data on vessel fragmentations. Specifically, it is suggested to develop priors with two Bayesian models known as compound Poisson-gamma and multinomial-Dirichlet probability distributions. The available data is used to specify non-informative prior for Poisson parameter that is subsequently transformed into priors of individual fragment number probabilities. Alternatively, the data is applied to a specification of Dirichlet concentration parameters. The latter priors directly express epistemic uncertainty in the fragment number probabilities. Example calculations presented in the study demonstrate that the suggested non-informative prior distributions are responsive to updates with scarce data on vessel explosions. It is shown that priors specified with Poisson-gamma and multinomial-Dirichlet models differ tangibly; however, this difference decreases with increasing amount of new data. For the sake of brevity and concreteness, the study was limited to fire induced vessel bursts known as boiling liquid expanding vapour explosions (BLEVEs).
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Dong, Yalun, Martina Jelocnik, Amber Gillett, Ludovica Valenza, Gabriel Conroy, Dominique Potvin, and Renfu Shao. "Mitochondrial Genome Fragmentation Occurred Multiple Times Independently in Bird Lice of the Families Menoponidae and Laemobothriidae." Animals 13, no. 12 (June 20, 2023): 2046. http://dx.doi.org/10.3390/ani13122046.
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Mitochondrial (mt) genome fragmentation has been discovered in all five parvorders of parasitic lice (Phthiraptera). To explore whether minichromosomal characters derived from mt genome fragmentation are informative for phylogenetic studies, we sequenced the mt genomes of 17 species of bird lice in Menoponidae and Laemobothriidae (Amblycera). Four species of Menoponidae (Actornithophilus sp. 1 ex [pied oystercatcher], Act. sp. 2 ex [masked lapwing], Austromenopon sp. 2 ex [sooty tern and crested tern], Myr. sp. 1 ex [satin bowerbird]) have fragmented mt genomes, whereas the other 13 species retain the single-chromosome mt genomes. The two Actornithophilus species have five and six mt minichromosomes, respectively. Aus. sp. 2 ex [sooty tern and crested tern] has two mt minichromosomes, in contrast to Aus. sp. 1 ex [sooty shearwater], which has a single mt chromosome. Myr. sp. 1 ex [satin bowerbird] has four mt minichromosomes. When mapped on the phylogeny of Menoponidae and Laemobothriidae, it is evident that mt genome fragmentation has occurred multiple times independently among Menoponidae and Laemobothriidae species. We found derived mt minichromosomal characters shared between Myrsidea species, between Actornithophilus species, and between and among different ischnoceran genera, respectively. We conclude that while mt genome fragmentation as a general feature does not unite all the parasitic lice that have this feature, each independent mt genome fragmentation event does produce minichromosomal characters that can be informative for phylogenetic studies of parasitic lice at different taxonomic levels.
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van Veelen, P. A., U. R. Tjaden, J. van der Greef, and N. D. de With. "Sequence-Informative fragmentation in an 8.9 kDa oligopeptide using plasma desorption mass spectrometry." Organic Mass Spectrometry 26, no. 4 (April 1991): 345–46. http://dx.doi.org/10.1002/oms.1210260429.
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Zauner, Gerhild, Radoslaw P. Kozak, Richard A. Gardner, Daryl L. Fernandes, André M. Deelder, and Manfred Wuhrer. "Protein O-glycosylation analysis." Biological Chemistry 393, no. 8 (August 1, 2012): 687–708. http://dx.doi.org/10.1515/hsz-2012-0144.
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Abstract This review provides an overview on the methods available for analysis of O-glycosylation. Three major themes are addressed: analysis of released O-glycans including different O-glycan liberation, derivatization, and detection methods; analysis of formerly O-glycosylated peptides yielding information on O-glycan attachment sites; analysis of O-glycopeptides, representing by far the most informative but also most challenging approach for O-glycan analysis. Although there are various techniques available for the identification of O-linked oligosaccharides, the focus here is on MS fragmentation techniques such as collision-induced fragmentation, electron capture dissociation, and electron transfer dissociation. Finally, the O-glycan analytical challenges that need to be met will be discussed.
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Kong, Feng, Shao Sun, and Yifei Wang. "Comprehensive Understanding the Disaster-Causing Mechanism, Governance Dilemma and Targeted Countermeasures of Urban Pluvial Flooding in China." Water 13, no. 13 (June 25, 2021): 1762. http://dx.doi.org/10.3390/w13131762.
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Urban pluvial flooding in China has become one of the major challenges for sustainable development. This paper analyzes the impact of climate change, urbanization, and integrated disaster drivers on urban pluvial flooding hazards, starting from the disaster-causing mechanisms of urban pluvial flooding in China. This paper then analyzes the main features and progress of urban pluvial flooding governance in China. In particular, this paper describes the progress of sponge cities in China. On the basis of the above contents, this paper describes three manifestations of the fragmentation dilemma at the level of governance, namely, fragmentation in value integration due to conflicting management orders and service values, fragmentation in resource and power allocation due to the lack of vertical top-level design and blurred horizontal departmental management boundaries, and fragmentation in policy formulation and implementation due to outdated urban flood control standards and interdepartmental information compartmentalization. In response to the fragmentation dilemma in urban pluvial flooding management in China, this paper introduces the concept of holistic governance and clarifies the path of urban waterlogging management, i.e., forming a collaborative and diversified governance subjects, deeply optimizing the organizational structure of urban waterlogging management, creating a mature information-based governance platform, and improving the legal and rule of law construction model. This paper is informative for understanding the governance of urban pluvial flooding in China from a government-led management level.
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Nishikaze, Takashi. "Sensitive and Structure-Informative N-Glycosylation Analysis by MALDI-MS; Ionization, Fragmentation, and Derivatization." Mass Spectrometry 6, no. 1 (2017): A0060. http://dx.doi.org/10.5702/massspectrometry.a0060.
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Dolgikh, O. V., D. G. Dianova, and A. V. Krivtsov. "Sperm DNA fragmentation and total antiradical activity of sperm in men with exaggerated anamnesis." Russian Journal of Immunology 24, no. 3 (July 15, 2021): 387–90. http://dx.doi.org/10.46235/1028-7221-1033-sdf.
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Various intracellular and extracellular stimuli can promote excessive accumulation of reactive oxygen species and lead to detrimental effects on sperm function, in particular, damage to sperm DNA, thus often resulting into infertility. The aim of the study was to assess the degree of sperm DNA fragmentation by flow cytometry and to study total antiradical activity of sperm in men with infertility and chronic prostatitis using spectrophotometric technique. A total of 75 men were examined. The comparison group consisted of 45 men with chronic prostatitis beyond exacerbation. The observation group included 30 men with chronic prostatitis in remission state. We have found that in the subjects during the period of acute inflammation, pathological fragmentation of sperm DNA was revealed, being statistically significant (p = 0.004). It was registered 1.7 times more often than in the examined men during the remission of chronic prostatitis. Increased fragmentation of the sperm DNA was noted in 50% of men from comparison group. In the patients from observation group, the degree of sperm DNA fragmentation over reference ranges was observed in 80% of the subjects. In men diagnosed with chronic prostatitis at the exacerbation stage, there is a statistically significant (p 0.05) relationship between sperm DNA fragmentation and development of acute inflammatory process. It was shown that in the subjects from observation group, the mean value of antiradical sperm activity did not show statistically significant differences (p = 0.378) compared with results found in men from the comparison group. The presented results suggest a higher degree of sperm DNA fragmentation in the examined patients with chronic prostatitis at the stage of decompensation, which may point to excessively increased production of free radicals during the acute inflammatory process. Obviously, exacerbation of chronic prostatitis contributes to imbalance in the redox homeostatic system in men, thus creating prerequisites for excess of reactive oxygen species and significant fragmentation of sperm DNA. The identified changes, i.e., an increased sperm DNA fragmentation levels and a deficiency of total antiradical activity of sperm in men with chronic urogenital diseases, may play a pathogenetic role in occurrence and further development of infertility. The degree of sperm DNA fragmentation and markers of redox processes may serve as informative activity indices of the inflammatory process.
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Gao, Yang, Jiexun Bu, Zhou Peng, and Biwei Yang. "Radical Reactions in the Gas Phase: Recent Development and Application in Biomolecules." Journal of Spectroscopy 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/570863.
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This review summarizes recent literature describing the use of gas phase radical reactions for structural characterization of complex biomolecules other than peptides. Specifically, chemical derivatization, in-source chemical reaction, and gas phase ion/ion reactions have been demonstrated as effective ways to generate radical precursor ions that yield structural informative fragments complementary to those from conventional collision-induced dissociation (CID). Radical driven dissociation has been applied to a variety of biomolecules including peptides, nucleic acids, carbohydrates, and phospholipids. The majority of the molecules discussed in this review see limited fragmentation from conventional CID, and the gas phase radical reactions open up completely new dissociation channels for these molecules and therefore yield high fidelity confirmation of the structures of the target molecules. Due to the extensively studied peptide fragmentation, this review focuses only on nonpeptide biomolecules such as nucleic acids, carbohydrates, and phospholipids.
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Mosely, Jackie A., Benjamin S. Murray, and David Parker. "Electron-Capture Dissociation and Collision-Induced Dissociation of Lanthanide Metal–Ligand Complexes and Lanthanide Metal–Ligand Complexes Bound to Phosphopeptides." European Journal of Mass Spectrometry 15, no. 2 (April 2009): 145–55. http://dx.doi.org/10.1255/ejms.941.
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Collision-induced dissociation (CID) and electron-capture dissociation (ECD) of lanthanide metal(III)–ligand complexes and lanthanide metal(III)–ligand–phosphopeptide complexes have been investigated using a Fourier transform-ion cyclotron resonance mass spectrometer (FT-ICR MS). Ternary adducts were formed for [LnL3+ + solvent anion(s) n–](3– n)+ [Ln = europium, terbium and ytterbium, L = heptadentate ligand, solvent anion = acetate or trifluoromethane-sulphonate (triflate)]. Results show that ECD provides much more diagnostically useful information than CID. ECD was found to systematically cleave N–C bonds in the “arms” of the ligand, similar to the N–Cα cleavage of peptides, generating two fragmentation sites per arm of the ligand. The most intense and informative fragment ions were obtained from the terbium complex and it is believed that this is a consequence of terbium's greater reduction potential: the greater the reduction potential, the greater the ligand fragmentation; the lower the reduction potential, the more likely the molecule is to relinquish the solvent anion. The choice of solvent is also shown to be important. In general, the complexes studied fragment easily to lose CH3CO2H; however, particularly for ECD, the complexes retain the triflate anion causing the ligand to fragment instead, thus providing much more useful information. The triflate anion can be displaced by a phosphopeptide to create a lanthanide metal–ligand–phosphopeptide adduct. ECD is able to sequence the phosphopeptide, locating the site of phosphorylation bound to [LnL]3+ and also confirm the identity of the ligand. Small differences in the fragmentation of the lanthanide metal–ligand–phosphopeptide adducts follow the trend Eu < Tb < Yb suggesting that charge density may now be a more significant factor than metal ion reduction potential. ECD analysis of the triflate salts of the terbium complexes is most informative in developing a method to optimise structural information that can be gained from this group of molecules by mass spectrometry.
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Borunova, Seidfatima M., Dmitry A. Rudnyaev, and Pavel N. Abramov. "Evaluation of the reproductive qualities of rams-producers and the quality of sperm in terms of the DNA fragmentation index." Veterinariya, Zootekhniya i Biotekhnologiya 4, no. 113 (2023): 157–65. http://dx.doi.org/10.36871/vet.zoo.bio.202304017.
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The study of physical, biological and morphological parameters of sperm production, despite the strict criteria established by regulatory documents, does not always allow an objective assessment of fertility ram producers. The study of sperm production in terms of the DNA fragmentation index in addition to studies on morphological parameters will allow the most complete and objective assessment of the reproductive ability of the studied spermatozoa of ram producers. The informative value of this method of research, coupled with simplicity and low cost, allows us to recommend this study in the practice of evaluating sperm quality.
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Vorst, H. J., M. W. E. M. van Tilborg, P. A. van Veelen, U. R. Tjaden, and J. van der Greef. "Sequence-informative fragmentation of peptides up to a molecular weight of 4.6 kDa in plasma-desorption mass spectrometry." Rapid Communications in Mass Spectrometry 4, no. 6 (June 1990): 202–5. http://dx.doi.org/10.1002/rcm.1290040607.
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Gordeeva, M. S., I. A. Serdiukova, A. S. Krasichkov, and E. V. Parmon. "Analysis of Fragmentation QRS Complex and Early Repolarization Pattern in Patients with Myocardial Inflammatory Changes." Effective Pharmacotherapy 19, no. 5 (March 30, 2023): 14–22. http://dx.doi.org/10.33978/2307-3586-2023-19-5-14-22.
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Inflammatory changes in the myocardium create the prerequisites for the electrical instability of the myocardium, which can affect the ECG. It is promising to study relatively new electrocardiographic patterns: fragmentation of QRS (FQRS) and premature ventricular beats (FPVB) and early repolarization pattern (ERP) to improve the screening of patients with suspected myocarditis. Aim. To study FQRS, FPVB and ERP in patients with inflammatory changes in the myocardium. Material and methods. The study included 46 patients (78.3% male, 21.7% women) with suspected myocarditis. Age: median 47.5, quartile 37; 56.5. In all patients, the anamnesis, results of ECG, echocardiography, cardiac magnetic resonance imaging and endomyocardial biopsy were analyzed. Results. The patients were divided into three groups: the 1st – 20 patients with inflammatory and fibrotic changes in the myocardium, the 2nd – 20 patients with myocardial fibrosis without inflammatory, the 3rd – 6 patients without structural changes in the myocardium. FQRS in the 1st group was detected in 35% of the examined, in the 2nd – in 25%, in the 3rd – not registered. FPVB in the 1st group was determined in 55% of the examined, in the 2nd – in 30%, in the 3rd – in 33.3%. ERP in the 1st group was registered in 30% of the examined, in the 2nd group it was not detected, in the 3rd group – in 16.7%. FPVB and ERP were informative for the detection of inflammation (sensitivity – 57.9 and 85% respectively, specificity – 69.2 and 53.8% respectively). For the detection of fibrosis, FPVB proved to be the most informative (sensitivity – 80.0%, specificity – 59.1%). Conclusions. FQRS, FPVB, and ERP are significant ECG-markers for detecting both inflammatory changes in the myocardium and fibrosis. The use of these ECG-markers in routine clinical practice may have an impact on further management of patients with suspected myocarditis.
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Ershov, M. V. "The world and Russia in the environment of transformation: Is the economic recovery sustainable?" Voprosy Ekonomiki, no. 12 (December 6, 2023): 31–47. http://dx.doi.org/10.32609/0042-8736-2023-12-31-47.
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In 2023, there is an improvement in the trends of economic dynamics in the global economy, but there is a high probability that it will be only temporal. The processes of fragmentation of the world economy are intensifying, previous indicators of the state of the economy are becoming less informative. Regulators face a difficult choice regarding the mechanisms of economic policy. Russia is in no less difficult conditions, given the negative effect of the sanctions that are being implemented against it. Increasing the strength of the domestic economy and forming stable conditions in the financial market are the most important prerequisites for the successful solution of emerging problems.
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De Montis, Andrea, Vittorio Serra, Giovanna Calia, Daniele Trogu, and Antonio Ledda. "To Weight or Not to Weight, That Is the Question: The Design of a Composite Indicator of Landscape Fragmentation." Applied Sciences 11, no. 7 (April 2, 2021): 3208. http://dx.doi.org/10.3390/app11073208.
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Composite indicators (CIs), i.e., combinations of many indicators in a unique synthetizing measure, are useful for disentangling multisector phenomena. Prominent questions concern indicators’ weighting, which implies time-consuming activities and should be properly justified. Landscape fragmentation (LF), the subdivision of habitats in smaller and more isolated patches, has been studied through the composite index of landscape fragmentation (CILF). It was originally proposed by us as an unweighted combination of three LF indicators for the study of the phenomenon in Sardinia, Italy. In this paper, we aim at presenting a weighted release of the CILF and at developing the Hamletian question of whether weighting is worthwhile or not. We focus on the sensitivity of the composite to different algorithms combining three weighting patterns (equalization, extraction by principal component analysis, and expert judgment) and three indicators aggregation rules (weighted average mean, weighted geometric mean, and weighted generalized geometric mean). The exercise provides the reader with meaningful results. Higher sensitivity values signal that the effort of weighting leads to more informative composites. Otherwise, high robustness does not mean that weighting was not worthwhile. Weighting per se can be beneficial for more acceptable and viable decisional processes.
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MacLaurin, Cindy Lee, Jack Martin Miller, and Mary Frances Richardson. "Synthesis and fast atom bombardment mass spectrometry of the coordination complexes of the ligand 5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane." Canadian Journal of Chemistry 67, no. 5 (May 1, 1989): 797–803. http://dx.doi.org/10.1139/v89-121.
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Metal complexes containing the ligand 5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazatetradecane were synthesized and characterized using electron impact (EI) and fast atom bombardment (FAB). The FAB mass spectra were obtained in positive and negative ion mode. FAB in the positive ion mode proved to be the most successful technique for the identification of these compounds. The majority of the FAB spectra obtained were structurally informative, although not all showed molecular (M+) or quasimolecular ([M + H]+) ions. The fragmentations observed were characteristic of the ligands and the metal, and were interpreted based on the chemical and spectroscopic properties of these compounds. Keywords: FAB mass spectroscopy, tetraazacyclotetradecane complexes.
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Pacenti, Marco, Stefano Dugheri, Pietro Traldi, Filippo Degli Esposti, Nicola Perchiazzi, Elena Franchi, Massimo Calamante, et al. "New Automated and High-Throughput Quantitative Analysis of Urinary Ketones by Multifiber Exchange-Solid Phase Microextraction Coupled to Fast Gas Chromatography/Negative Chemical-Electron Ionization/Mass Spectrometry." Journal of Automated Methods and Management in Chemistry 2010 (2010): 1–13. http://dx.doi.org/10.1155/2010/972926.
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The present research is focused on automation, miniaturization, and system interaction with high throughput for multiple and specific Direct Immersion-Solid Phase Microextraction/Fast Gas Chromatography analysis of the urinary ketones. The specific Mass Spectrometry instrumentation, capable of supporting such the automated changeover from Negative Chemical to Electron Ionization mode, as well as the automation of the preparation procedure by new device called MultiFiber Exchange, through change of the fibers, allowed a friendly use of mass spectrometry apparatus with a number of advantages including reduced analyst time and greater reproducibility (2.01–5.32%). The detection limits for the seven ketones were less than 0.004 mg/L. For an innovative powerful meaning in high-throughput routine, the generality of the structurally informative Mass Spectrometry fragmentation patterns together with the chromatographic separation and software automation are also investigated.
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Curi, Rogério Abdallah, Monique Marcondes Krauskopf, Janaína Conte Hadlich, Marina Rufino Salinas Fortes, Dianne Margaret Vankan, Josineudson Augusto II Vasconcelos Silva, Henrique Nunes de Oliveira, and Marcílio Dias Silveira da Mota. "Candidate SNPs for carcass and meat traits in Nelore animals and in their crosses with Bos taurus." Pesquisa Agropecuária Brasileira 47, no. 2 (February 2012): 294–301. http://dx.doi.org/10.1590/s0100-204x2012000200019.
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The objective of this work was to evaluate the effects of single-nucleotide polymorphisms (SNPs) in the genes IGF1 (AF_017143.1:g.198C>T), MSTN (AF_320998.1:g.433C>A), MYOD1 (NC_007313:g.1274A>G) and MYF5 (NC_007303:g.1911A>G) on carcass and meat traits in Nelore (Bos indicus) and Nelore x B. taurus. A total of 300 animals were genotyped and phenotyped for rib eye area (REA), backfat thickness (BT), intramuscular fat (IF), shear force (SF) and myofibrillar fragmentation index (MFI). The effects of allele substitution for each SNP were estimated by regression of the evaluated phenotypes on the number of copies of a particular allele using the general linear model. The polymorphism at IGF1 was non-informative in Nelore animals. In crossbred animals, the IGF1 C allele was associated with greater REA. However, this relation was not significant after Bonferroni correction for multiple testing. The A allele of the MSTN polymorphism was absent in Nelore cattle and was only found in two crossbred animals. The polymorphisms of MYOD1 and MYF5 were little informative in Nelore animals with G allele frequency of 0.097 and A allele frequency of 0.031, respectively. These markers show no association with the analyzed traits in the total sample of evaluated animals.
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Goldstein, Rise B., Awapuhi K. Lee, Denise L. Haynie, Jeremy W. Luk, Brian J. Fairman, Danping Liu, Jacob S. Jeffers, Bruce G. Simons-Morton, and Stephen E. Gilman. "Neighbourhood disadvantage and depressive symptoms among adolescents followed into emerging adulthood." Journal of Epidemiology and Community Health 73, no. 7 (March 30, 2019): 590–97. http://dx.doi.org/10.1136/jech-2018-212004.
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BackgroundResidents of disadvantaged neighbourhoods report higher levels of depressive symptoms; however, few studies have employed prospective designs during adolescence, when depression tends to emerge. We examined associations of neighbourhood social fragmentation, income inequality and median household income with depressive symptoms in a nationally representative survey of adolescents.MethodsThe NEXT Generation Health Study enrolled 10th-grade students from 81 US high schools in the 2009–2010 school year. Depressive symptoms were assessed with the Modified Depression Scale (wave 1) and the paediatric Patient-Reported Outcome Measurement Information System (waves 2–6). Neighbourhood characteristics at waves 1, 3, 4, and 5 were measured at the census tract level using geolinked data from the American Community Survey 5-year estimates. We used linear mixed models to relate neighbourhood disadvantage to depressive symptoms controlling for neighbourhood and individual sociodemographic factors.ResultsNone of the models demonstrated evidence for associations of social fragmentation, income inequality or median household income with depressive symptoms.ConclusionDespite the prospective design, repeated measures and nationally representative sample, we detected no association between neighbourhood disadvantage and depressive symptoms. This association may not exist or may be too small to detect in a geographically dispersed sample. Given the public health significance of neighbourhood effects, future research should examine the developmental timing of neighbourhood effects across a wider range of ages than in the current sample, consider both objective and subjective measures of neighbourhood conditions, and use spatially informative techniques that account for conditions of nearby neighbourhoods.
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Helleur, R. J., and Pierre Thibault. "Optimization of pyrolysis–desorption chemical ionization mass spectrometry and tandem mass spectrometry of polysaccharides." Canadian Journal of Chemistry 72, no. 2 (February 1, 1994): 345–51. http://dx.doi.org/10.1139/v94-053.
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The operating conditions for pyrolysis–desorption ammonia chemical ionization mass spectrometry and tandem mass spectrometry have been optimized and the technique evaluated for the production and analysis of structurally-informative pyrolytic fragmentation ions corresponding to intact anhydrohexose oligosaccharides, using amylose as the model polysaccharide. Among the various parameters examined it was found that the nature of the solvent used to adhere the sample to the emitter coil and the configuration of the emitter and the rate at which it is heated all play important roles in determining the efficiency of the pyrolytic process and the production of high mass fragment ions. Adjustment of reagent gas pressure together with source temperature also influence the chemical integrity of high mass oligomeric pyrolysis products. Under optimal operating conditions using ammonia reagent gas, the analyses of cellulose, laminarin, agars, and chitin gave relatively abundant ions corresponding to ammonium (or protonated) adducts of up to anhydrohexose tetrasaccharide. More importantly, the generation of such higher mass fragment ions provided a sustained ionic current of sufficient duration to perform tandem mass spectrometric analyses.
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Zakic, Mirjana. "The complementary nature of poetic and musical systems in ritual visits to households." Muzikologija, no. 9 (2009): 133–52. http://dx.doi.org/10.2298/muz0909133z.
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Analysis of poetic texts of the ritual - processions (koledari, lazarice kraljice) in Southeastern Serbia has proved that poetical systems facilitate the differentiation at all levels of semantic relations connected to ritual practice: from denotatum (the current, real objects to which the individual ritual acts refers), specific designatum (mutual concept of given ritual marked with existing denotata), to universal designata (general concept of all rituals, marked with specific designata and content denotata). However with the frequent absence of indexic references (refrains, specific frames and lexemes), poetic texts have become universal in the denotation area of the general idea of fertility among all rituals, and the possibility of fragmentation/ analysis and reality segmentation, which derive from the high communication potential of the verbal system, which contributes towards making key connections with denotata on the syntagmatic plan of the ritual process. In contrast with that, musical texts (as articulated entities or music 'gestalts') are always contextualized and ritually recognizable on a paradigmatic level. In this article the differentiation of poetic and music informative values are stressed: semantic (under which meaning, the presence of objects in the text as a sign, is considered) and numeric (which assigns a numerical quantity of innovation in the text). In a semantic sense, the musical message (in relation to the idea of the ritual) and poetic message (according to a concrete object and possibly the idea of the given ritual) are highly informative. In a numerical sense, again, the values of this message are different. The musical message, at the level of the initial model (starting pattern) holds a highly informative value relating to extramusical concept (designatum). However, its numerical informative value is rapidly reduced by model repetition in further melostrophic appearances. A different principle is at stake when it comes to poetic structuralisation, in which a continuous flow of new verses (new content) produces increscent information. With such a mechanism, in a perceptual sense, the high redundancies of the musical model are being commutated. This redundancy of music content has the function of impacting and integrating it into individual and collective memory. The very thought of this parallel testifies to the frequently stressed differentiality of non-verbal and verbal communicational forms. During informational transfer 'syntax of non-verbal 'language' has to be much simpler than the syntax of spoken or written language'.
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Bai, Xiangqi, Billy T. Lau, Alison Almada, Sue Grimes, Tianqi Chen, Hojoon Lee, and Hanlee P. Ji. "Abstract 4920: A nanopore sequencing approach characterizes cell-free DNA methylation-fragmentomics profiles indicative of breast cancer in a large cohort." Cancer Research 84, no. 6_Supplement (March 22, 2024): 4920. http://dx.doi.org/10.1158/1538-7445.am2024-4920.
Full textAbstract:
Abstract The detection of breast cancer from cell-free DNA (cfDNA) offers a new approach with the potential to benefit individual screening and early detection. However, identifying breast cancer from cfDNA remains a major challenge when one uses conventional short-read sequencing. Methylation and DNA fragmentation characteristics provide highly informative biomarkers for detecting and monitoring cancer. To characterize these genomic features from cfDNA, we developed an approach using single molecule Nanopore sequencing. Single cfDNA molecules are sequenced intact with the methylation and fragment size directly extrapolated from Nanopore data. Moreover, our approach requires small amounts of cfDNA to discern specific genomic features from individual molecules. Thus, the use of Nanopore sequencing provides both methylation and fragment size as directly measured from native cfDNA without the use of any chemical processing or other molecular manipulation. We studied an extended breast cancer cohort with in total 1080 of samples, consisting of 440 untreated breast cancer patients and 640 healthy controls. Nanopore sequencing analysis of these cfDNA samples identified a range of 1 to 4 million CpG sites from 1 ml of plasma. Leveraging the cohort, we developed an ensemble classifier for breast cancer detection based on cfDNA methylation and fragmentation. The classifier leveraged a leave-one-out cross-validation (LOOCV) to generate predicted probability. We created nucleosome-specific methylation scores as the input features to the classifier, which scores quantified the similarity of each sample's methylation profile to a training set on a selected set of CpG sites associated with cancers. Furthermore, we also identified DNA fragmentation features, revealing distinct mono-nucleosome and di-nucleosome patterns that distinguish cancers from healthy controls. Aggregating the DNA nucleosome-specific scores and fragmentation features, we built an ensemble LOOCV random forest model. We applied the model to the breast cancer cohort and achieved a detection specificity of 74%, a sensitivity of 71%, and an overall accuracy of approximately 73%. The area under the receiver operating characteristic curve (AUROC) reached 80%. We validated the classifier with two external independent cohorts. Validation cohort 1 demonstrated as a specificity of 85%, a sensitivity of 80%, and overall accuracy of 83% with AUROC of 90%. Validation cohort 2 without controls demonstrated that the classifier achieved a sensitivity of 94%. Both validation sets confirm that our model can achieve excellent performance for early breast cancer detection. In summary, our findings demonstrate that nanopore sequencing provides cfDNA methylation and fragment profiling that enables breast cancer detection. This approach holds the potential to improve cancer diagnosis and treatment outcomes. Citation Format: Xiangqi Bai, Billy T. Lau, Alison Almada, Sue Grimes, Tianqi Chen, Hojoon Lee, Hanlee P. Ji. A nanopore sequencing approach characterizes cell-free DNA methylation-fragmentomics profiles indicative of breast cancer in a large cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4920.
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Cimatti, Irene, Silviya Ninova, Valeria Lanzilotto, Luigi Malavolti, Luca Rigamonti, Brunetto Cortigiani, Matteo Mannini, et al. "UHV deposition and characterization of a mononuclear iron(III) β-diketonate complex on Au(111)." Beilstein Journal of Nanotechnology 5 (November 18, 2014): 2139–48. http://dx.doi.org/10.3762/bjnano.5.223.
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The adsorption of the sterically hindered β-diketonate complex Fe(dpm)3, where Hdpm = dipivaloylmethane, on Au(111) was investigated by ultraviolet photoelectron spectroscopy (UPS) and scanning tunnelling microscopy (STM). The high volatility of the molecule limited the growth of the film to a few monolayers. While UPS evidenced the presence of the β-diketonate ligands on the surface, the integrity of the molecule on the surface could not be assessed. The low temperature STM images were more informative and at submonolayer coverage they showed the presence of regular domains characterized by a flat morphology and height of ≈0.3 nm. Along with these domains, tetra-lobed features adsorbed on the kinks of the herringbone were also observed. DFT-simulated images of the pristine molecule and its possible decomposition products allowed to assess the partial fragmentation of Fe(dpm)3 upon adsorption on the Au(111) surface. Structural features with intact molecules were only observed for the saturation coverage. An ex situ prepared thick film of the complex was also investigated by X-ray magnetic circular dichroism (XMCD) and features typical of high-spin iron(III) in octahedral environment were observed.
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Pös, Zuzana, Ondrej Pös, Jakub Styk, Angelika Mocova, Lucia Strieskova, Jaroslav Budis, Ludevit Kadasi, Jan Radvanszky, and Tomas Szemes. "Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes." International Journal of Molecular Sciences 21, no. 22 (November 16, 2020): 8634. http://dx.doi.org/10.3390/ijms21228634.
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Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.
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Spickett, Corinne M., and Norsyahida Mohd Fauzi. "Analysis of oxidized and chlorinated lipids by mass spectrometry and relevance to signalling." Biochemical Society Transactions 39, no. 5 (September 21, 2011): 1233–39. http://dx.doi.org/10.1042/bst0391233.
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Oxidized and chlorinated phospholipids are generated under inflammatory conditions and are increasingly understood to play important roles in diseases involving oxidative stress. MS is a sensitive and informative technique for monitoring phospholipid oxidation that can provide structural information and simultaneously detect a wide variety of oxidation products, including chain-shortened and -chlorinated phospholipids. MSn technologies involve fragmentation of the compounds to yield diagnostic fragment ions and thus assist in identification. Advanced methods such as neutral loss and precursor ion scanning can facilitate the analysis of specific oxidation products in complex biological samples. This is essential for determining the contributions of different phospholipid oxidation products in disease. While many pro-inflammatory signalling effects of oxPLs (oxidized phospholipids) have been reported, it has more recently become clear that they can also have anti-inflammatory effects in conditions such as infection and endotoxaemia. In contrast with free radical-generated oxPLs, the signalling effects of chlorinated lipids are much less well understood, but they appear to demonstrate mainly pro-inflammatory effects. Specific analysis of oxidized and chlorinated lipids and the determination of their molecular effects are crucial to understanding their role in disease pathology.
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Taylor, Zachary S., and Susan M. G. Hoffman. "Mitochondrial DNA genetic structure transcends natural boundaries in Great Lakes populations of woodland deer mice (Peromyscus maniculatus gracilis)." Canadian Journal of Zoology 88, no. 4 (April 2010): 404–15. http://dx.doi.org/10.1139/z10-010.
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The landscape of the Great Lakes region has been fragmented since the lakes formed starting about 20 000 years ago. Small mammals, such as deer mice ( Peromyscus maniculatus (Wagner, 1845)), inhabiting the region therefore face barriers to migration and gene flow, which could complicate ongoing range shifts related to climate change. We analyzed DNA sequences for 481 base pairs of the mitochondrial D-loop to compare mouse genetic structure with the fragmented landscape and geological history of the region. Phylogenetic analyses reveal two distinct lineages of mice in the Great Lakes region. The spatial distribution of these two groups is not congruent with the fragmentation of the landscape; rather, a western group is found from Minnesota through the western Upper Peninsula of Michigan, whereas an eastern group spans southern Ontario and the rest of northern Michigan. The genetic data suggest that the eastern clade colonized Michigan through Ontario from a source shared with southern Appalachian mice, but are less informative for the western clade. Together, these findings suggest that the Great Lakes are relatively porous barriers in the long term but may still have implications for the response of small-mammal communities to climate change.
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Chmelík, Josef, Pavel Řehulka, Vladimír Kováčik, Vladimír Pätoprstý, and Pavol Kováč. "Negative Matrix-Assisted Laser Desorption/Ionization Time-of-Flight/Time-of-Flight Tandem Mass Spectrometry Fragmentation of Synthetic Analogs of the O-Specific Polysaccharide of Vibrio Cholerae O:1 in the Presence of Anionic Dopants." European Journal of Mass Spectrometry 13, no. 5 (October 2007): 347–53. http://dx.doi.org/10.1255/ejms.891.
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Oligosaccharides (tri- to hexamers) that represent terminal epitopes of O-antigens of Vibrio cholerae O:1, serotypes Ogawa and Inaba, have been studied by negative matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDI-ToF/ToF MS). The [M – H+]− ions are formed after expulsion of a proton from molecules studied under MALDI/MS analysis conditions in the negative mode. Several ammonium salts (chloride, nitrate, hydrogencarbonate and hydrogensulfate) were used as additives to increase the formation of negative ions from saccharides. The most efficient was the addition of ammonium hydrogencarbonate, which increased the number of [M – H+]− ions more than six times. Between three fragmentation pathways, the new conjugated transfer of electrons within the second downstream unit of oligosaccharides was discovered. Production of these ions, which has not been observed in any other kinds of measurement, distinguishes substances belonging to Ogawa and Inaba serotypes. The negative MALDI-ToF/ToF mass spectra are simpler and, at the same time, more informative, as compared with positive and negative electrospray ionization ion trap as well as with positive MALDI-ToF/ToF analysis.
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Lacalle, Estíbaliz, Estela Fernández-Alegre, Belén Gómez-Giménez, Manuel Álvarez-Rodríguez, Beatriz Martín-Fernández, Cristina Soriano-Úbeda, and Felipe Martínez-Pastor. "Application of Flow Cytometry Using Advanced Chromatin Analyses for Assessing Changes in Sperm Structure and DNA Integrity in a Porcine Model." International Journal of Molecular Sciences 25, no. 4 (February 6, 2024): 1953. http://dx.doi.org/10.3390/ijms25041953.
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Chromatin status is critical for sperm fertility and reflects spermatogenic success. We tested a multivariate approach for studying pig sperm chromatin structure to capture its complexity with a set of quick and simple techniques, going beyond the usual assessment of DNA damage. Sperm doses from 36 boars (3 ejaculates/boar) were stored at 17 °C and analyzed on days 0 and 11. Analyses were: CASA (motility) and flow cytometry to assess sperm functionality and chromatin structure by SCSA (%DFI, DNA fragmentation; %HDS, chromatin maturity), monobromobimane (mBBr, tiol status/disulfide bridges between protamines), chromomycin A3 (CMA3, protamination), and 8-hydroxy-2′-deoxyguanosine (8-oxo-dG, DNA oxidative damage). Data were analyzed using linear models for the effects of boar and storage, correlations, and multivariate analysis as hierarchical clustering and principal component analysis (PCA). Storage reduced sperm quality parameters, mainly motility, with no critical oxidative stress increases, while chromatin status worsened slightly (%DFI and 8-oxo-dG increased while mBBr MFI—median fluorescence intensity—and disulfide bridge levels decreased). Boar significantly affected most chromatin variables except CMA3; storage also affected most variables except %HDS. At day 0, sperm chromatin variables clustered closely, except for CMA3, and %HDS and 8-oxo-dG correlated with many variables (notably, mBBr). After storage, the relation between %HDS and 8-oxo-dG remained, but correlations among other variables disappeared, and mBBr variables clustered separately. The PCA suggested a considerable influence of mBBr on sample variance, especially regarding storage, with SCSA and 8-oxo-dG affecting between-sample variability. Overall, CMA3 was the least informative, in contrast with results in other species. The combination of DNA fragmentation, DNA oxidation, chromatin compaction, and tiol status seems a good candidate for obtaining a complete picture of pig sperm nucleus status. It raises many questions for future molecular studies and deserves further research to establish its usefulness as a fertility predictor in multivariate models. The usefulness of CMA3 should be clarified.
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Abdel-Khalik, Jonas, Peter J. Crick, Eylan Yutuc, Yuqin Wang, and William J. Griffiths. "Developing an Enzyme-Assisted Derivatization Method for Analysis of C27 Bile Alcohols and Acids by Electrospray Ionization-Mass Spectrometry." Molecules 24, no. 3 (February 7, 2019): 597. http://dx.doi.org/10.3390/molecules24030597.
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Enzyme-assisted derivatization for sterol analysis (EADSA) is a technology designed to enhance sensitivity and specificity for sterol analysis using electrospray ionization–mass spectrometry. To date it has only been exploited on sterols with a 3β-hydroxy-5-ene or 3β-hydroxy-5α-hydrogen structure, using bacterial cholesterol oxidase enzyme to convert the 3β-hydroxy group to a 3-oxo group for subsequent derivatization with the positively charged Girard hydrazine reagents, or on substrates with a native oxo group. Here we describe an extension of the technology by substituting 3α-hydroxysteroid dehydrogenase (3α-HSD) for cholesterol oxidase, making the method applicable to sterols with a 3α-hydroxy-5β-hydrogen structure. The 3α-HSD enzyme works efficiently on bile alcohols and bile acids with this stereochemistry. However, as found by others, derivatization of the resultant 3-oxo group with a hydrazine reagent does not go to completion in the absence of a conjugating double bond in the sterol structure. Nevertheless, Girard P derivatives of bile alcohols and C27 acids give an intense molecular ion ([M]+) upon electrospray ionization and informative fragmentation spectra. The method shows promise for analysis of bile alcohols and 3α-hydroxy-5β-C27-acids, enhancing the range of sterols that can be analyzed at high sensitivity in sterolomic studies.
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Stukan, Maciej, Piotr Rutkowski, Jeremy Smadja, and Sylvie Bonvalot. "Ultrasound-Guided Trans-Uterine Cavity Core Needle Biopsy of Uterine Myometrial Tumors to Differentiate Sarcoma from a Benign Lesion—Description of the Method and Review of the Literature." Diagnostics 12, no. 6 (May 29, 2022): 1348. http://dx.doi.org/10.3390/diagnostics12061348.
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Uterine sarcomas are rare, aggressive tumors with poor prognosis that can be further negatively affected by inadequate surgical approaches such as morcellation. There are no clinical and radiologic criteria for differentiating leiomyoma from malignant uterine tumors. However, some ultrasonography and magnetic resonance imaging findings may be informative. We present a technique of ultrasound-guided trans-uterine cavity (UG-TUC) core needle biopsy for uterine lesions. As the procedure is an in-organ biopsy, there is no risk of needle canal contamination. The technique also enables the biopsy of lesions inaccessible by the transvaginal tru-cut biopsy. The core needle of the automatic biopsy system is inserted via the cervical canal into the uterine cavity and is directed and activated at the myometrial lesion under ultrasound control. The standard local treatment of localized uterine sarcomas is en bloc total hysterectomy; for fibroids, there are multiple options including conservative management or tumorectomy and tumor morcellation using minimally invasive techniques. Fragmentation of the sarcoma significantly worsens oncologic outcomes and should therefore be avoided. The UG-TUC core needle biopsy of uterine lesions can complement imaging to obtain sufficient material for histologic and molecular analyses of suspected or undetermined lesions, thus facilitating treatment planning and decreasing the risk of unsuspected sarcomas.
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Gordeeva, Mariya S., Elena V. Parmon, Veronika A. Karlina, and Darya V. Ryzhkova. "Fragmented QRS complex as a marker of myocardial fibrosis in patients with coronary artery disease." Science and Innovations in Medicine 7, no. 2 (April 29, 2022): 95–102. http://dx.doi.org/10.35693/2500-1388-2022-7-2-95-102.
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Aim to analyze the relationship between fQRS and myocardial fibrosis in CAD patients using SPECT.
Material and methods. Retrospectively, we have analyzed the anamnesis and examinations of 116 patients with suspected coronary heart disease. The fQRS was assessed according to the criteria of Das M. et al., 2006, along with the presence of a pathological Q wave and a slow increase in the amplitude of the R wave. We analysed the transient myocardial ischemia and/or myocardial scarring using stress/rest SPECT with technetium-99m.
Results. fQRS was significantly more frequently detected in patients with stable and partially reversible perfusion defects 44.1% and 52.2%, respectively, versus 13.0% and 5.5% in patients without perfusion defects or with reversible perfusion defects, p 0.05. Among 28 patients with QRS fragmentation and myocardial fibrosis, 19 (67.8%) had classical signs of fibrosis on the ECG, 9 (32.1%) had no ECG-registered fibrosis but fQRS was detected. The sensitivity of fQRS marker in detecting myocardial fibrosis reached 84.4%, the specificity was 63.3%.
Conclusion. fQRS complex is an informative marker for detecting myocardial scarring in patients with coronary artery disease. Analysis of fQRS in daily clinical practice may increase the diagnostic value of electrocardiography in the detection of fibrosis.
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Fukutome, Asuka, and Haruo Kawamoto. "Dehydration Leads to Hydrocarbon Gas Formation in Thermal Degradation of Gas-Phase Polyalcohols." Energies 13, no. 14 (July 20, 2020): 3726. http://dx.doi.org/10.3390/en13143726.
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To understand the molecular mechanisms of hydrocarbon gas formation in biomass gasification, gasification of simple polyalcohols (glycerol, propylene glycol, and ethylene glycol) were studied at 400, 600, and 800 °C (residence times: 0.9–1.4 s) from the viewpoint of dehydration reactions that form aldehydes with various substituents as intermediates to produce hydrocarbon gases. The results were also compared with those of glyceraldehyde and dihydroxyacetone, which are reported to produce syngas (H2 and CO) selectively. All polyalcohols became reactive at 600 °C to form condensable products in 15.7–24.7% yields (C-based), corresponding to 33.9–38.4% based on the amounts of reacted polyalcohols. These condensable products, mostly aldehydes, act as gas-forming intermediates, because the polyalcohols were completely gasified at 800 °C (hydrocarbon gas contents: 20.3–35.3%, C-based). Yields of the intermediates bearing alkyl groups at 600 °C were proportionally correlated to the yields of hydrocarbon gases at 800 °C, suggesting that the alkyl groups are further converted into hydrocarbon gases via the fragmentation of acyl radicals. Dehydration reactions were suggested to occur in both heterolytic and radical mechanisms by theoretical calculations. Glyceraldehyde tended to fragment directly into CO and H2, instead of forming a dehydration intermediate. These results are informative for controlling the product gas composition in biomass gasification.
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Quéméner, Bernard, Cédric Désiré, Marc Lahaye, Laurent Debrauwer, and Luc Negroni. "Structural Characterisation by Both Positive- and Negative-Ion Electrospray Mass Spectrometry of Partially Methyl-Esterified Oligogalacturonides Purified by Semi-Preparative High-Performance Anion-Exchange Chromatography." European Journal of Mass Spectrometry 9, no. 1 (February 2003): 45–60. http://dx.doi.org/10.1255/ejms.526.
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The off-line coupling of high-performance anion-exchange chromatography (HPAEC) to electrospray ionisation/ion trap mass spectrometry (ESI-ITMS) is described. The Dionex carbohydrate membrane desalter (CMD) has been assessed as an on-line chromatographic desalting system to remove the high sodium concentration necessary for the HPAEC separation of partially methyl-esterified oligogalacturonides. The developed HPAEC configuration proved to be suitable for indirect coupling with ESI-ITMS. This paper provides some interesting features of positive- and negative-ion multistage tandem mass spectrometry (MSn) analysis of these acidic oligosaccharides. The spectra acquired in both negative- and positive-ion modes show characteristic fragment ions resulting from glycosidic bond and cross-ring cleavages. Some new mass spectrometric fragmentation routes are also described. The positive-ion mode gave more complex spectra but was as informative as the negative-ion mode. ESI-ITMS was revealed to be, as previously reported from direct use on an unseparated enzymatic digest, a powerful sequencing technique for the determination of linkage type and the methyl ester distribution of partially methyl-esterified oligogalacturonides. Moreover, unlike matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-ToF MS), it gives valuable information on the elution behaviour of these oligomers in relation to their structure, namely the HPAEC co-elution of isomeric structures.
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Maslova, M. N. "Quantitative analysis of the ecological and economic balance and the structure of land use in the basin of the Tumannaya River." Geosystems of Transition Zones 7, no. 3 (2023): 316–30. http://dx.doi.org/10.30730/gtrz.2023.7.3.316-330.
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The article is devoted to the study of the structure of land use in the transboundary basin of the Tumannaya River. The map of land use within the Tumannaya River basin was compiled using remote sensing data. According to the basin approach, the territory was divided into the tributary basins of the first, second and third order using the ArcGIS software suite – a total of 21. The mapping results were analyzed by means of mathematical methods and quantitative techniques. The ecological and economic state of the transboundary basin has been found to have a low level of tension. The ecological and economic state of the floodplain is less balanced, for which low values of the natural protection coefficient have been identified. The minimum value of this coefficient is typical for the DPRK territory. The entropic measure of complexity and its derivatives as well as the Margalef index are more informative among the quantitative indicators. The floodplain parts of the basin within the PRC and the DPRK also have high values for most of the complexity indicators. Unlike the peripheral parts of the basin, they are more susceptible to anthropogenic effect. The Russian territory of the basin is the smallest in terms of the area, with less diversity in types of land use and greater fragmentation
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Perreault, Hélène, and Catherine E. Costello. "Differentiation of cerebroside isomers and study of fragmentation by liquid secondary ion mass spectrometry and mass spectrometry/mass spectrometry of selected derivatives." Canadian Journal of Chemistry 74, no. 9 (September 1, 1996): 1682–95. http://dx.doi.org/10.1139/v96-185.
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The possibility of distinguishing two cerebroside isomers, whose structural variation is in the sugar rings, was investigated by liquid secondary ion mass spectrometry (LSIMS) and tandem mass spectrometry (MS/MS). In addition to the native materials, four types of derivatives of these cerebroside isomers were prepared and studied using these techniques. A first level of comparison between isomers consisted of seeking differences in the conventional LSIMS spectra. Native compounds, galactosyl and glucosyl ceramides, did not yield consistent and meaningful elements of comparison and a few nanomoles of material were required to produce significant spectra. Permethylated cerebrosides gave rise to abundant ceramide ions that do not reveal information about sugar structure; relative abundances of low-mass sugar-related ions allowed isomeric discrimination to a limited extent. Peracetylated and perbenzoylated derivatives of both cerebrosides yielded several sugar-related ions whose relative abundances in the spectra varied systematically between species and allowed distinction of glucosyl- from galacto-cerebrosides. At a second level of comparison, collision-induced dissociation (CID) MS/MS spectra of selected ions containing the hexosyl residues and observed in the LSIMS spectra were recorded to study the extent and pathways of fragmentation for each isomer. Native and permethylated compounds led to disappointing results; on the other hand, peracetylated and perbenzoylated derivatives yielded informative spectra where isomeric differentiation was possible, mostly owing to the production of carbohydrate-related product ions, whereas native and permethylated compounds only produced ceramide-related ions upon CID MS/MS. Key words: glycosphingolipids, cerebrosides, derivatization, mass spectrometry, MS/MS, LSIMS.
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Zeng, Wenjuan, Yanyan Zhang, Wei Zheng, Qun Luo, Juanjuan Han, Jian’an Liu, Yao Zhao, Feifei Jia, Kui Wu, and Fuyi Wang. "Discovery of Cisplatin Binding to Thymine and Cytosine on a Single-Stranded Oligodeoxynucleotide by High Resolution FT-ICR Mass Spectrometry." Molecules 24, no. 10 (May 14, 2019): 1852. http://dx.doi.org/10.3390/molecules24101852.
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The clinically widely-used anticancer drug, cisplatin, binds strongly to DNA as a DNA-damaging agent. Herein, we investigated the interaction of cisplatin with a 15-mer single-stranded C,T-rich oligodeoxynucleotide, 5′-CCTT4CTT7G8C9T10TCTCC-3′ (ODN15), using ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in conjunction with tandem mass spectrometry (top-down MS). Top-down MS analysis with collision-induced dissociation (CID) fragmentation of the mono-platinated and di-platinated ODN15 provided abundant and informative Pt-containing or Pt-free a/[a − B], w and internal fragments, allowing the unambiguous identification of T4, T7, C9, and T10 as the platination sites on the cisplatin-ODN15 adducts. These results revealed that, in addition to the well-established guanine site, the unexpected thermodynamic binding of cisplatin to cytosine and thymine bases was also evident at the oligonucleotide level. Furthermore, the binding models of cisplatin with cytosine and thymine bases were built as the Pt coordinated to cytosine-N(3) and thymine-N(3) with displacement of the proton or tautomerization of thymine. These findings contribute to a better understanding of the mechanism of action of cisplatin and its preference for gene loci when the drug binds to cellular DNA, and also demonstrate the great potential and superiority of FT-ICR MS in studying the interactions of metallodrugs with large biomolecules.
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Sritongchuay, Tuanjit, Claire Kremen, and Sara Bumrungsri. "Effects of forest and cave proximity on fruit set of tree crops in tropical orchards in Southern Thailand." Journal of Tropical Ecology 32, no. 4 (July 2016): 269–79. http://dx.doi.org/10.1017/s0266467416000353.
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Abstract:Deforestation and forest fragmentation are contributing to declines in crop pollinator populations worldwide. Several studies have examined the impact of forest proximity on plant pollination ecology, but concentrated on single crop species. However, it can be more informative to investigate multiple crop and pollinator species in a community, because different pollinator groups may respond differently to forest distance. We evaluated flower visitor diversity, visitation frequency, and fruit set for three crop species (rambutan, durian and mango) in 10 pairs of mixed fruit orchards. Each pair consisted of one orchard near to (< 1 km) and one orchard far from (> 7 km) the forest edge. Rambutan fruit set was significantly influenced by distance to forest. The main visitors of rambutan flowers were stingless bees. In contrast, the dominant visitors to durian and mango flowers were nectarivorous bats and flies, respectively, and the fruit set of these crops were not significantly influenced by distance to forest. However, durian fruit set was negatively affected by distance to the nearest cave inhabited by nectarivorous bats. This study demonstrates that both caves and forests can be important pollinator sources for agricultural crops, and that the dispersal success of pollinators is related to isolation from source habitats. Maintaining forest patches and limestone karsts may provide stepping stones across fragmented landscapes, and attract greater numbers of pollinators to agricultural areas.
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Pernold, Karin, Eric Rullman, and Brun Ulfhake. "Bouts of rest and physical activity in C57BL/6J mice." PLOS ONE 18, no. 6 (June 26, 2023): e0280416. http://dx.doi.org/10.1371/journal.pone.0280416.
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The objective was to exploit the raw data output from a scalable home cage (type IIL IVC) monitoring (HCM) system (DVC®), to characterize pattern of undisrupted rest and physical activity (PA) of C57BL/6J mice. The system’s tracking algorithm show that mice in isolation spend 67% of the time in bouts of long rest (≥40s). Sixteen percent is physical activity (PA), split between local movements (6%) and locomotion (10%). Decomposition revealed that a day contains ˜7100 discrete bouts of short and long rest, local and locomotor movements. Mice travel ˜330m per day, mainly during the dark hours, while travelling speed is similar through the light-dark cycle. Locomotor bouts are usually <0.2m and <1% are >1m. Tracking revealed also fits of abnormal behaviour. The starting positions of the bouts showed no preference for the rear over the front of the cage floor, while there was a strong bias for the peripheral (75%) over the central floor area. The composition of bouts has a characteristic circadian pattern, however, intrusive husbandry routines increased bout fragmentation by ˜40%. Extracting electrode activations density (EAD) from the raw data yielded results close to those obtained with the tracking algorithm, with 81% of time in rest (<1 EAD s-1) and 19% in PA. Periods ≥40 s of file when no movement occurs and there is no EAD may correspond to periods of sleep (˜59% of file time). We confirm that EAD correlates closely with movement distance (rs>0.95) and the data agreed in ˜97% of the file time. Thus, albeit EAD being less informative it may serve as a proxy for PA and rest, enabling monitoring group housed mice. The data show that increasing density from one female to two males, and further to three male or female mice had the same effect size on EAD (˜2). In contrast, the EAD deviated significantly from this stepwise increase with 4 mice per cage, suggesting a crowdedness stress inducing sex specific adaptations. We conclude that informative metrics on rest and PA can be automatically extracted from the raw data flow in near-real time (< 1 hrs). As discussed, these metrics relay useful longitudinal information to those that use or care for the animals.
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Santibáñez-López, Carlos E., Oscar F. Francke, and L. Prendini. "Shining a light into the world’s deepest caves: phylogenetic systematics of the troglobiotic scorpion genus Alacran Francke, 1982 (Typhlochactidae : Alacraninae)." Invertebrate Systematics 28, no. 6 (2014): 643. http://dx.doi.org/10.1071/is14035.
Full textAbstract:
The scorpion genus Alacran Francke, 1982, endemic to eastern Mexico, was created to accommodate Alacran tartarus Francke, 1982. This remarkable troglobiotic species is adapted for life in some of the world’s deepest caves, 720–916 m below the surface in the Sistema Huautla of the state of Oaxaca (the deepest records at which a scorpion has been found). A second species, Alacran chamuco Francke, 2009, was later described from Te Cimutaá, also in Oaxaca. In the present contribution, we describe a third species, Alacran triquimera, sp. nov., recently discovered in a cave system in the state of Puebla, and test the monophyly and internal relationships of Alacran, based on a cladistic analysis of 10 terminal taxa (including seven species representing all four genera of Typhlochactidae) and 151 informative morphological characters, building on a previously published matrix. The single most parsimonious tree obtained, supports the monophyly of Alacran and the following relationships among its component species: (A. chamuco (A. tartarus + A. triquimera, sp. nov.)). The phylogenetic relationships among the three species of Alacran are consistent with the biogeographical history of the caves they inhabit. Based on the geological history of the Sierra Madre del Sur and the likely similar speleogenesis of the Tres Quimeras, Sistema Huautla and Te Cimutaá caves, we propose a vicariance hypothesis to account for the disjunct distribution of the three species of Alacran, whereby an initially more widespread, panmictic ancestral population speciated into three geographically isolated taxa following fragmentation of the southern Sierra Madre del Sur.
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Wehmas, Leah C., Charles E. Wood, Brian N. Chorley, Carole L. Yauk, Gail M. Nelson, and Susan D. Hester. "Enhanced Quality Metrics for Assessing RNA Derived From Archival Formalin-Fixed Paraffin-Embedded Tissue Samples." Toxicological Sciences 170, no. 2 (May 15, 2019): 357–73. http://dx.doi.org/10.1093/toxsci/kfz113.
Full textAbstract:
Abstract Formalin-fixed paraffin-embedded (FFPE) tissues provide an important resource for toxicogenomic research. However, variability in the integrity or quality of RNA obtained from archival FFPE specimens can lead to unreliable data and wasted resources, and standard protocols for measuring RNA integrity do not adequately assess the suitability of FFPE RNA. The main goal of this study was to identify improved methods for evaluating FFPE RNA quality for whole-genome sequencing. We examined RNA quality metrics conducted prior to RNA-sequencing in paired frozen and FFPE samples with varying levels of quality based on age in block and time in formalin. RNA quality was measured by the RNA integrity number (RIN), a modified RIN called the paraffin-embedded RNA metric, the percentage of RNA fragments >100–300 nucleotides in size (DV100–300), and 2 quantitative PCR-based methods. This information was correlated to sequencing read quality, mapping, and gene detection. Among fragmentation-based methods, DV and PCR-based metrics were more informative than RIN or paraffin-embedded RNA metric in determining sequencing success. Across low- and high-quality FFPE samples, a minimum of 80% of RNA fragments >100 nucleotides (DV100 > 80) provided the best indication of gene diversity and read counts upon sequencing. The PCR-based methods further showed quantitative reductions in amplifiable RNA of target genes related to sample age and time in formalin that inform input quantity of FFPE RNA for sequencing. These results should aid in screening and prioritizing archival FFPE samples for retrospective analyses of gene expression.
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Rosyid, Fathur. "Pragmatics of the Qur’an: Model Pemahaman Kisah Sayyidah Maryam yang Terikat Konteks." SUHUF 9, no. 2 (August 14, 2017): 321–42. http://dx.doi.org/10.22548/shf.v9i2.149.
Full textAbstract:
Abstrak
Kata Kunci: Pragamtik, Tindak Tutur, Implikatur, Kisah Sayyidah Maryam
Kisah Sayyidah Maryam dalam al-Qur’a>n merupakan salah-satu kisah yang menarik dikaji dengan pendekatan pragmatik. Hal ini disebabkan, secara tekstual, beliau adalah publik figur yang fenomenal, bahkan mengalahkan status sosial perempuan lainnya, sehingga namanya terdokumentasikan dalam satu surat khusus yang populer dengan sebutan â€Surat Maryamâ€. Kecuali itu, kisah tersebut juga termasuk kisah yang kaya dengan nuansa konteks. Sementara posisi ilmu prgamatik sendiri merupakan disiplin keilmuan yang mengkaji satuan bahasa dari sudut pandang relasi antara konteks linguistik yang bersifat diadik dan konteks non-linguistik yang bersifat triadik.
Penelitian ini hendak mengungkap dua hal; Pertama, apa yang dimaksud pragmatika al-Qur’a>n?. Kedua, bagaimana bentuk aplikasi pragmatik tindak tutur dan implikatur terhadap fragmentasi kisah kelahiran Sayyidah Maryam dalam al-Qur’an?. Tujuan kedua pertanyaan tersebut untuk memahami konsep prgamtika al-Qur’an, juga untuk mengungkap bentuk tindak tutur dan implikatur fragmentasi kisah kelahiran Sayyidah Maryam.
Penelitian ini menghasilkan kesimpulan; Pertama, pragmatika al-Qur’an adalah suatu disiplin ilmu yang mengkaji al-Qur’a>n dari sudut pandang relasi antara konteks kebahasaan dengan konteks non-kebahasaan. Kedua, tindak tutur fragmentasi kisah kelahiran Sayyidah Maryam yang terdapat dalam Qs. A<li ‘Imra>n (03): 36, lokusinya berupa kalimat informatif, sementara illokusinya merupakan bentuk kalimat asertif yang bermakna mengeluh. Adapun implikaturnya sebagai pelajaran, bahwa jika segala sesuatu telah dipasrahkan sama Allah swt. maka tidak pantas mencari kesalahan atas peraturan yang telah ditetapkan-Nya.
Abstract
Keywords: Pragamtik, Speech Acts, implicatures, Story of Sayyidah Maryam
The story of Sayyidah Maryam in the al-Qur'a>n is one-on-one interesting stories studied with a pragmatic approach. This is due, textually, he is a public figure who is phenomenal, even beating out other women's social status, so the name is documented in a special letter that is popularly known as "Surah Maryam". Except that, the story also included a story rich with nuances of context. While the position pragamatic science itself is a scientific discipline that examines unit of language from the perspective of the relationship between linguistic context that is both dyadic and non-linguistic context that is triadic.
This research seeks to reveal two things; First, what is meant pragmatic al-Qur'a>n?. Second, how the application form pragmatics of speech acts and implicatures to fragmentation birth story of Sayyidah Maryam in the al-Qur'a>n?. The second purpose of these questions to understand the concept pragamtic al-Qur'a>n, as well as to reveal the shape of speech acts and implicatures fragmentation of the birth story of Sayyidah Maryam.
This research resulted in the conclusion; First, the pragmatics of the al-Qur’a>n is a discipline that examines al-Qur'a>n from the viewpoint of the relationship between linguistic context with non-linguistic context. Second, the speech act fragmentation birth story of Sayyidah Maryam contained in Qs. A<li 'Imra>n (03): 36, locutionary acts be informative sentence, while illocutionary acts an assertive form meaningful sentences complaining. The implicature as a lesson,
that if everything was handled the same God, it is inappropriate to find fault with the regulations set his.
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Baygildiev, T. M., A. V. Braun, M. F. Vokuev, I. V. Rybalchenko, and I. A. Rodin. "Determination of nitrogen mustard metabolites in urine using high-performance liquid chromatography and high-resolution mass spectrometry." Industrial laboratory. Diagnostics of materials 87, no. 10 (October 18, 2021): 18–25. http://dx.doi.org/10.26896/1028-6861-2021-87-10-18-25.
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Detection of biologically active components in mixtures of complex composition which include biological fluids (blood, urine, etc.) is the most difficult problem of the analytical chemistry and requires the use of modern highly informative research methods. One of the most effective and universal ways to study the structure of unknown substances is the method of liquid chromatography- high resolution mass spectrometry that combines the possibility of highly selective separation of the mixtures under study, the reliable detection of unknown substances and high sensitivity of the procedure. We propose a method for the simultaneous extraction of highly polar biomarkers of nitrogen mustard — N-triethanolamine (TEA), N-ethyl diethanolamine (EDEA) and N-methyldiethanolamine (MDEA) — from urine with subsequent determination by HPLC and detection by high resolution tandem mass spectrometry. The mass spectra of fragmentation of protonated molecular ions of TEA, EDEA, and MDEA have been studied and possible structural formulas of the fragment ions are given. The sample preparation of urine and mass spectrometric detection in the multiple reaction monitoring mode were optimized. The five-fold dilution with deionized water was chosen as a method of urine sample preparation for analysis. Separation of the components was performed in the reversed-phase chromatography mode with retention times for TEA, EDEA, and MDEA of 2.00, 2.05, and 1.92 min, respectively. The time required to complete all steps of the urine sample analysis did not exceed 25 min. The detection limits in urine were 1 ng/ml for TEA and 2 ng/ml for EDEA and MDEA. The developed approach provides determination of the fact of application of specific nitrogen mustard in enquiry of possible exposure of living organism to the blister agents.
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Glybochko, Peter Vitalevich, Yuri Gennadevich Alyaev, Vadim Igorevich Rudenko, Leonid Mikhailovich Rapoport, Vagarshak Aramaisovich Grigoryan, Denis Victorovich Butnaru, Anna Nikolaevna Perekalina, Igor Georgievich Kraev, and Dmitry Olegovich Korolev. "The clinical role of X-ray computed tomography to predict the clinical efficiency of extracorporeal shock wave lithotripsy." Urologia Journal 86, no. 2 (March 26, 2018): 63–68. http://dx.doi.org/10.1177/0391560317749422.
Full textAbstract:
Aim: To evaluate the clinical efficiency of computed tomography for diagnostics of patients with urolithiasis and the choice of treatment strategy. Material and methods: The study was carried out at the Urological Clinic of I.M. Sechenov First Moscow State Medical University and included 1044 patients with urinary stones. The ultimate goal of this study was to predict the clinical efficiency of extracorporeal shock wave lithotripsy using a combination of computed tomography and densitometry. Extracorporeal shock wave lithotripsy was performed on “Siemens Lithostar Plus,” “Siemens Modularis Uro,” and “Dornier Gemini” lithotripters. Statistical analysis of clinical data included evaluation of individual sampling groups and calculation of weighted arithmetic mean ( M). Results: The efficiency of extracorporeal shock wave lithotripsy has been determined primarily using X-ray analysis of the concrement outlines and the structure (homogeneous or heterogeneous) of its central zone. However, in terms of efficiency and repetition rate (the number of fragmentation procedures required for complete clearance) of extracorporeal shock wave lithotripsy, the mean density of the concrement along the whole length of its three-dimensional structure (expressed in Hounsfield units) appeared to be the most reliable and informative predictive index in this study. Conclusion: The combination of computed tomography with densitometry in the treatment of patients with urolithiasis allows one (1) to determine the exact localization, size, X-ray structure, and structural density of urinary stones and (2) to predict, on the basis of densitometric data histograms, the clinical efficiency and repetition rate of extracorporeal shock wave lithotripsy with due regard to the X-ray structure of peripheral and central zones, and mean density (in Hounsfield units) of urinary concrements.
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Sarre, Stephen D., and Arthur Georges. "Genetics in conservation and wildlife management: a revolution since Caughley." Wildlife Research 36, no. 1 (2009): 70. http://dx.doi.org/10.1071/wr08066.
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In his 1994 review of conservation biology, Graeme Caughley questioned the central role for genetics in that discipline. His central theme was that there was no known case of genetic malfunction leading to the extinction of a population or species, and that driving forces such as overkill, habitat fragmentation and introduced predators as well as environmental and demographic stochasticity of small populations should be considered ahead of genetics in the debate about extinction prevention. At the time, only indirect and theoretical evidence existed for genetic contributions to the declines of wildlife and most of the debate revolved around the impact of genetic variation on fitness and long-term persistence. In addition, the application of DNA technologies to the study of wildlife was in its infancy. Though this was not Caughley’s intention, many within wildlife management took his criticisms of genetic aspects of species decline as the cue to dismiss this branch of science as of minor relevance to conservation biology. Since Caughley’s critique, there has been a revolution in genetic technologies for non-model organisms with the arrival of highly informative hypervariable DNA markers. Perhaps even more importantly, developments in DNA and gene technologies have provided the opportunity to study fundamental life-history traits such as disease resistance in more direct ways than previously possible. In concert with these tools, conservation geneticists have risen to Caughley’s challenge and demonstrated unambiguously a clear role for genetic analysis in conservation biology. Despite these impressive advances, there remains an important gap between the genetic approaches available and their uptake by managers. Bridging this gap will greatly increase the capacity of wildlife managers to generate the data necessary for sound management.
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Kusnerik, Kristopher M., Guy H. Means, Roger W. Portell, Mark Brenner, Quan Hua, Alshina Kannai, Ryan Means, Mariah A. Monroe, and Michał Kowalewski. "Live, dead, and fossil mollusks in Florida freshwater springs and spring-fed rivers: Taphonomic pathways and the formation of multisourced, time-averaged death assemblages." Paleobiology 46, no. 3 (July 20, 2020): 356–78. http://dx.doi.org/10.1017/pab.2020.25.
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AbstractTaphonomic processes are informative about the magnitude and timing of paleoecological changes but remain poorly understood with respect to freshwater invertebrates in spring-fed rivers and streams. We compared taphonomic alteration among freshwater gastropods in live, dead (surficial shell accumulations), and fossil (late Pleistocene–early Holocene in situ sediments) assemblages from two Florida spring-fed systems, the Wakulla and Silver/Ocklawaha Rivers. We assessed taphonomy of two gastropod species: the native Elimia floridensis (n = 2504) and introduced Melanoides tuberculata (n = 168). We quantified seven taphonomic attributes (aperture condition, color, fragmentation, abrasion, juvenile spire condition, dissolution, and exterior luster) and combined those attributes into a total taphonomic score (TT). Fossil E. floridensis specimens exhibited the greatest degradation (highest TT scores), whereas live specimens of both species were least degraded. Specimens of E. floridensis from death assemblages were less altered than fossil specimens of the same species. Within death assemblages, specimens of M. tuberculata were significantly less altered than specimens of E. floridensis, but highly degraded specimens dominated in both species. Radiocarbon dates on fossils clustered between 9792 and 7087 cal BP, whereas death assemblage ages ranged from 10,692 to 1173 cal BP. Possible explanations for the observed taphonomic patterns include: (1) rapid taphonomic shell alteration, (2) prolonged near-surface exposure to moderate alteration rates, and/or (3) introduction of reworked fossil shells into surficial assemblages. Combined radiocarbon dates and taphonomic analyses suggest that all these processes may have played a role in death assemblage formation. In these fluvial settings, shell accumulations develop as a complex mixture of specimens derived from multiple sources and characterized by multimillennial time-averaging. These findings suggest that, when available, fossil assemblages may be more appropriate than death assemblages for assessing preindustrial faunal associations and recent anthropogenic changes in freshwater ecosystems.
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McElwain, Mark A., Janice M. Olson, Camila Zanette, Karen Nguyen, Devon M. Fitzgerald, Isabel Y. Lee, Elizabeth Schmidt, et al. "Analytical Validation of a Duplex Sequencing AML Assay with a Limit of Detection Below 0.01% VAF for SNVs and Indels." Blood 142, Supplement 1 (November 28, 2023): 6020. http://dx.doi.org/10.1182/blood-2023-189955.
Full textAbstract:
Sensitive, specific, precise, and accurate detection of low frequency mutations in acute myeloid leukemia (AML) is critical to assess measurable residual disease (MRD). Next generation sequencing (NGS) assays are powerful tools for this, permitting interrogation of thousands of base positions across genomic regions of interest. However, PCR and sequencing errors in these assays limit accurate mutation detection at variant allele frequencies (VAF) below approximately 1%. Duplex sequencing (DS), an error-corrected NGS (ecNGS) method, greatly reduces such errors by relating original top and bottom DNA strands to make double stranded consensus sequences, thus enabling sensitive, specific, accurate, and precise detection of variants below 0.01% VAF. Here, we report analytical validation of an updated DuplexSeq™ AML assay, a 36-gene panel informed by 2022 European LeukemiaNet (ELN) recommendations combined with kitted library preparation reagents and a cloud-based analysis pipeline. The assay uniformly targets regions that harbor AML-associated mutations: 82% of targeted regions exhibit sequencing depth >80% of the panel-wide mean and >99.5% of targeted regions exhibit depth >20% of the panel-wide mean. These analytical studies also validate an improved “v2 chemistry” version of a DS library preparation kit. This improved chemistry provides an enzymatic fragmentation step that replaces time-consuming mechanical fragmentation methods while increasing the yield of duplex data for a given input mass of DNA sample and eliminating damage that results from mechanical fragmentation. A contrived human genomic DNA sample carrying 26 variants targeted by the panel, DNA extracted from AML-positive peripheral blood (PB) and bone marrow aspirate (BMA) specimens, and DNA extracted from healthy normal PB specimens were used as test samples to execute limit of detection (LoD), limit of blank (LoB), accuracy, linearity, and repeatability & reproducibility studies. In this assay a duplex depth threshold of ≥20,000x is applied; ≥91.8% of the 42,605 genomic base positions targeted by the panel are consistently (in 95% of analyzed libraries) above this threshold. The LoD study assayed samples carrying variants from 0.37% to 0.00055% VAF. The assay demonstrated excellent sensitivity, with variants down to 0.00055% VAF detected. A probit model was used to estimate the VAF at which 95% of variants would be detected, establishing an LoD of 0.008% VAF for single-nucleotide variants (SNVs) and insertions and deletions (indels) (see Figure 1). The LoB study assessed the background detection rate in DNA samples derived from healthy normal specimens. In >95% of sites surveyed, no variants were observed, establishing an assay LoB of 0 (0% VAF). Accuracy of the assay was determined by interrogating PB and BMA samples from AML-positive and -negative donors along with contrived test samples. Results were compared to data acquired via orthogonal methods. For variants above the LoD of 0.008% VAF, accuracy was high, with overall percent agreement (OPA) of 98.3%, positive percent agreement (PPA) of 100.0%, and negative percent agreement (NPA) of 98.3%. Data were linear from 0.0016% VAF to 96.1% VAF with R 2 = 0.95. All 6 expected FLT3-ITD variants, and all 5 expected NPM1 insertions were detected by the assay. Precision study data showed that the assay was highly repeatable, with OPA of 97.5%, PPA of 98.0%, and NPA of 97.3%. Reproducibility across 2 operators, 2 lots of reagents, and 3 independent runs of library preparation was also very high, with OPA of 97.5%, PPA of 98.8%, and NPA of 96.9%. Current ELN guidelines provisionally define NGS-MRD positivity as ≥0.1% VAF, but recent evidence suggests lower frequency variants may be informative. With an LoD of 0.008% VAF for SNVs and indels, and an LoB of 0, this novel AML assay comprising an updated gene panel coupled with improved duplex sequencing chemistry and software represents a highly sensitive, specific, accurate, and precise ecNGS assay for detecting variants associated with AML MRD.
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MCHUGH, JULIA B., STEPHANIE K. DRUMHELLER, MIRIAM KANE, ANJA RIEDEL, and JENNIFER H. NESTLER. "ASSESSING PALEOECOLOGICAL DATA RETENTION AMONG DISPARATE FIELD COLLECTION REGIMES: A CASE STUDY AT THE MYGATT-MOORE QUARRY (MORRISON FORMATION)." Palaios 38, no. 5 (May 31, 2023): 233–39. http://dx.doi.org/10.2110/palo.2022.048.
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ABSTRACT Field work protocols in the recovery of vertebrate fossils can vary between sites, and also within sites, due to differing researcher goals. Disparate researcher priorities can affect the resulting collections in terms of species richness, size distribution, specimen completeness, taphonomic condition, and aesthetic value. We examined paleoecological data, in the form of bone surface modifications (e.g., abrasion, feeding traces, etc.), from a single site worked by multiple collectors to determine the sensitivity of this type of data to collector bias. We examined 2,368 fossils from the Mygatt-Moore Quarry and divided them into two cohorts: 2016–2019 (bulk collection under a single collector) and pre-2016 (mixed collectors and priorities). Frequencies of modified bone surfaces were then calculated in each cohort among the recovered specimens. However, the specimens within the cohorts were of unequal size, completeness, and amount of preserved surface area, making inferences of modified bone surface frequencies difficult. To correct for unequal morphologies and preservation, we estimated the percentage of altered surface area among specimens by overlaying photos with a 4.0 cm2 digital grid to create a digital set of equal sized fragments. With such a large dataset, we took a random 10% subsample of specimens from each cohort for the grid study. We estimated the sample size needed to accurately reflect the frequency of bone surface modifications by specimen and surface area for each cohort. Results show the recovery of modified bone surfaces between the two cohorts was highly disparate, and potentially sensitive to the effects of collector bias when using specimen-level data. However, frequencies based on estimates of surface area were much more consistent and appeared to equalize data between cohorts and showed little influence of collector bias on data recovery. Thus, the traditional method of calculating frequencies using specimen-level data may create an illusion of bias that is removed when frequencies are calculated from estimated bone surface area. We posit that the digital fragmentation method is more informative when comparing paleoecological traces between datasets and should be applied to fossil assemblages going forward, especially when collection protocols between assemblages are significantly different or unknown.