scholarly journals A computational EXFOR database

2020 ◽  
Vol 239 ◽  
pp. 16001
Author(s):  
Georg Schnabel
Keyword(s):  
Experimental Data ◽  
Programming Languages ◽  
Nuclear Physics ◽  
Nuclear Data ◽  
Important Ingredient ◽  
Starting Point ◽  
Exfor Library ◽  
High Level ◽  
Exfor Database ◽  
Programmatic Access

The EXFOR library is a useful resource for many people in the field of nuclear physics. In particular, the experimental data in the EXFOR library serves as a starting point for nuclear data evaluations. There is an ongoing discussion about how to make evaluations more transparent and reproducible. One important ingredient may be convenient programmatic access to the data in the EXFOR library from high-level languages. To this end, the complete EXFOR library can be converted to a MongoDB database. This database can be conveniently searched and accessed from a wide variety of programming languages, such as C++, Python, Java, Matlab, and R. This contribution provides some details about the successful conversion of the EXFOR library to a MongoDB database and shows simple usage examples to underline its merits. All codes required for the conversion have been made available online and are open-source. In addition, a Dockerfile has been created to facilitate the installation process.

scholarly journals Synergy of Nuclear Data and Nuclear Theory Online

2020 ◽  
Vol 239 ◽  
pp. 03021
Author(s):  
Andrey Denikin ◽  
Alexander Karpov ◽  
Mikhail Naumenko ◽  
Vladimir Rachkov ◽  
Viacheslav Samarin ◽  
...  
Keyword(s):  
Experimental Data ◽  
Knowledge Base ◽  
Cross Sections ◽  
Nuclear Physics ◽  
Nuclear Research ◽  
Nuclear Data ◽  
Reaction Cross ◽  
Nuclear Dynamics ◽  
Wide Range ◽  
Educational Applications

The paper describes the NRV web knowledge base on low-energy nuclear physics developed in the Joint Institute for Nuclear Research. The NRV knowledge base working through the Internet integrates a large amount of digitized experimental data on the properties of nuclei and nuclear reaction cross sections with a wide range of computational programs for modeling of nuclear properties and nuclear dynamics. Today, the NRV becomes a powerful instrument for nuclear physics research as well as for educational applications. Advantages of the functioning scheme of the knowledge base provide the synergy of coexistence of the experimental data and computational codes within one platform.

scholarly journals THE PRINCESS PROJECT: FROM DIFFERENTIAL TO INTEGRAL EXPERIMENTS

2021 ◽  
Vol 247 ◽  
pp. 20002
Author(s):  
Isabelle Duhamel ◽  
Mariya Brovchenko ◽  
Jean-Baptiste Clavel ◽  
Matthieu Duluc ◽  
Raphaëlle Ichou ◽  
...  
Keyword(s):  
Experimental Data ◽  
Nuclear Physics ◽  
Nuclear Data ◽  
Nuclear Safety ◽  
Reactor Physics ◽  
Neutron Physics ◽  
Experimental Facilities ◽  
Integral Data ◽  
Criticality Safety

Following the shutdown of the CEA Valduc experimental facilities, where, for more than 50 years, IRSN used to perform experiments related to criticality safety, IRSN initiated a new project named PRINCESS (PRoject for IRSN Neutron physics and Criticality Experimental data Supporting Safety). The objective is to continue collecting experimental data necessary for the IRSN missions in nuclear safety. For this purpose, collaborations with various national and international laboratories have been established. The PRINCESS project covers various nuclear physics fields from nuclear data to criticality-safety and reactor physics providing information to both differential and integral data improvements.

CSim 2

2021 ◽  
Vol 43 (1) ◽  
pp. 1-46
Author(s):  
David Sanan ◽  
Yongwang Zhao ◽  
Shang-Wei Lin ◽  
Liu Yang
Keyword(s):  
Programming Languages ◽  
Concurrent Systems ◽  
Theorem Prover ◽  
Compositional Techniques ◽  
Machine Code ◽  
Top Down ◽  
Hol Theorem Prover ◽  
High Level ◽  
High Degree

To make feasible and scalable the verification of large and complex concurrent systems, it is necessary the use of compositional techniques even at the highest abstraction layers. When focusing on the lowest software abstraction layers, such as the implementation or the machine code, the high level of detail of those layers makes the direct verification of properties very difficult and expensive. It is therefore essential to use techniques allowing to simplify the verification on these layers. One technique to tackle this challenge is top-down verification where by means of simulation properties verified on top layers (representing abstract specifications of a system) are propagated down to the lowest layers (that are an implementation of the top layers). There is no need to say that simulation of concurrent systems implies a greater level of complexity, and having compositional techniques to check simulation between layers is also desirable when seeking for both feasibility and scalability of the refinement verification. In this article, we present CSim 2 a (compositional) rely-guarantee-based framework for the top-down verification of complex concurrent systems in the Isabelle/HOL theorem prover. CSim 2 uses CSimpl, a language with a high degree of expressiveness designed for the specification of concurrent programs. Thanks to its expressibility, CSimpl is able to model many of the features found in real world programming languages like exceptions, assertions, and procedures. CSim 2 provides a framework for the verification of rely-guarantee properties to compositionally reason on CSimpl specifications. Focusing on top-down verification, CSim 2 provides a simulation-based framework for the preservation of CSimpl rely-guarantee properties from specifications to implementations. By using the simulation framework, properties proven on the top layers (abstract specifications) are compositionally propagated down to the lowest layers (source or machine code) in each concurrent component of the system. Finally, we show the usability of CSim 2 by running a case study over two CSimpl specifications of an Arinc-653 communication service. In this case study, we prove a complex property on a specification, and we use CSim 2 to preserve the property on lower abstraction layers.

scholarly journals Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yi Chen ◽  
Fons. J. Verbeek ◽  
Katherine Wolstencroft
Keyword(s):  
Gene Ontology ◽  
Enrichment Analysis ◽  
Biological Data ◽  
Hallmarks Of Cancer ◽  
High Throughput Analysis ◽  
Knowledge Resources ◽  
Gene Set ◽  
Cancer Hallmarks ◽  
Starting Point ◽  
High Level

Abstract Background The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development and tumourigenesis. However, methods for translating these high-level concepts into data-level associations between hallmarks and genes (for high throughput analysis), vary widely between studies. The examination of different strategies to associate and map cancer hallmarks reveals significant differences, but also consensus. Results Here we present the results of a comparative analysis of cancer hallmark mapping strategies, based on Gene Ontology and biological pathway annotation, from different studies. By analysing the semantic similarity between annotations, and the resulting gene set overlap, we identify emerging consensus knowledge. In addition, we analyse the differences between hallmark and gene set associations using Weighted Gene Co-expression Network Analysis and enrichment analysis. Conclusions Reaching a community-wide consensus on how to identify cancer hallmark activity from research data would enable more systematic data integration and comparison between studies. These results highlight the current state of the consensus and offer a starting point for further convergence. In addition, we show how a lack of consensus can lead to large differences in the biological interpretation of downstream analyses and discuss the challenges of annotating changing and accumulating biological data, using intermediate knowledge resources that are also changing over time.

Application of C Sharp and MATLAB Mixed Programming Based on .Net Assembly in Blind Source Separation

2014 ◽  
Vol 599-601 ◽  
pp. 1407-1410
Author(s):  
Xu Liang ◽  
Ke Ming Wang ◽  
Gui Yu Xin
Keyword(s):  
Numerical Calculation ◽  
Programming Languages ◽  
Blind Source Separation ◽  
Source Separation ◽  
Processing System ◽  
Signal Processing System ◽  
Blind Signal Processing ◽  
Blind Signal ◽  
Mixed Programming ◽  
High Level

Comparing with other High-level programming languages, C Sharp (C#) is more efficient in software development. While MATLAB language provides a series of powerful functions of numerical calculation that facilitate adoption of algorithms, which are widely applied in blind source separation (BSS). Combining the advantages of the two languages, this paper presents an implementation of mixed programming and the development of a simplified blind signal processing system. Application results show the system developed by mixed programming is successful.

Theoretical determination of the structures of CaSiO3 perovskites

2006 ◽  
Vol 62 (6) ◽  
pp. 1025-1030 ◽  
Author(s):  
Razvan Caracas ◽  
Renata M. Wentzcovitch
Keyword(s):  
Crystal Structure ◽  
Experimental Data ◽  
Density Functional Theory ◽  
Density Functional ◽  
Theoretical Determination ◽  
Functional Theory ◽  
Starting Point ◽  
Atomic Coordinates ◽  
The Ideal

Density functional theory is used to determine the possible crystal structure of the CaSiO3 perovskites and their evolution under pressure. The ideal cubic perovskite is considered as a starting point for studying several possible lower-symmetry distorted structures. The theoretical lattice parameters and the atomic coordinates for all the structures are determined, and the results are discussed with respect to experimental data.

NENOK — A SOFTWARE ARCHITECTURE FOR GENERIC INFERENCE

2010 ◽  
Vol 19 (01) ◽  
pp. 65-99 ◽  
Author(s):  
MARC POULY
Keyword(s):  
Programming Languages ◽  
Software Library ◽  
Inference Process ◽  
Software Projects ◽  
Open Problems ◽  
Constraint Systems ◽  
Fast Prototyping ◽  
Inference Algorithms ◽  
Key Competences ◽  
High Level

Computing inference from a given knowledgebase is one of the key competences of computer science. Therefore, numerous formalisms and specialized inference routines have been introduced and implemented for this task. Typical examples are Bayesian networks, constraint systems or different kinds of logic. It is known today that these formalisms can be unified under a common algebraic roof called valuation algebra. Based on this system, generic inference algorithms for the processing of arbitrary valuation algebras can be defined. Researchers benefit from this high level of abstraction to address open problems independently of the underlying formalism. It is therefore all the more astonishing that this theory did not find its way into concrete software projects. Indeed, all modern programming languages for example provide generic sorting procedures, but generic inference algorithms are still mythical creatures. NENOK breaks a new ground and offers an extensive library of generic inference tools based on the valuation algebra framework. All methods are implemented as distributed algorithms that process local and remote knowledgebases in a transparent manner. Besides its main purpose as software library, NENOK also provides a sophisticated graphical user interface to inspect the inference process and the involved graphical structures. This can be used for educational purposes but also as a fast prototyping architecture for inference formalisms.

scholarly journals Evidence for Inhibition of Topoisomerase 1A by Gold(III) Macrocycles and Chelates TargetingMycobacterium tuberculosisandMycobacterium abscessus

2018 ◽  
Vol 62 (5) ◽  
Author(s):  
Rashmi Gupta ◽  
Carolina Rodrigues Felix ◽  
Matthew P. Akerman ◽  
Kate J. Akerman ◽  
Cathryn A. Slabber ◽  
...  
Keyword(s):  
Mycobacterium Abscessus ◽  
Cross Resistance ◽  
Human Pathogens ◽  
Intrinsic Resistance ◽  
Content Type ◽  
Starting Point ◽  
Scalable Synthesis ◽  
High Level ◽  
Novel Drug

ABSTRACTMycobacterium tuberculosisand the fast-growing speciesMycobacterium abscessusare two important human pathogens causing persistent pulmonary infections that are difficult to cure and require long treatment times. The emergence of drug-resistantM. tuberculosisstrains and the high level of intrinsic resistance ofM. abscessuscall for novel drug scaffolds that effectively target both pathogens. In this study, we evaluated the activity of bis(pyrrolide-imine) gold(III) macrocycles and chelates, originally designed as DNA intercalators capable of targeting human topoisomerase types I and II (Topo1 and Topo2), againstM. abscessusandM. tuberculosis. We identified a total of 5 noncytotoxic compounds active against both mycobacterial pathogens under replicatingin vitroconditions. We chose one of these hits, compound 14, for detailed analysis due to its potent bactericidal mode of inhibition and scalable synthesis. The clinical relevance of this compound was demonstrated by its ability to inhibit a panel of diverseM. tuberculosisandM. abscessusclinical isolates. Prompted by previous data suggesting that compound 14 may target topoisomerase/gyrase enzymes, we demonstrated that it lacked cross-resistance with fluoroquinolones, which target theM. tuberculosisgyrase.In vitroenzyme assays confirmed the potent activity of compound 14 against bacterial topoisomerase 1A (Topo1) enzymes but not gyrase. Novel scaffolds like compound 14 with potent, selective bactericidal activity againstM. tuberculosisandM. abscessusthat act on validated but underexploited targets like Topo1 represent a promising starting point for the development of novel therapeutics for infections by pathogenic mycobacteria.

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