Chemostratigraphy of Neoproterozoic carbonates: implications for 'blind dating'

The delta C-13(carb) and Sr-87/Sr-86 secular variations in Neoproteozoic seawater have been used for the purpose of 'isotope stratigraphy' but there are a number of problems that can preclude its routine use. In particular, it cannot be used with confidence for 'blind dating'. The compilation of isotopic data on carbonate rocks reveals a high level of inconsistency between various carbon isotope age curves constructed for Neoproteozoic seawater, caused by a relatively high frequency of both global and local delta C-13(carb) fluctuations combined with few reliable age determinations. Further complication is caused by the unresolved problem as to whether two or four glaciations, and associated negative delta C-13(carb) excursions, can be reliably documented. Carbon isotope stratigraphy cannot be used alone for geological correlation and 'blind dating'. Strontium isotope stratigraphy is a more reliable and precise tool for stratigraphic correlations and indirect age determinations. Combining strontium and carbon isotope stratigraphy, several discrete ages within the 590-544 Myr interval, and two age-groups at 660-610 and 740-690 Myr can be resolved

The flyby anomaly: a multivariate analysis approach

[EN] The flyby anomaly is the unexpected variation of the asymptotic post-encounter velocity of a spacecraft with respect to the pre-encounter velocity as it performs a slingshot manoeuvre. This effect has been detected in, at least, six flybys of the Earth but it has not appeared in other recent flybys. In order to find a pattern in these, apparently contradictory, data several phenomenological formulas have been proposed but all have failed to predict a new result in agreement with the observations. In this paper we use a multivariate dimensional analysis approach to propose a fitting of the data in terms of the local parameters at perigee, as it would occur if this anomaly comes from an unknown fifth force with latitude dependence. Under this assumption, we estimate the range of this force around 300 km .Acedo Rodríguez, L. (2017). The flyby anomaly: a multivariate analysis approach. Astrophysics and Space Science. 362(2):1-7. doi:10.1007/s10509-017-3025-zS173622Acedo, L.: Adv. Space Res. 54, 788 (2014). 1505.06884Acedo, L.: Universe 1, 422 (2015a)Acedo, L.: Galaxies 3, 113 (2015b)Acedo, L.: Mon. Not. R. Astron. Soc. 463(2), 2119 (2016)Acedo, L., Bel, L.: Astron. Nachr. (2016). 1602.03669Adler, S.L.: Int. J. Mod. Phys. A 25, 4577 (2010). 0908.2414 . doi: 10.1142/S0217751X10050706Adler, S.L.: In: Proceedings of the Conference in Honour of Murray Gellimann’s 80th Birthday, p. 352 (2011). doi: 10.1142/9789814335614_0032Anderson, J.D., Laing, P.A., Lau, E.L., Liu, A.S., Nieto, M.M., Turyshev, S.G.: Phys. Rev. D 65(8), 082004 (2002). gr-qc/0104064 . doi: 10.1103/PhysRevD.65.082004Anderson, J.D., Campbell, J.K., Ekelund, J.E., Ellis, J., Jordan, J.F.: Phys. Rev. Lett. 100(9), 091102 (2008). doi: 10.1103/PhysRevLett.100.091102Atchison, J.A., Peck, M.A., Streetman, B.J.: J. Guid. Control Dyn. 33, 1115 (2010). doi: 10.2514/1.47413Border, J.S., Pham, T., Bedrossian, A., Chang, C.: 2015 Delta Differential One-way Ranging in Dsn Telecommunication Link Design Handbook (810-005). http://deepspace.jpl.nasa.gov/dsndocs/810-005/210/210A.pdf . Accessed: 2016-11-17Burns, J.A.: Am. J. Phys. 44(10), 944 (1976). doi: 10.1119/1.10237Busack, H.-J.: arXiv e-prints 1312.1139 (2013)Butrica, A.J.: In: From Engineering Science to Big Science: The NACA and NASA Collier Trophy Research Project Winners, p. 251 (1998)Cahill, R.T.: arXiv e-prints 0804.0039 (2008)Chamberlin, A., Yeomans, D., Giorgini, J., Chodas, P.: 2016 Horizons Ephemeris System. http://ssd.jpl.nasa.gov/horizons.cgi . Accessed: 2016-10-27Danby, J.M.A.: Fundamentals of Celestial Mechanics, 2nd edn. 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Effects of cleaning methods upon preservation of stable isotopes and trace elements in shells of Cyprideis torosa (Crustacea, Ostracoda): implications for palaeoenvironmental reconstruction

The trace element (Sr/Ca and Mg/Ca) and stable isotope (δ¹⁸O and δ¹³C) geochemistry of fossil ostracod valves provide valuable information, particularly in lacustrine settings, on palaeo-water composition and palaeotemperature. The removal of sedimentary and organic contamination prior to geochemical analysis is essential to avoid bias of the results. Previous stable isotope and trace element work on ostracod shells has, however, employed different treatments for the removal of contamination beyond simple ‘manual’ cleaning using a paint brush and methanol under a low-power binocular microscope. For isotopic work pre-treatments include chemical oxidation, vacuum roasting and plasma ashing, and for trace element work sonication, chemical oxidation and reductive cleaning. The impact of different treatments on the geochemical composition of the valve calcite has not been evaluated in full, and a universal protocol has not been established. Here, a systematic investigation of the cleaning methods is undertaken using specimens of the ubiquitous euryhaline species, Cyprideis torosa. Cleaning methods are evaluated by undertaking paired analyses on a single carapace (comprising two valves); in modern ostracods, whose valves are assumed to be unaltered, the two valves should have identical geochemical and isotopic composition. Hence, when one valve is subjected to the chosen treatment and the other to simple manual cleaning any difference in composition can confidently be assigned to the treatment method. We show that certain cleaning methods have the potential to cause alteration to the geochemical signal, particularly Mg/Ca and δ¹⁸O, and hence have implications for palaeoenvironmental reconstructions. For trace element determinations we recommend cleaning by sonication and for stable isotope analysis, oxidation by hydrogen peroxide. These methods remove contamination, yet do not significantly alter the geochemical signal

Anomalous accelerations in spacecraft flybys of the Earth

[EN] The flyby anomaly is a persistent riddle in astrodynamics. Orbital analysis in several flybys of the Earth since the Galileo spacecraft flyby of the Earth in 1990 have shown that the asymptotic post-encounter velocity exhibits a difference with the initial velocity that cannot be attributed to conventional effects. To elucidate its origin, we have developed an orbital program for analyzing the trajectory of the spacecraft in the vicinity of the perigee, including both the Sun and the Moon¿s tidal perturbations and the geopotential zonal, tesseral and sectorial harmonics provided by the EGM96 model. The magnitude and direction of the anomalous acceleration acting upon the spacecraft can be estimated from the orbital determination program by comparing with the trajectories fitted to telemetry data as provided by the mission teams. This acceleration amounts to a fraction of a mm/s2 and decays very fast with altitude. The possibility of some new physics of gravity in the altitude range for spacecraft flybys is discussed.Acedo Rodríguez, L. (2017). Anomalous accelerations in spacecraft flybys of the Earth. Astrophysics and Space Science. 362(12):1-15. doi:10.1007/s10509-017-3205-xS11536212Acedo, L.: Galaxies 3, 113 (2015)Acedo, L.: Mon. Not. R. Astron. Soc. 463(2), 2119 (2016)Acedo, L.: Adv. Space Res. 59(7), 1715 (2017). 1701.06939Acedo, L., Bel, L.: Astron. Nachr. 338(1), 117 (2017). 1602.03669Adler, S.L.: Int. J. Mod. Phys. A 25, 4577 (2010). 0908.2414 . doi: 10.1142/S0217751X10050706Adler, S.L.: In: Proceedings of the Conference in Honour of Murray Gellimann’s 80th Birthday, p. 352 (2011). doi: 10.1142/9789814335614_0032Anderson, J.D., Nieto, M.M.: In: Klioner, S.A., Seidelmann, P.K., Soffel, M.H. (eds.) Relativity in Fundamental Astronomy: Dynamics, Reference Frames, and Data Analysis. 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Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures

BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which emerged in late 2019 has spread globally, causing a pandemic of respiratory illness designated coronavirus disease 2019 (COVID-19). A better definition of the pulmonary host response to SARS-CoV-2 infection is required to understand viral pathogenesis and to validate putative COVID-19 biomarkers that have been proposed in clinical studies. METHODS: Here, we use targeted transcriptomics of formalin-fixed paraffin-embedded tissue using the NanoString GeoMX platform to generate an in-depth picture of the pulmonary transcriptional landscape of COVID-19, pandemic H1N1 influenza and uninfected control patients. RESULTS: Host transcriptomics showed a significant upregulation of genes associated with inflammation, type I interferon production, coagulation and angiogenesis in the lungs of COVID-19 patients compared to non-infected controls. SARS-CoV-2 was non-uniformly distributed in lungs (emphasising the advantages of spatial transcriptomics) with the areas of high viral load associated with an increased type I interferon response. Once the dominant cell type present in the sample, within patient correlations and patient-patient variation, had been controlled for, only a very limited number of genes were differentially expressed between the lungs of fatal influenza and COVID-19 patients. Strikingly, the interferon-associated gene IFI27, previously identified as a useful blood biomarker to differentiate bacterial and viral lung infections, was significantly upregulated in the lungs of COVID-19 patients compared to patients with influenza. CONCLUSION: Collectively, these data demonstrate that spatial transcriptomics is a powerful tool to identify novel gene signatures within tissues, offering new insights into the pathogenesis of SARS-COV-2 to aid in patient triage and treatment.Arutha Kulasinghe, Chin Wee Tan, Anna Flavia Ribeiro dos Santos Miggiolaro, James Monkman, Habib SadeghiRad, Dharmesh D. Bhuva, Jarbas da Silva Motta Junior, Caroline Busatta Vaz de Paula, Seigo Nagashima, Cristina Pellegrino Baena, Paulo Souza-Fonseca-Guimaraes, Lucia de Noronha, Timothy McCulloch, Gustavo Rodrigues Rossi, Caroline Cooper, Benjamin Tang, Kirsty R. Short, Melissa J. Davis, Fernando Souza-Fonseca-Guimaraes, Gabrielle T. Belz, and Ken O, Byrn

Parental origin of sequence variants associated with complex diseases

To access publisher full text version of this article. Please click on the hyperlink in Additional Links fieldEffects of susceptibility variants may depend on from which parent they are inherited. Although many associations between sequence variants and human traits have been discovered through genome-wide associations, the impact of parental origin has largely been ignored. Here we show that for 38,167 Icelanders genotyped using single nucleotide polymorphism (SNP) chips, the parental origin of most alleles can be determined. For this we used a combination of genealogy and long-range phasing. We then focused on SNPs that associate with diseases and are within 500 kilobases of known imprinted genes. Seven independent SNP associations were examined. Five-one with breast cancer, one with basal-cell carcinoma and three with type 2 diabetes-have parental-origin-specific associations. These variants are located in two genomic regions, 11p15 and 7q32, each harbouring a cluster of imprinted genes. Furthermore, we observed a novel association between the SNP rs2334499 at 11p15 and type 2 diabetes. Here the allele that confers risk when paternally inherited is protective when maternally transmitted. We identified a differentially methylated CTCF-binding site at 11p15 and demonstrated correlation of rs2334499 with decreased methylation of that site.info:eu-repo/grantAgreement/EC/FP7/21807

Random effects diagonal metric multidimensional scaling models

By assuming a distribution for the subject weights in a diagonal metric (INDSCAL) multidimensional scaling model, the subject weights become random effects. Including random effects in multidimensional scaling models offers several advantages over traditional diagonal metric models such as those fitted by the INDSCAL, ALSCAL, and other multidimensional scaling programs. Unlike traditional models, the number of parameters does not increase with the number of subjects, and, because the distribution of the subject weights is modeled, the construction of linear models of the subject weights and the testing of those models is immediate. Here we define a random effects diagonal metric multidimensional scaling model, give computational algorithms, describe our experiences with these algorithms, and provide an example illustrating the use of the model and algorithms.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45758/1/11336_2005_Article_BF02295730.pd

Meta-analysis of type 2 Diabetes in African Americans Consortium

Type 2 diabetes (T2D) is more prevalent in African Americans than in Europeans. However, little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies (GWAS) in individuals of European ancestry. In order to investigate the genetic architecture of T2D in African Americans, the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium examined 17 GWAS on T2D comprising 8,284 cases and 15,543 controls in African Americans in stage 1 analysis. Single nucleotide polymorphisms (SNPs) association analysis was conducted in each study under the additive model after adjustment for age, sex, study site, and principal components. Meta-analysis of approximately 2.6 million genotyped and imputed SNPs in all studies was conducted using an inverse variance-weighted fixed effect model. Replications were performed to follow up 21 loci in up to 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry. We identified three known loci (TCF7L2, HMGA2 and KCNQ1) and two novel loci (HLA-B and INS-IGF2) at genome-wide significance (4.15 × 10(-94)<P<5 × 10(-8), odds ratio (OR)  = 1.09 to 1.36). Fine-mapping revealed that 88 of 158 previously identified T2D or glucose homeostasis loci demonstrated nominal to highly significant association (2.2 × 10(-23) < locus-wide P<0.05). These novel and previously identified loci yielded a sibling relative risk of 1.19, explaining 17.5% of the phenotypic variance of T2D on the liability scale in African Americans. Overall, this study identified two novel susceptibility loci for T2D in African Americans. A substantial number of previously reported loci are transferable to African Americans after accounting for linkage disequilibrium, enabling fine mapping of causal variants in trans-ethnic meta-analysis studies.Peer reviewe

Novel Loci for Adiponectin Levels and Their Influence on Type 2 Diabetes and Metabolic Traits : A Multi-Ethnic Meta-Analysis of 45,891 Individuals

J. Kaprio, S. Ripatti ja M.-L. Lokki työryhmien jäseniä.Peer reviewe