13 research outputs found
Petrus Hispanus O.P. Auctor Summularum (III) ¿”Petrus Alfonsi” o “Petrus Ferrandi”?
No full textThis article aims to be a complement and continuation of my earlier work on the figure of Petrus Hispanus O. P., Auctor Summularum. First I bring to light some new documents in connection with the issues already examined in my 1997 and 2001 articles. Next, I deal with the questions postponed in my 2001 article: the problems concerning the figure of “Petrus Ferrandi” and his possible connection with the “auctor Summularum”, as well as Tugwell’s arguments against the hypothesis of the possible identity of the two figures, now examined from the perspective of the author of the Legenda prima. After analysing evidences from very diverse origin, I affirm, on the one hand, that the hypothesis of the identity of “Petrus Ferrandi” and “Petrus Hispanus” might be correct and, on the other hand, that there are no conclusive arguments that force us to affirm with certainty that the author of the Legenda prima is Pedro Ferrando. Although the analyses do not allow yet to determine whether the “auctor Summularum” is “Petrus Alfonsi” or “Petrus Ferrandi”, the evidence gathered and the connections set up will no doubt contribute to guide future research around the figure of “Petrus Hispanus”.Este artículo pretende ser complemento y continuación de mis anteriores trabajos sobre la figura de Petrus Hispanus O. P., Auctor Summularum. Comienzo presentando algunos nuevos documentos relacionados con las cuestiones ya examinadas en mis artículos de 1997 y 2001. A continuación, me ocupo de las cuestiones aplazadas en el artículo de 2001: los problemas relativos a la figura de “Petrus Ferrandi” y su posible relación con el “auctor Summularum”, así como los argumentos de Tugwell contra la hipótesis de la posible identidad de estas dos figuras, examinados ahora desde la perspectiva del autor de la Legenda prima. Tras analizar testimonios procedentes de muy diversos ámbitos, afirmo, por una parte, que la hipótesis de la identidad entre “Petrus Ferrandi” y “Petrus Hispanus” podría ser correcta y, por otra parte, que no hay argumentos concluyentes que obliguen a afirmar con seguridad que el autor de la Legenda prima es Pedro Ferrando. Aunque los análisis no permiten por el momento determinar si es “Petrus Alfonsi” o “Petrus Ferrandi” el “auctor Summularum”, los testimonios recogidos y las conexiones establecidas contribuirán, sin duda, a orientar futuras investigaciones en torno a la figura de “Petrus Hispanus”
HaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2
No full textAccurate and timely monitoring of the evolution of SARS-CoV-2 is crucial for identifying and tracking potentially more transmissible/virulent viral variants, and implement mitigation strategies to limit their spread. Here we introduce HaploCoV, a novel software framework that enables the exploration of SARS-CoV-2 genomic diversity through space and time, to identify novel emerging viral variants and prioritize variants of potential epidemiological interest in a rapid and unsupervised manner. HaploCoV can integrate with any classification/nomenclature and incorporates an effective scoring system for the prioritization of SARS-CoV-2 variants. By performing retrospective analyses of more than 11.5 M genome sequences we show that HaploCoV demonstrates high levels of accuracy and reproducibility and identifies the large majority of epidemiologically relevant viral variants - as flagged by international health authorities - automatically and with rapid turn-around times.Our results highlight the importance of the application of strategies based on the systematic analysis and integration of regional data for rapid identification of novel, emerging variants of SARS-CoV-2. We believe that the approach outlined in this study will contribute to relevant advances to current and future genomic surveillance methods
VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants
No full textWith the progression of the COVID-19 pandemic, large datasets of SARS-CoV-2 genome sequences were collected to closely monitor the evolution of the virus and identify the novel variants/strains. By analyzing genome sequencing data, health authorities can 'hunt' novel emerging variants of SARS-CoV-2 as early as possible, and then monitor their evolution and spread. We designed VariantHunter, a highly flexible and user-friendly tool for systematically monitoring the evolution of SARS-CoV-2 at global and regional levels. In VariantHunter, amino acid changes are analyzed over an interval of 4 weeks in an arbitrary geographical area (continent, country, or region); for every week in the interval, the prevalence is computed and changes are ranked based on their increase or decrease in prevalence. VariantHunter supports two main types of analysis: lineage-independent and lineage-specific. The former considers all the available data and aims to discover new viral variants. The latter evaluates specific lineages/viral variants to identify novel candidate designations (sub-lineages and sub-variants). Both analyses use simple statistics and visual representations (diffusion charts and heatmaps) to track viral evolution. A dataset explorer allows users to visualize available data and refine their selection. VariantHunter is a web application free to all users. The two types of supported analysis (lineage-independent and lineage-specific) allow user-friendly monitoring of the viral evolution, empowering genomic surveillance without requiring any computational background. Database URL http://gmql.eu/variant_hunter/
mapPat: tracking pathogens evolution in space and time
No full textMotivation: The COVID-19 pandemic highlighted the importance of genomic surveillance for monitoring pathogens evolution, mitigating the spread of infectious disorders, and informing decision-making by public health authorities. Since the need for the summarization and interpretation of large bodies of data, computational methods are critical for the implementation of effective genomic surveillance strategies. Results: Here, we introduce mapPat, an R Shiny application for the interactive visualization of pathogens genomic data in space and time. mapPat is designed as a user-friendly dashboard and allows the dynamic monitoring of the evolution of variants, lineages, and mutations in the genome of a pathogen at glance through informative geographic maps and elegant data visuals. mapPat provides a fine-grained map of pathogens evolution and circulation and represents a useful addition to the catalogue of bioinformatics methods for the genomic surveillance of pathogens. Availability and implementation: mapPat is available at GitHub (https://github.com/F3rika/mapPat.git)
Ascan: a novel method for the study of allele specific expression in single individuals
No full textIn diploid organisms, two copies of each allele are normally inherited from parents. Paternal and maternal alleles can be regulated and expressed unequally, which is referred to as allele-specific expression (ASE). In this work, we present aScan, a novel method for the identification of ASE from the analysis of matched individual genomic and RNA sequencing data. By performing extensive analyses of both real and simulated data, we demonstrate that aScan can correctly identify ASE with high accuracy and sensitivity in different experimental settings. Additionally, by applying our method to a small cohort of individuals that are not included in publicly available databases of human genetic variation, we outline the value of possible applications of ASE analysis in single individuals for deriving a more accurate annotation of "private" low-frequency genetic variants associated with regulatory effects on transcription. All in all, we believe that aScan will represent a beneficial addition to the set of bioinformatics tools for the analysis of ASE. Finally, while our method was initially conceived for the analysis of RNA-seq data, it can in principle be applied to any quantitative NGS assay for which matched genotypic and expression data are available. Availability: aScan is currently available in the form of an open source standalone software package at: https://github.com/Federico77z/aScan/. aScan version 1.0.3, available at https://github.com/Federico77z/aScan/releases/tag/1.0.3, has been used for all the analyses included in this manuscript. A Docker image of the tool has also been made available at https://github.com/pmandreoli/aScanDocker
Adducin- and Ouabain-Related Gene Variants Predict the Antihypertensive Activity of Rostafuroxin. Part 2: Clinical Studies
No full textTwenty years of genetic studies have not contributed to improvement in the clinical management of primary arterial hypertension. Genetic heterogeneity, epistatic-environmental-biological interactions, and the pathophysiological complexity of hypertension have hampered the clinical application of genetic findings. In the companion article, we furnished data from rodents and human cells demonstrating two hypertension-triggering mechanisms-variants of adducin and elevated concentrations of endogenous ouabain (within a particular range)-and their selective inhibition by the drug rostafuroxin. Here, we have investigated the relationship between variants of genes encoding enzymes for ouabain synthesis [LSS (lanosterol synthase) and HSD3B1 (hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1)], ouabain transport {MDR1/ABCB1 [ATP-binding cassette, sub-family B (MDR/TAP), member 1]}, and adducin activity [ADD1 (adducin 1) and ADD3], and the responses to antihypertensive medications. We determined the presence of these variants in newly recruited, never-treated patients. The genetic profile defined by these variants predicted the antihypertensive effect of rostafuroxin (a mean placebo-corrected systolic blood pressure fall of 14 millimeters of mercury) but not that of losartan or hydrochlorothiazide. The magnitude of the rostafuroxin antihypertensive effect was twice that of antihypertensive drugs recently tested in phase 2 clinical trials. One-quarter of patients with primary hypertension display these variants of adducin or concentrations of endogenous ouabain and would be expected to respond to therapy with rostafuroxin. Because the mechanisms that are inhibited by rostafuroxin also underlie hypertension-related organ damage, this drug may also reduce the cardiovascular risk in these patients beyond that expected by the reduction in systolic blood pressure alone
MorphoSys reconfigurable hardware for cryptography: The twofish case
No full textThis paper presents the mapping and performance analysis of the Twofish algorithm on MorphoSys. MorphoSys is a reconfigurable architecture that can provide high performance compared to custom hardware and yet preserves a level of flexibility compared to general-purpose processors.With today's high demand for secure data transfer mediums including wired and wireless networks, there is a growing demand for real-time implementation of cryptographic algorithms. The choice of the Twofish algorithm, one of the five AES finalists, is because it is computationally intensive algorithm. It requires lookup tables, logical and arithmetic computations that stipulate high flexibility and performance. So it is a perfect algorithm to be mapped in order to evaluate such hardware. © 2010 Springer Science + Business Media, Inc.Al-Khalidy M, 2004, INT C CURR ISS BUS I; Almaini AEA, 1994, ELECT LOGIC SYSTEMS; Bagherzadeh N, 2000, J VLSI SIGNAL PR MAR; Damaj I, 2002, LECT NOTES COMPUT SC, V2438, P1076; Diab H, 2003, ACS IEEE INT C COMP; Ferrandi F., 2005, Proceedings. 19th IEEE International Parallel and Distributed Processing Symposium; Galanis MD, 2005, IEEE INT SYMP CIRC S, P1206, DOI 10.1109-ISCAS.2005.1464810; Galanis MD, 2004, P FPGA FEBR 2004; Galanis MD, 2004, P 13 INT C FIELD PRO; Ghaffari F, 2007, LECT NOTES COMPUT SC, V4050, P179, DOI 10.1007-978-3-540-71528-3_12; Green D.H., 1986, MODERN LOGIC DESIGN; Hartenstein R, 2001, DESIGN AUTOMATION TE; Hauck S, 1998, CAN C FIELD PROGR DE; Itani M, 2004, IEEE ACS INT C PERV; Majzoub S, 2006, IEEE S SIGN PROC INF, P496; Majzoub S, 2003, ACS IEEE INT C COMP; Majzoub S, 2006, 6 INT WORKSH SYST ON; MOLLER L., 2006, P 19 ANN S INT CIRC, P44, DOI 10.1145-1150343.1150360; Nollet V, 2003, P INT C ENG REC SYST, P81; Pan CZ, 2003, DESIGN, AUTOMATION AND TEST IN EUROPE CONFERENCE AND EXHIBITION, PROCEEDINGS, P468; Schneier B., 1996, APPL CRYPTOGRAPHY PR; Schneier B., 1998, TWOFISH 128 BIT BLOC; Singh H, 2000, IEEE T COMPUT, V49, P465, DOI 10.1109-12.8595400
Author Correction: Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology
No full textCorrection to: Nature Genetics https://doi.org/10.1038/s41588-021-00973-1, published online 6 December 2021.
In the version of this article initially published, the affiliation for Nazli Başak appeared incorrectly. Nazli Başak is at Koç University, School of Medicine, KUTTAM-NDAL, Istanbul, Turkey, and not Bogazici University. The error has been corrected in the HTML and PDF versions of the article
Author Correction: Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology
No full textMeasurement of non-prompt D -meson elliptic flow in Pb–Pb collisions at √sNN=5.02 TeV
No full textThe elliptic flow (v2) of D mesons from beauty-hadron decays (non-prompt D) was measured in midcentral (30–50%) Pb–Pb collisions at a centre-of-mass energy per nucleon pair sNN=5.02 TeV with the ALICE detector at the LHC. The D mesons were reconstructed at midrapidity (| y| < 0.8) from their hadronic decay D → K -π + , in the transverse momentum interval 2 < pT< 12 GeV/c. The result indicates a positive v2 for non-prompt D mesons with a significance of 2.7 σ . The non-prompt D -meson v2 is lower than that of prompt non-strange D mesons with 3.2 σ significance in 2<pT<8GeV/c , and compatible with the v2 of beauty-decay electrons. Theoretical calculations of beauty-quark transport in a hydrodynamically expanding medium describe the measurement within uncertainties. © 2023, The Author(s)
