Non-Standard Errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Assessment of 53Mn deposition on Earth via accelerator mass spectrometry

The 53Mn flux onto Earth is a quantity relevant for different extraterrestrial and astrophysical questions. It is a proxy for related fluxes, such as supernova-produced material or interplanetary dust particles. In this work, we performed a first attempt to assess the 53Mn flux by measuring the 53Mn/10Be isotopic ratio in a 1400 L sample of molten Antarctic snow by AMS (Accelerator Mass Spectrometry). Using the 10Be production rate in the atmosphere, an upper limit of 5.5 × 103 atoms cm−2 yr−1 was estimated for the deposition of extraterrestrial 53Mn. This result is compatible with one of the two discrepant values existing in the literature.Fil: Rodrigues Ferreira Maltez, Dario Pablo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Comisión Nacional de Energía Atómica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Negri, Agustín E.. Universidad Nacional de San Martín. Instituto de Investigación en Ingeniería Ambiental; ArgentinaFil: Balpardo, Christian Guillermo. Comisión Nacional de Energía Atómica. Centro Atómico Ezeiza; ArgentinaFil: Arazi, Andres. Comisión Nacional de Energía Atómica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Faestermann, Thomas. Technische Universität München; AlemaniaFil: Fernandez Niello, Jorge Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Comisión Nacional de Energía Atómica; Argentina. Universidad Nacional de San Martín. Instituto de Investigación en Ingeniería Ambiental; ArgentinaFil: Fimiani, Leticia. Technische Universität München; AlemaniaFil: Gómez Guzmán, José Manuel. Technische Universität München; AlemaniaFil: Hain, Karin. Technische Universität München; AlemaniaFil: Korschinek, Gunther. Technische Universität München; AlemaniaFil: Ludwig, Peter. Technische Universität München; AlemaniaFil: Marti, Guillermo V.. Comisión Nacional de Energía Atómica; Argentin

Quality Control (2004/2005) Performed By The Latin American Society For Forensic Genetics (Sociedad Latinoamericana De Genética Forense)

Los estudios de genética forense en Latinoamérica son efectuados por laboratorios públicos y privados. La Sociedad Latinoamericana de Genética Forense (www.slagf.or g) posee un programa para favorecer la colaboración y la mejora de la calidad de los resultados obtenidos. El concepto básico del programa es que un caso de paternidad o forense ficticio es enviado y analizado por todos los laboratorios participantes. Además, se incluye un caso teórico para el cálculo del índice correspondiente. Este procedimiento es repetido una vez por año desde 2003, cuando la SLAGF fue creada, y los resultados se comparan con otros controles regionales llevados a cabo durante los años 1998 y 2003. Las muestras deben ser analizadas de acuerdo con los procedimientos y marcadores empleados habitualmente por cada participante. Los resultados se distribuyen a cada uno, y se detectan las variaciones intra e inter-laboratorio. El resultado de cada control de calidad es la base de una discusión para mejorar la calidad de los análisis de ADN, lo cual se ha ido produciendo desde 1998 hasta la fecha.Studies on forensic genetics in Latin America are performed at public and private laboratories. The Latin American Society for Forensic Genetics ( Sociedad Latinoamericana de Genética Forense ) (www.slagf.or g) has a joint program to increase the collaboration and to give support in quality improvement. The basic concept for the program is that one fictitious paternity or forensic case is shipped to and analyzed in all participating laboratories. In addition, a theoretical case is sent in order to do the index calculation. This procedure is repeated once a year since 2003, when the Society was created, and the results were compared with other regional controls performed before (1998 and 2000). The samples should be analyzed according to the local procedures and with the marker systems typically used. The results are distributed to the participating laboratories and both the intra and inter laboratory variations are to be focused upon. The results of each quality control are the basis for a discussion to improve the quality of the tests, as seen from 1998 to date.Fil: Penacino, G.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Álvarez, M.. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; Argentina. Sociedad Latinoamericana de Genética Forense; ArgentinaFil: Arce, V.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Arévalo, J.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Arrieta, G.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Barretto, R.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Basso, Nestor Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; Argentina. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Borja, L.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Carbajal, L. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Chiarello, A.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: de Santi, V.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Domínguez, V.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Espinoza, M.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Estrada, M.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Fortín, M.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Gaviria, A.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Gélvez, X.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Gentili, A.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Giugliani, R.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Gómez, M.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: González, P.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Gónzalez, S.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Gutiérrez, A.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Hau, J.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Iannacone, G.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Ibarra, A.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Iglesias, M.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Jaime, J.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: León, A.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Martínez, M.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Marti, M.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Martins, J.. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; ArgentinaFil: Olivera, Nelda Lila. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; Argentina. Sociedad Latinoamericana de Genética Forense; Argentina. Unidad de Análisis de ADN del Colegio Oficial de Farmacéuticos y Bioquímicos de Capital Federal; Argentin

Can the Inca site of Choqek'iraw be considered an agro-pastoral calendar?

International audience"Situated in the heart of the Vilcabamba cordillera in Peru, some 150 km northwest of Cuzco, the ancient Inca state capital, Choqek'iraw or Choquequirao (“the golden cradle” in Quechua), is one of the most beautiful achievements of Inca architecture, and one of the very few pre-Hispanic sites displaying large wall mosaics, the only one known from Inca times. This article will attempt to demonstrate that the figures represented on the walls convey cosmological significance and are laid out following textile principles. After describing the site and its geo-cultural setting, the mosaics' main characteristics will be examined in detail, in an attempt to grasp their meaning. Finally, the author suggests that some of the scenes depicted could have been inspired by pre-Columbian myths and could be linked to astronomical concepts." (source éditeur)"Ubicado en el corazón de la cordillera de Vilcabamba, a unos 150 kilómetros de Cuzco, la antigua capital del estado inca, Choqek'iraw o Choquequirao (la cuna del oro en quechua), es uno de los logros más hermosos de la arquitectura Inca y el único sitio de época inca, con un gran mosaico mural. En este trabajo se intentará demostrar que las figuras representadas en las paredes podrían transmitir significado cosmológico y se distribuyen siguiendo principios textiles. Asimismo, después de hacer una breve descripción del sitio, ubicándolo en sus contextos geográfico y cultural, se analizarán las principales decoraciones que allí se encuentran para tratar de entenderlas. Los temas representados podrían referirse a antiguos mitos andinos y concepciones de orden astronómicos." (source éditeur