The amount of data coming from modern acquisition systems, especially working in extreme experimental conditions, is significantly rising over the years. Combined with complex algorithms, the ...computation time and power consumption are considerably increasing. The issue usually occurs in many world laboratories, such as CERN, Brookhaven National Laboratory, GSI Helmholtzzentrum für Schwerionenforschung, and tokamak devices (JET, WEST, MAST, and more). Often well verified, but legacy codes are used as a main computational engine, resulting in weak performance unsuitable for current needs. The paper presents a methodology to appropriately adapt the legacy C/C++ high-energy physics (HEP) algorithms for computation acceleration using FPGAs, which may improve the designing of real-time systems based on verified codes. The main idea is to separate the HLS-FPGA code work areas between groups of experts: physicists and electronics. The methodology consists of several parts: interfacing, storage, verification methods, defining the algorithm and data structures, program refactoring in the scope of CPU and FPGA, performance and results analysis, FPGA verification methods, FPGA performance estimation, and automatization of the process. The methodology has been successfully tested by implementing a legacy, complex HEP algorithm for femtoscopy correlations in the HLS framework for FPGA. It works with extensive input data from international experiments, like STAR at RHIC. The implementation and verification were done successfully on the FPGA hardware platform. Following the methodology results in a clearer to analyze and debug HEP code than a machine-generated version by tools. We also confirmed that it is possible to make a working, HLS-compliant program designed by non-FPGA experts. Using the modern implementation tools, FPGA resource usage is low despite unoptimized syntax. It gives a large field for further significant optimizations and good performance. The proposed approach should be interesting to introduce in devices like tokamaks, synchrotrons, and similar, where the real-time monitoring of the experimental processes is essential.
•Methodology for complex algorithm conversion from legacy code to hardware accelerated in FPGA in high level synthesis (HLS) languages.•Guidelines to achieve the performance improvement of legacy (C, Fortran etc.) high energy physics algorithms.•Discussion about the pros and cons of using the high-level synthesis (HLS) languages for acceleration.•Preliminary in-hardware FPGA laboratory tests of the presented approach based on Monte-Carlo HEP algorithm for heavy-ion collisions.•Use for high energy physics experiments, however not limited to.
The global polarization of {\Lambda} hyperons along the total orbital angular momentum of a relativistic heavy-ion collision is presented based on the high statistics data samples collected in Au+Au ...collisions at \sqrt{s_{NN}} = 2.4 GeV and Ag+Ag at 2.55 GeV with the High-Acceptance Di-Electron Spectrometer (HADES) at GSI, Darmstadt. This is the first measurement below the strangeness production threshold in nucleon-nucleon collisions. Results are reported as a function of the collision centrality as well as a function of the hyperon transverse momentum (p_T) and rapidity (y_{CM}) for the range of centrality 0--40%. We observe a strong centrality dependence of the polarization with an increasing signal towards peripheral collisions. For mid-central (20--40%) collisions the polarization magnitudes are <P_{\Lambda}>(%) = 6.8 \pm 1.3 (stat.) \pm 2.1 (syst.) for Au+Au and <P_{\Lambda}>(%) = 6.2 \pm 0.4 (stat.) \pm 0.6 (syst.) for Ag+Ag, which are the largest values observed so far. This observation thus provides a continuation of the increasing trend previously observed by STAR and contrasts expectations from recent theoretical calculations predicting a maximum in the region of collision energies about 3 GeV. The observed polarization is of a similar magnitude as predicted by 3D fluid dynamics and the UrQMD plus thermal vorticity model and significantly above results from the AMPT model.
The aim of the paper is to reconstruct the theoretical background and practical meaning of the so called war writings which emerged within the phenomenological movement during the First World War. ...The author exemplifies it by researching the works of two German representatives of this movement, Max Scheler and Kurt Stavenhagen. He focuses on their application of the phenomenological method to the analysis of Russian national identity, and historical as well as cultural foundations of Russian state. The paper’s main thesis is that the politicization and militarization of phenomenology consisted in both “personalization” and “sociologization” of the phenomenological approach to the problem of the state. While interpreting Scheler’s personalism as an exemplification of the approach to the state as a problem of social ontology, the author reconstructs the theoretical conditions of analyzing the Russian imperial state in terms of the “world.” The focus of the paper is particularly on the phenomenology of, as Scheler put it, Russian collective personality and Russian national consciousness or “soul” as well as on the question of legitimacy of Ukrainian resistance against Russian imperialism.
Roman Ingarden the early phenomenologist is regarded as a theorist in the area of aesthetics and ontology rather than being a political philosopher. The aim of the article is to reconstruct ...a non-existent philosophy of the state, one that could have been developed by Ingarden by taking as a starting point his ontological analysis of the structure of a literary work of art. In his book of 1931 Ingarden defined very broadly the literary work of art, including as its borderline cases among others scientific works, letters, memoirs etc. The thesis of the article is that state constitution may be also interpreted as a borderline case of that work. In reference to Ingarden’s analysis of stage play as the concretisation of a piece of drama, an attempt will be made to reconstruct in terms of his ontology the relation between the state constitution and the state itself.
Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for emerging pathogen detection directly from clinical specimens. In contrast to targeted methods, mNGS also provides ...valuable information on the composition of the microbiome and might uncover coinfections that may associate with disease progression and impact prognosis. To evaluate the use of mNGS for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or other infecting pathogens, we applied direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing. Nasopharyngeal (NP) swab specimens from 50 patients under investigation for CoV disease 2019 (COVID-19) were sequenced, and the data were analyzed by the CosmosID bioinformatics platform. Further, we characterized coinfections and the microbiome associated with a four-point severity index. SARS-CoV-2 was identified in 77.5% (31/40) of samples positive by RT-PCR, correlating with lower cycle threshold (Ct) values and fewer days from symptom onset. At the time of sampling, possible bacterial or viral coinfections were detected in 12.5% of SARS-CoV-2-positive specimens. A decrease in microbial diversity was observed among COVID-19-confirmed patients (Shannon diversity index,
= 0.0082; Chao richness estimate,
= 0.0097; Simpson diversity index,
= 0.018), and differences in microbial communities were linked to disease severity (
= 0.022). Furthermore, statistically significant shifts in the microbiome were identified among SARS-CoV-2-positive and -negative patients, in the latter of whom a higher abundance of
(
= 0.028) and a reduction in the abundance of
(
= 0.025) were observed. Our study corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages rather than the severity of COVID-19. Further, we demonstrate that SARS-CoV-2 causes a significant change in the respiratory microbiome. This work illustrates the utility of mNGS for the detection of SARS-CoV-2, for diagnosing coinfections without viral target enrichment or amplification, and for the analysis of the respiratory microbiome.
SARS-CoV-2 has presented a rapidly accelerating global public health crisis. The ability to detect and analyze viral RNA from minimally invasive patient specimens is critical to the public health response. Metagenomic next-generation sequencing (mNGS) offers an opportunity to detect SARS-CoV-2 from nasopharyngeal (NP) swabs. This approach also provides information on the composition of the respiratory microbiome and its relationship to coinfections or the presence of other organisms that may impact SARS-CoV-2 disease progression and prognosis. Here, using direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing of NP swab specimens from 50 patients under investigation for COVID-19, we detected SARS-CoV-2 sequences by applying the CosmosID bioinformatics platform. Further, we characterized coinfections and detected a decrease in the diversity of the microbiomes in these patients. Statistically significant shifts in the microbiome were identified among COVID-19-positive and -negative patients, in the latter of whom a higher abundance of
and a reduction in the abundance of
were observed. Our study also corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages of disease rather than with severity of disease. This work illustrates the utility of mNGS for the detection and analysis of SARS-CoV-2 from NP swabs without viral target enrichment or amplification and for the analysis of the respiratory microbiome.
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