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2022 ◽  
Author(s):  
Lara A. M. Zaki ◽  
Meike W. Vernooij ◽  
Marion Smits ◽  
Christine Tolman ◽  
Janne M. Papma ◽  
...  

Abstract Purpose To compare two artificial intelligence software packages performing normative brain volumetry and explore whether they could differently impact dementia diagnostics in a clinical context. Methods Sixty patients (20 Alzheimer’s disease, 20 frontotemporal dementia, 20 mild cognitive impairment) and 20 controls were included retrospectively. One MRI per subject was processed by software packages from two proprietary manufacturers, producing two quantitative reports per subject. Two neuroradiologists assigned forced-choice diagnoses using only the normative volumetry data in these reports. They classified the volumetric profile as “normal,” or “abnormal”, and if “abnormal,” they specified the most likely dementia subtype. Differences between the packages’ clinical impact were assessed by comparing (1) agreement between diagnoses based on software output; (2) diagnostic accuracy, sensitivity, and specificity; and (3) diagnostic confidence. Quantitative outputs were also compared to provide context to any diagnostic differences. Results Diagnostic agreement between packages was moderate, for distinguishing normal and abnormal volumetry (K = .41–.43) and for specific diagnoses (K = .36–.38). However, each package yielded high inter-observer agreement when distinguishing normal and abnormal profiles (K = .73–.82). Accuracy, sensitivity, and specificity were not different between packages. Diagnostic confidence was different between packages for one rater. Whole brain intracranial volume output differed between software packages (10.73%, p < .001), and normative regional data interpreted for diagnosis correlated weakly to moderately (rs = .12–.80). Conclusion Different artificial intelligence software packages for quantitative normative assessment of brain MRI can produce distinct effects at the level of clinical interpretation. Clinics should not assume that different packages are interchangeable, thus recommending internal evaluation of packages before adoption.


Drones ◽  
2022 ◽  
Vol 6 (1) ◽  
pp. 24
Author(s):  
Taleatha Pell ◽  
Joan Y. Q. Li ◽  
Karen E. Joyce

With the increased availability of low-cost, off-the-shelf drone platforms, drone data become easy to capture and are now a key component of environmental assessments and monitoring. Once the data are collected, there are many structure-from-motion (SfM) photogrammetry software options available to pre-process the data into digital elevation models (DEMs) and orthomosaics for further environmental analysis. However, not all software packages are created equal, nor are their outputs. Here, we evaluated the workflows and output products of four desktop SfM packages (AgiSoft Metashape, Correlator3D, Pix4Dmapper, WebODM), across five input datasets representing various ecosystems. We considered the processing times, output file characteristics, colour representation of orthomosaics, geographic shift, visual artefacts, and digital surface model (DSM) elevation values. No single software package was determined the “winner” across all metrics, but we hope our results help others demystify the differences between the options, allowing users to make an informed decision about which software and parameters to select for their specific application. Our comparisons highlight some of the challenges that may arise when comparing datasets that have been processed using different parameters and different software packages, thus demonstrating a need to provide metadata associated with processing workflows.


2022 ◽  
Author(s):  
Hao Gong ◽  
Bin Han

Abstract Many software packages and pipelines had been developed to handle the sequence data of the model species. However, Genotyping from complex heterozygous plant genome needs further improvement on the previous methods. Here we present a new pipeline available at https://github.com/Ncgrhg/HetMapv1) for variant calling and missing genotype imputation from low coverage sequence data for heterozygous plant genomes. To check the performance of the HetMap on the real sequence data, HetMap was applied to both the F1 hybrid rice population which consists of 1495 samples and wild rice population with 446 samples. Four high coverage sequence hybrid rice accessions and two high coverage sequence wild rice accessions, which were also included in low coverage sequence data, are used to validate the genotype inference accuracy. The validation results showed that HetMap archived significant improvement in heterozygous genotype inference accuracy (13.65% for hybrid rice, 26.05% for wild rice) and total accuracy compared with other similar software packages. The application of the new genotype with the genome wide association study also showed improvement of association power in two wild rice phenotypes. It could archive high genotype inference accuracy with low sequence coverage with a small population size with both the natural population and constructed recombination population. HetMap provided a powerful tool for the heterozygous plant genome sequence data analysis, which may help the discover of new phenotype regions for the plant species with complex heterozygous genome.


2022 ◽  
Author(s):  
Yi Nian Niu ◽  
Eric G. Roberts ◽  
Danielle Denisko ◽  
Michael M. Hoffman

Background: Bioinformatics software tools operate largely through the use of specialized genomics file formats. Often these formats lack formal specification, and only rarely do the creators of these tools robustly test them for correct handling of input and output. This causes problems in interoperability between different tools that, at best, wastes time and frustrates users. At worst, interoperability issues could lead to undetected errors in scientific results. Methods: We sought (1) to assess the interoperability of a wide range of bioinformatics software using a shared genomics file format and (2) to provide a simple, reproducible method for enhancing interoperability. As a focus, we selected the popular BED file format for genomic interval data. Based on the file format's original documentation, we created a formal specification. We developed a new verification system, Acidbio (https://github.com/hoffmangroup/acidbio), which tests for correct behavior in bioinformatics software packages. We crafted tests to unify correct behavior when tools encounter various edge cases—potentially unexpected inputs that exemplify the limits of the format. To analyze the performance of existing software, we tested the input validation of 80 Bioconda packages that parsed the BED format. We also used a fuzzing approach to automatically perform additional testing. Results: Of 80 software packages examined, 75 achieved less than 70% correctness on our test suite. We categorized multiple root causes for the poor performance of different types of software. Fuzzing detected other errors that the manually designed test suite could not. We also created a badge system that developers can use to indicate more precisely which BED variants their software accepts and to advertise the software's performance on the test suite. Discussion: Acidbio makes it easy to assess interoperability of software using the BED format, and therefore to identify areas for improvement in individual software packages. Applying our approach to other file formats would increase the reliability of bioinformatics software and data.


2022 ◽  
pp. 49-59
Author(s):  
MARYNA SHOVKALIUK ◽  
ROMAN VASHCHYSHYN

There are many approaches to assessing the energy performance of buildings. In Ukraine, previously, when developing the energy passport of buildings, a method based on stationary calculations using degree-days of the heating period was used. Then, for the tasks of energy certification of buildings, a national calculation method based on the monthly quasi-stationary method was introduced. The simplified hourly method of calculation allows to consider thermal inertia of protections. In recent years, the methods of dynamic energy modeling using software packages have become increasingly relevant, because it allows at the preliminary design stage to estimate energy costs for different building needs before and after the implementation of energy efficiency projects and provides the ability to create 3D models based on geometric and thermal parameters, tasks of different configurations and types of engineering systems of the building. To build an energy model, a training building was chosen to determine energy consumption indicators and identify measures that have the greatest impact on the energy performance of the building.Purpose. Evaluation of energy characteristics of the educational building of a higher education institution with modeling of energy consumption in specialized software, technical and economic evaluation of opportunities to increase energy efficiency.Research methods. Energy inspection of the object of research and technical and economic analysis with the use of engineering methods of calculation, experimental measurements of the parameters of the microclimate of the building with the use of laboratory equipment were performed. Simulations are used in specialized software products RETScreen, EnergyPlus, DesignBuilder.Result. With the help of the developed models the structure of energy consumption of the educational building is obtained and the assessment of energy saving potential is carried out; in case of implementation of the proposed measures it is expected to reduce the consumption of energy resources and monetary costs for their payment, as well as improve the quality of educational services. The research was conducted as part of a master's thesis.Scientific novelty. The technical potential of this software for modeling the energy performance of a building of complex configuration on the example of the educational building of the educational institution, analyzed the methods of processing initial data for programs, comparative analysis of calculation results for the actual condition of the building, baseline and after implementing energy saving measures.Practical significance. As a result of the research, the potential of using different software packages to perform applied research of the master's dissertation was determined and a project of complex thermal modernization of the building of the educational building was developed.


2022 ◽  
Vol 81 (1) ◽  
Author(s):  
Kiril Vassilev ◽  
Momchil Nazarov ◽  
Constantin Mardari ◽  
Borislav Grigorov ◽  
Stoyan Georgiev ◽  
...  

Class Polygono-Poetea annuae Rivas-Mart. 1975 includes therophyte-rich vegetation on trampled habitats. The study presents the first analysis of the syntaxonomy of this class and its ecology in Bulgaria. One hundred seventy-five relevés from this class were collected and stored in the Balkan Vegetation Database during 2017–2020. Numerical classification (hierarchical divisive) and ordination were performed by JUICE and CANOCO software packages. Diagnostic species were determined by calculating the Phi-coefficient. Four associations, Sclerochloo durae-Polygonetum arenastri, Polygonetum arenastri, Lolio-Polygonetum arenastri and Poëtum annuae, were recognized. Their floristic composition has been shaped mainly by climatic and soil conditions. Sclerochloo durae-Polygonetum arenastri association has been found at lower altitudes, occurring in fully lighted habitats with high radiation, whereas Poëtum annuae has been found at higher altitudes in wetter and cooler areas. On the other hand, stands of Polygonetum arenastri have been found on nutrient-rich soils, whereas communities of Lolio-Polygonetum arenastri were distributed in warmer and nutrient-poor areas. The Polygono-Poetea annuae class is still poorly studied in Bulgaria and much more information from all regions of the country needs to be collected and analyzed.


2022 ◽  
Vol 12 (1) ◽  
pp. 130-142
Author(s):  
Leen Al-Khalafat ◽  
Ahmad S. Haider

Translation is defined as transferring meaning and style from one language to another, taking the text producer's intended purpose and the audience culture into account. This paper uses a 256,000-word Arabic-English parallel corpus of the speeches of King Abdullah II of Jordan from 1999 to 2015 to examine how some culture-bound expressions were translated from Arabic into English. To do so, two software packages were used, namely Wordsmith 6 and SketchEngine. Comparing the size of the Arabic corpus with its English counterpart using the wordlist tool of WS6, the researchers found that the number of words (tokens) in the English translation is more than the Arabic source text. However, the results showed that the Arabic language has more unique words, which means that it has more lexical density than its English counterpart. The researchers carried out a keyword analysis and compared the Arabic corpus with the ArTenTen corpus to identify the words that King Abdullah II saliently used in his speeches. Most of the keywords were culture-bound and related to the Jordanian context, which might be challenging to render. Using the parallel concordance tool and comparing the Arabic text with its English translation showed that the translator/s mainly resorted to the strategies of deletion, addition, substitution, and transliteration. The researchers recommend that further studies be conducted using the same approach but on larger corpora of other genres, such as legal, religious, press, and scientific texts.


Seizure ◽  
2022 ◽  
Author(s):  
E.E.M. Reus ◽  
G.H. Visser ◽  
J.G. van Dijk ◽  
F.M.E. Cox

2021 ◽  
Vol 7 (4) ◽  
pp. 111-120
Author(s):  
Kateryna Kovbasiuk ◽  
Kamil Židek ◽  
Michal Balog ◽  
Liudmyla Dobrovolska

The simulation software market is becoming more complex and universal. Computer simulations are thus more accessible and are becoming a modern tool that has a wide application in industry. Their potential and benefits can be used in small and large projects. A simulation model can take into account inventory, assembly, production and human resources, leading to decisions that can maintain or improve efficiency at the lowest possible cost. The data obtained through the simulation allow to test different combinations and scenarios in the virtual world. The benefits of manufacturing simulation include reducing investment risk, minimizing waste, improving efficiency, reducing energy consumption and even increasing worker health. The question arises as to which of the possible simulation packages is the most suitable for a given company, so that the investments made are the best possible. In the first part of the paper the theoretical basis of simulation in Industry 4.0 is presented, including the description of the possible simulation modelling tools. The second part of the paper offers comparative and descriptive analysis of six selected discrete-event simulation software packages – AnyLogic, Arena, FlexSim, SIMUL8, Tecnomatix Plant Simulation and WITNESS. The given simulation tools are compared based on their main characteristics, simulation features, application areas and popularity among the companies which use simulation software packages.


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