Multiscale machine-learning interatomic potentials for ferromagnetic and liquid iron.

A large and increasing number of different types of interatomic potentials exist, either based on parametrised analytical functions or machine learning. The choice of potential to be used in a molecular dynamics simulation should be based on the affordable computational cost and required accuracy. We develop and compare four interatomic potentials of different complexity for iron: a simple machine-learned embedded atom method (EAM) potential, a potential with machine-learned two- and three-body-dependent terms, a potential with machine-learned EAM and three-body terms, and a Gaussian approximation potential with the smooth overlap of atomic positions descriptor. All potentials are trained to the same diverse database of body-centred cubic and liquid structures computed with density functional theory. The first three potentials are tabulated and evaluated efficiently using cubic spline interpolations, while the fourth one is implemented without additional optimisation. The four potentials span three orders of magnitude in computational cost. We compare and discuss the advantages of each potential in terms of transferability and the balance between accuracy and computational cost.

Absence of a Crystal Direction Regime in which Sputtering Corresponds to Amorphous Material.

Erosion of material by energetic ions, i.e., sputtering, is widely used in industry and research. Using experiments and simulations that, independently of each other, obtain the sputter yield of thousands of individual grains, we demonstrate here that the sputter yield for heavy keV ions on metals changes as a continuous function of the crystal direction. Moreover, we show that polycrystalline metals with randomly oriented grains do not sputter with the same yield as the amorphous material. The key reason for this is attributed to linear collision sequences rather than channeling.

Collision cascades overlapping with self-interstitial defect clusters in Fe and W.

Overlap of collision cascades with previously formed defect clusters become increasingly likely at radiation doses typical for materials in nuclear reactors. Using molecular dynamics, we systematically investigate the effects of different pre-existing self-interstitial clusters on the damage produced by an overlapping cascade in bcc iron and tungsten. We find that the number of new Frenkel pairs created in direct overlap with an interstitial cluster is reduced to essentially zero, when the size of the defect cluster is comparable to that of the disordered cascade volume. We develop an analytical model for this reduced defect production as a function of the spatial overlap between a cascade and a defect cluster of a given size. Furthermore, we discuss cascade-induced changes in the morphology of self-interstitial clusters, including transformations between [Formula: see text] and [Formula: see text] dislocation loops in iron and tungsten, and between C15 clusters and dislocation loops in iron. Our results provide crucial new cascade-overlap effects to be taken into account in multi-scale modelling of radiation damage in bcc metals.

No evidence of enteric viral involvement in the new neonatal porcine diarrhoea syndrome in Danish pigs.

BACKGROUND: The aim of this study was to investigate whether the syndrome New Neonatal Porcine Diarrhoea Syndrome (NNPDS) is associated with a viral aetiology. Four well-managed herds experiencing neonatal diarrhoea and suspected to be affected by NNPDS were included in a case-control set up. A total of 989 piglets were clinically examined on a daily basis. Samples from diarrhoeic and non-diarrhoeic piglets at the age of three to seven days were selected for extensive virological examination using specific real time polymerase chain reactions (qPCRs) and general virus detection methods. RESULTS: A total of 91.7% of the animals tested positive by reverse transcription qPCR (RT-qPCR) for porcine kobuvirus 1 (PKV-1) while 9% and 3% were found to be positive for rotavirus A and porcine teschovirus (PTV), respectively. The overall prevalence of porcine astrovirus (PAstV) was 75% with 69.8% of the PAstV positive pigs infected with PAstV type 3. No animals tested positive for rotavirus C, coronavirus (TGEV, PEDV and PRCV), sapovirus, enterovirus, parechovirus, saffoldvirus, cosavirus, klassevirus or porcine circovirus type 2 (PCV2). Microarray analyses performed on a total of 18 animals were all negative, as were eight animals examined by Transmission Electron Microscopy (TEM). Using Next Generation de novo sequencing (de novo NGS) on pools of samples from case animals within all herds, PKV-1 was detected in four herds and rotavirus A, rotavirus C and PTV were detected in one herd each. CONCLUSIONS: Our detailed analyses of piglets from NNPDS-affected herds demonstrated that viruses did not pose a significant contribution to NNPDS. However, further investigations are needed to investigate if a systemic virus infection plays a role in the pathogenesis of NNPDS.

Novel technologies applied to the nucleotide sequencing and comparative sequence analysis of the genomes of infectious agents in veterinary medicine.

Next-generation sequencing (NGS), also referred to as deep, high-throughput or massively parallel sequencing, is a powerful new tool that can be used for the complex diagnosis and intensive monitoring of infectious disease in veterinary medicine. NGS technologies are also being increasingly used to study the aetiology, genomics, evolution and epidemiology of infectious disease, as well as host-pathogen interactions and other aspects of infection biology. This review briefly summarises recent progress and achievements in this field by first introducing a range of novel techniques and then presenting examples of NGS applications in veterinary infection biology. Various work steps and processes for sampling and sample preparation, sequence analysis and comparative genomics, and improving the accuracy of genomic prediction are discussed, as are bioinformatics requirements. Examples of sequencing-based applications and comparative genomics in veterinary medicine are then provided. This review is based on novel references selected from the literature and on experiences of the World Organisation for Animal Health (OIE) Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden.

Le séquençage de nouvelle génération (également désigné « séquençage à très haut débit ¼ ou « séquençage massivement parallèle ¼) est un nouvel outil extrêmement puissant permettant de procéder à des diagnostics sophistiqués et d'assurer un contrôle vétérinaire intensif de maladies infectieuses complexes. Les technologies du séquençage de nouvelle génération sont également d'un grand secours pour étudier l'étiologie, la génomique, l'évolution et l'épidémiologie des maladies infectieuses ainsi que les interactions hôtes­agents pathogènes et bien d'autres aspects de la biologie des maladies infectieuses. Pour présenter les progrès et les accomplissements les plus récents dans ce domaine, les auteurs décrivent d'abord une série de techniques innovantes puis quelques exemples d'applications du séquençage de nouvelle génération dans le champ de la biologie des maladies animales infectieuses. Ils exposent un certain nombre d'étapes et de processus opérationnels régissant la sélection et la préparation des échantillons, l'analyse séquentielle et les études de génomique comparative, ainsi que ceux qui permettent d'améliorer la justesse prédictive de la génomique ; les exigences particulières de la bio-informatique sont également évoquées. Cette analyse est complétée par quelques exemples d'applications de l'analyse séquentielle et de la génomique comparative en médecine vétérinaire. Cette synthèse est basée sur une sélection de références bibliographiques récentes ainsi que sur l'expérience acquise par le Centre collaborateur de l'Organisation mondiale de la santé animale (OIE) pour le diagnostic basé sur la biotechnologie des maladies infectieuses en médecine vétérinaire, situé à Uppsala (Suède).

La secuenciación de próxima generación, también denominada secuenciación profunda, de alto rendimiento o masivamente paralela, es una nueva y poderosa herramienta para efectuar diagnósticos complejos y vigilar muy de cerca enfermedades infecciosas complejas en el ámbito de la medicina veterinaria. Estas técnicas también se utilizan cada vez más para estudiar la etiología, genómica, evolución y epidemiología de las enfermedades infecciosas, así como las interacciones entre patógeno y anfitrión y otros aspectos de la biología de las infecciones. Los autores resumen brevemente una serie de logros y adelantos obtenidos últimamente en este ámbito, presentando en primer lugar un conjunto de técnicas novedosas y ofreciendo después ejemplos de aplicaciones de la secuenciación de próxima generación a la biología de las infecciones veterinarias. También describen varios protocolos y procesos de trabajo para la obtención y preparación de muestras, el análisis de secuencias y las labores de genómica comparada, explican cómo mejorar la exactitud de la predicción genómica y examinan las herramientas bioinformáticas necesarias para ello. A continuación presentan ejemplos de aplicaciones basadas en técnicas de secuenciación y en la genómica comparada en medicina veterinaria. Este artículo está basado en referencias muy recientes, tomadas de publicaciones científicas, y en la experiencia del Centro Colaborador de la Organización Mundial de Sanidad Animal (OIE) para el Diagnóstico de las enfermedades infecciosas de la medicina veterinaria basado en la biotecnología, sito en Upsala (Suecia).

Next-generation sequencing workflows in veterinary infection biology: towards validation and quality assurance.

Recent advancements in DNA sequencing methodologies and sequence data analysis have revolutionised research in many areas of biology and medicine, including veterinary infection biology. New technology is poised to bridge the gap between the research and diagnostic laboratory. This paper defines the potential diagnostic value and purposes of next-generation sequencing (NGS) applications in veterinary infection biology and explores their compatibility with the existing validation principles and methods of the World Organisation for Animal Health. Critical parameters for validation and quality control (quality metrics) are suggested, with reference to established validation and quality assurance guidelines for NGS-based methods of diagnosing human heritable diseases. Although most currently described NGS applications in veterinary infection biology are not primary diagnostic tests that directly result in control measures, this critical reflection on the advantages and remaining challenges of NGS technology should stimulate discussion on its diagnostic value and on the potential to validate NGS methods and monitor their diagnostic performance.

Les avancées récentes enregistrées en matière de séquençage de l'ADN et d'analyse des données de séquences ont révolutionné la recherche dans de nombreux domaines de la biologie et de la médecine, notamment la biologie des maladies animales infectieuses. Ces nouvelles technologies vont permettre de combler le fossé qui séparait la recherche fondamentale du laboratoire de diagnostic. Après avoir défini l'intérêt diagnostique des applications du séquençage de nouvelle génération (SNG) ainsi que leurs finalités dans le domaine de la biologie des maladies animales infectieuses, les auteurs examinent leur compatibilité avec les méthodes et les principes actuels de validation recommandés par l'Organisation mondiale de la santé animale. Ils proposent quelques paramètres critiques de validation et de contrôle qualité (mesure de la qualité), en se référant aux lignes directrices de validation et d'assurance qualité des techniques diagnostiques basées sur le séquençage de nouvelle génération visant à détecter les maladies humaines héréditaires. Certes, la plupart des applications actuelles des méthodes de séquençage de nouvelle génération en biologie des maladies animales infectieuses ne constituent pas des tests de diagnostic primaire (dont dépendent directement les décisions de contrôle sanitaire) ; toutefois, l'analyse critique proposée par les auteurs sur les avantages de cette technologie et sur les difficultés restant à résoudre devrait ouvrir la voie à des discussions sur l'intérêt diagnostique des méthodes recourant au séquençage de nouvelle génération ainsi que sur les perspectives de validation et de contrôle de leurs performances diagnostiques.

Los recientes avances en los métodos de secuenciación del ADN y el análisis de los datos de secuencias han revolucionado la investigación en muchos ámbitos de la biología y la medicina, entre ellos la biología de las infecciones veterinarias. Las nuevas técnicas encierran la promesa de reducir la distancia entre el mundo de la investigación y los laboratorios de diagnóstico. Tras explicar el interés que pueden revestir las aplicaciones de la secuenciación de próxima generación y su posible uso con fines de diagnóstico de infecciones veterinarias, los autores examinan su compatibilidad con los principios y métodos de validación que tiene definidos la Organización Mundial de Sanidad Animal. Asimismo, proponen parámetros básicos para su validación y control de calidad (medición de la calidad), haciendo referencia a las pautas ya establecidas de validación y garantía de calidad de métodos de diagnóstico de enfermedades humanas hereditarias que reposan en técnicas de secuenciación de próxima generación. Aunque la mayoría de las aplicaciones de estas técnicas actualmente descritas en biología de las infecciones veterinarias no constituyen pruebas primarias de diagnóstico, esto es, cuyos resultados puedan inducir directamente medidas de control, esta crucial reflexión sobre las ventajas que entraña la secuenciación de próxima generación y los problemas que aún plantea debería alentar un debate sobre su interés para labores de diagnóstico y sobre la posibilidad de validar métodos basados en estas técnicas y de hacer un seguimiento de la eficacia diagnóstica que ofrezcan.

Mechanism of Radiation Damage Reduction in Equiatomic Multicomponent Single Phase Alloys.

Recently a new class of metal alloys, of single-phase multicomponent composition at roughly equal atomic concentrations ("equiatomic"), have been shown to exhibit promising mechanical, magnetic, and corrosion resistance properties, in particular, at high temperatures. These features make them potential candidates for components of next-generation nuclear reactors and other high-radiation environments that will involve high temperatures combined with corrosive environments and extreme radiation exposure. In spite of a wide range of recent studies of many important properties of these alloys, their radiation tolerance at high doses remains unexplored. In this work, a combination of experimental and modeling efforts reveals a substantial reduction of damage accumulation under prolonged irradiation in single-phase NiFe and NiCoCr alloys compared to elemental Ni. This effect is explained by reduced dislocation mobility, which leads to slower growth of large dislocation structures. Moreover, there is no observable phase separation, ordering, or amorphization, pointing to a high phase stability of this class of alloys.

High-throughput sequencing in veterinary infection biology and diagnostics.

Sequencing methods have improved rapidly since the first versions of the Sanger techniques, facilitating the development of very powerful tools for detecting and identifying various pathogens, such as viruses, bacteria and other microbes. The ongoing development of high-throughput sequencing (HTS; also known as next-generation sequencing) technologies has resulted in a dramatic reduction in DNA sequencing costs, making the technology more accessible to the average laboratory. In this White Paper of the World Organisation for Animal Health (OIE) Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine (Uppsala, Sweden), several approaches and examples of HTS are summarised, and their diagnostic applicability is briefly discussed. Selected future aspects of HTS are outlined, including the need for bioinformatic resources, with a focus on improving the diagnosis and control of infectious diseases in veterinary medicine.