Series Of Files Research Articles

Deciphering the Molecular Basis of Mutated Binding Site Bromodomain-Ligand Complexes: Insights from Molecular Dynamics Simulations and Decoded Interaction Fingerprint Analysis

This study aims to predict structural stability changes and to identify the molecular determinants of ligand-bromodomain complex interactions that undergo mutations in the ligand binding site (LBS) using computational chemistry methods. The stability changes of the complexes were investigated using Molecular Dynamics (MD) simulations during a 25 ns production run. The identification of molecular interaction determinants was performed by decoding the interaction fingerprint, utilizing the output of trajectory data of the MD simulations, which were converted into a series of pdb files along the time step. The system preparations were done using CHARMM-GUI. The MD simulations were carried out using the GROMACS program. Protein-ligand interaction fingerprints (PLIF) were identified using the PyPLIF-HIPPOS program. This study successfully predicted the stability of both wild-type and mutated ligand-bromodomain complex structures, where the W81A mutation led to a decrease in complex stability. The key residues and non-hydrophobic interaction types responsible for the stabilities were identified as TRP81 aromatic edge-to-face, TYR139 aromatic edge-to-face, and TYR139 aromatic face-to-face.

Discovering ecoacoustic codes in beehives: First evidence and perspectives

The sounds present inside a beehive originate from the overlap of honeybee buzzes with external sounds. They reveal patterns that support the hypothesis that the sonic context of the beehive may be utilized by honeybees as a source of ecoacoustic codes for communication and the coordination of social activity. Patterns were observed in a data series of acoustic files sampled at a frequency of 48 kHz during the period May–July 2023 in a beehive of Apis mellifera ligustica (Spinola, 1806). The acoustic information was extracted using the acoustic complexity index (ACItf) algorithm applied to a fast Fourier transform matrix. Data series, aggregated in 1368 min × 512 frequency bins × 61 days, were tentatively classified according to three temporal classes of aggregation (eight, six, and four clusters, respectively) using the hierarchical K-means clustering algorithm. The clusters obtained at these three resolutions were considered potential ecoacoustic codes (PECs) belonging to each minute of the data series.The number of discontinuities along the 24-h PEC sequence, the coefficient of variation of the number of PECs at daily and seasonal scales, and the PEC sample entropy confirmed a patterned distribution of PECs across the 24 h, modulated at a monthly scale. A significant correlation was found between these indices and the daily average wind speed, and temperature. Honeybee buzz is an informative medium used by honeybees to develop survival strategies.

Adaptive Mode Transformation for Wear Leveling in Nonvolatile FPGAs

Nowadays, field programmable gate arrays (FPGAs) have been widely adopted to serve as accelerators in artificial intelligence and big data related applications. Since the static random access memory (SRAM)-based FPGA is suffering from limited density and high leakage power, nonvolatile FPGAs have been proposed, where SRAM is replaced with emerging nonvolatile memories (NVMs). Multilevel cell (MLC), which can store multiple bits within one memory cell, further improves the density of nonvolatile FPGAs and shows great potential to enable large on-chip memory. However, it suffers from limited lifetime. In this article, we propose a wear leveling scheme to improve lifetime of MLC-based nonvolatile FPGAs. Instead of generating a series of configuration files for runtime reconfiguration, we propose to identify write-heavy MLC regions and dynamically transform them to durable single-level cell (SLC) mode. Specifically, we propose three modules: 1) pertaining to write behavior monitor; 2) approximate cost calculator; and 3) mode transformation manager to achieve adaptive mode transformations. We consider FPGA features to design these modules, which is different from implementations for MLC-SLC transformation in CPU architecture. Evaluation shows that the proposed scheme can improve lifetime for MLC nonvolatile FPGAs by <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$6.03\times $ </tex-math></inline-formula> , at cost of 12.5% storage overhead.

UNITE Species Hypotheses Matching Analysis

UNITE (User-friendly Nordic ITS Ectomycorrhizal Database) (Nilsson et al. 2018) is a theoretical and practical platform for calculating, identifying and communicating DNA-based species hypotheses that may not have been described as formal species yet. UNITE species hypotheses (SH) matching analysis is a digital service for the global species discovery from environmental DNA (eDNA). SH matching service is based on UNITE datasets hosted in PlutoF. The tool places a user's unknown DNA sequences in FASTA format into existing UNITE species hypotheses and forms SHs not yet present in the system. Its output in a series of CSV and HTML files (Fig. 1) includes information about what species are present in eDNA samples, whether they are potentially undescribed new species, where they are found in other studies, whether they are alien or threatened species, etc. The service is very useful for understanding species distribution patterns, host range, etc. Analysis output will provide Digital Object Identifier (DOI)-based stable identifiers for communicating species hypotheses found in eDNA. DOIs are connected to the taxonomic backbone of PlutoF and GBIF (Global Biodiversity Information Facility). In this way every DOI is accompanied by a taxon name, which is still widely used for the communication of species. In the case of undescribed species, DOIs will be issued by the PlutoF system. All UNITE services are focused on fungi but cover all Eukarya by using publicly available rDNA ITS (ribosomal DNA Internal Transcribed Spacer) marker sequences accompanied by sample metadata. SH matching analysis results can be published in GBIF as DNA-derived occurrence data where occurrences are linked to SH identifiers present in GBIF backbone taxonomy. Source code of the SH matching analysis tool is available in GitHub with an implementation accessible online on the PlutoF platform for registered users. PlutoF (Abarenkov et al. 2010) is an open data management platform for biology and related disciplines. Users can manage their bodiversity datasets through a full data life cycle—from uploading to publishing and archiving in FAIR (Findable, Accessible, Interoperable, Reusable) way. PlutoF also features an analysis module by providing analytical services for molecular sequence identification and species discovery from eDNA samples. There are more than 8 000 registrered users in PlutoF with more than 500 users who have used its analysis module (as of August, 2022).

Identification of a Diagnostic Signature and Immune Cell Infiltration Characteristics in Keloids.

Background: Keloid disorder is a recurrent fibroproliferative cutaneous tumor. Due to the lack of early identification of keloid patients before the formation of keloids, it is impossible to carry out pre-traumatic intervention and prevention for these patients. This led us to identify and determine signatures with diagnostic significance for keloids. Methods: Public series of matrix files were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were calculated from expression profiling data, and the diagnostic signature was identified by constructing a protein-protein interaction (PPI) network. The diagnostic efficacy of the screened signature was assessed by employing receiver operating characteristic (ROC) curves. Furthermore, we calculated the proportion of different immune cells in the gene expression matrix microenvironment by the “ssGSEA” algorithm, and assessed the difference in immune cell abundance between keloids and control groups and the relationship between the signature and immune cell infiltration. Clinical keloid and normal skin tissues were collected, and the expression of the screened diagnostic signature was validated by RT-qPCR and immunohistochemical assay. Results: By screening the key genes in PPI, TGM2 was recognized and validated as a diagnostic signature and the infiltrating abundance of 10 immune cells was significantly correlated with TGM2 expression. Gene ontology enrichment analysis demonstrated that TGM2 and molecules interacting with it were mainly enriched in processes involving wound healing and collagen fiber organization. TGM2 correlated positively with HIF-1A (R = 0.82, p-value = 1.4e-05), IL6 (R = 0.62, p-value = 0.0053), and FN1 (R = 0.66, p-value = 0.0019). Besides, TGM2 was significantly upregulated in clinical keloid samples compared to normal skin tissues. Conclusion: TGM2 may serve as an auxiliary diagnostic indicator for keloids. However, the role of TGM2 in keloids has not been adequately reported in the current literature, which may provide a new direction for molecular studies of keloids.

TRAINING PODCASTS IN THE TEACHING PROCESS UKRAINIAN AS A FOREIGN LANGUAGE

The article reveals the possibilities of using podcasting in the process of teaching foreign students of preparatory departments of the Ukrainian language as a foreign language, shows its didactic potential (resources Studyukrainian and Ukrainianlessons). The article analyzes the advantages and disadvantages of podcasting in the organization of the educational process and presents the types of work with podcasts. The modern educational process is inconceivable without the widespread use of such technology as “podcasting”. A podcast is a single audio or video file or a series of such files that are published at the same address on the Internet and have a certain frequency of publication, which depends on the creator of a particular podcast. One of the most productive platforms for online learning of Ukrainian as a foreign language is the Studyukrainian resource. The site already has 5 seasons of podcasts (about 160 recordings), and the resource is actively replenished. In the first season the podcasts are written in English, in the following seasons the share of English in the teacher’s explanations decreases significantly, in the fifth season the podcasts are written exclusively in Ukrainian. Each podcast lasts about 20 minutes. Foreign students have the opportunity to receive by e-mail a “script” in PDF format of the podcast and additional materials on the topic (grammar tables, explanations, examples, diagrams, a list of phrases and dialogues, exercises for more practice and vocabulary on the topic, etc.). In addition, the foreign student is given additional opportunities: sets of cards for learning words, videos of various songs and clips, which explain the Ukrainian realities or features of word usage (for example, national holidays, greetings etc.). The site provides foreign students with a dictionary, a list of phrases, a grammar block, a blog for communication with the teacher. In the process of learning the Ukrainian language as a foreign language, the fullest possible disclosure of the possibilities of podcasting technology is possible, because the language as a means of transmitting information in this context is also the object of study. The use of podcasts in teaching various activities helps to increase students’ motivation to learn the national language; the emergence of choice in the selection of interesting phonetic material; promotes the formation of listening skills and the ability to perceive different speech styles with different accents and intonations; improving speaking skills. Podcast as a media carrier of information is, along with other resources, an integral technical means of distance learning of Ukrainian as a foreign language, which allows to solve complex problems of foreign language education. Key words: podcasting, iPod, listening training, new information technologies in teaching Ukrainian as a foreign language, Studyukrainian and Ukrainianlessons resources.

FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies.

Multilocus Sequence Typing (MLST) is a precise microbial typing approach at the intra-species level for epidemiologic and evolutionary purposes. It operates by assigning a sequence type (ST) identifier to each specimen, based on a combination of alleles of multiple housekeeping genes included in a defined scheme. The use of MLST has multiplied due to the availability of large numbers of genomic sequences and epidemiologic data in public repositories. However, data processing speed has become problematic due to the massive size of modern datasets. Here, we present FastMLST, a tool that is designed to perform PubMLST searches using BLASTn and a divide-and-conquer approach that processes each genome assembly in parallel. The output offered by FastMLST includes a table with the ST, allelic profile, and clonal complex or clade (when available), detected for a query, as well as a multi-FASTA file or a series of FASTA files with the concatenated or single allele sequences detected, respectively. FastMLST was validated with 91 different species, with a wide range of guanine-cytosine content (%GC), genome sizes, and fragmentation levels, and a speed test was performed on 3 datasets with varying genome sizes. Compared with other tools such as mlst, CGE/MLST, MLSTar, and PubMLST, FastMLST takes advantage of multiple processors to simultaneously type up to 28 000 genomes in less than 10 minutes, reducing processing times by at least 3-fold with 100% concordance to PubMLST, if contaminated genomes are excluded from the analysis. The source code, installation instructions, and documentation of FastMLST are available at https://github.com/EnzoAndree/FastMLST

An open-source geospatial framework for beach litter monitoring.

Here, we present a framework for a beach litter monitoring process, based on free and open-source software (FOSS), which allows customization for any sampling design. The framework was developed by means of a GIS project (QGIS), a GIS collector (QField), and an R code, allowing further adjustments according to the area to be surveyed and research questions. The aim is to improve data collection, accessibility, and interoperability, as well as to help to fill the currently existing gap between fieldwork and data analysis, preventing typos and allowing better data processing. Therefore, it is expected to take less than an hour from ending fieldwork to obtaining up-to-date products. To test the developed open-source geospatial framework, it was applied in different sectors and dates on an important southern Brazilian touristic beach. Results obtained from the open-source geospatial framework application produce baseline information on beach litter issues, such as amounts, sources, and spatial and temporal patterns. Adoption of the framework can facilitate data collection by local and regional stakeholders, and the results obtained from it can be applied to support management strategies. For researchers, it produces spatialized data for each item in an already tidy format, which can be used for robust and complex models. A series of supplementary files support reproducibility and provide a guide to future users.

Regular and Oscillatory Motion of Coronal Bright Points

Long-term automatic tracking of coronal bright points has made it possible to study their proper motions using data from the AIA 193 A channel of SDO/AIA. Fits files for 95 visually long-lived bright points uniformly distributed in latitude have been chosen for processing. A specially developed program automatically fixes the heliographic coordinates of the centroid of the chosen coronal bright points in a series of Fits files. It was found that the proper motions of all the coronal bright points studied here have a distinct oscillatory character. The periods of the oscillations range from 5 to 60 h with an average of 20 h. Some tendencies in the latitudinal dependence of the oscillatory characteristics have been found. A possible explanation of these oscillations in terms of the propagation of helical waves along the magnetic loops that form the structure of the coronal bright points is pointed out. Linear trends in the latitudinal and longitudinal components of the motion of the coronal points are used to determine the rotational velocity and meridional migration of the coronal bright points. An analysis of the rotational velocities confirms the differential character of the latitudinal dependence. The problem of determining the direction and magnitude of the meridional migration is discussed.

Rapid Least Concern: towards automating Red List assessments.

BackgroundThe IUCN Red List of Threatened SpeciesTM (hereafter the Red List) is an important global resource for conservation that supports conservation planning, safeguarding critical habitat and monitoring biodiversity change (Rodrigues et al. 2006). However, a major shortcoming of the Red List is that most of the world's described species have not yet been assessed and published on the Red List (Bachman et al. 2019Eisenhauer et al. 2019). Conservation efforts can be better supported if the Red List is expanded to achieve greater coverage of mega-diverse groups of organisms such as plants, fungi and invertebrates. There is, therefore, an urgent need to speed up the Red List assessment and documentation workflow.One reason for this lack of species coverage is that a manual and relatively time-consuming procedure is usually employed to assess and document species. A recent update of Red List documentation standards (IUCN 2013) reduced the data requirements for publishing non-threatened or 'Least Concern' species on the Red List. The majority of the required fields for Least Concern plant species can be found in existing open-access data sources or can be easily calculated. There is an opportunity to consolidate these data and analyses into a simple application to fast-track the publication of Least Concern assessments for plants. There could be as many as 250,000 species of plants (60%) likely to be categorised as Least Concern (Bachman et al. 2019), for which automatically generated assessments could considerably reduce the outlay of time and valuable resources for Red Listing, allowing attention and resources to be dedicated to the assessment of those species most likely to be threatened.New informationWe present a web application, Rapid Least Concern, that addresses the challenge of accelerating the generation and documentation of Least Concern Red List assessments. Rapid Least Concern utilises open-source datasets, such as the Global Biodiversity Information Facility (GBIF) and Plants of the World Online (POWO) through a simple web interface. Initially, the application is intended for use on plants, but it could be extended to other groups, depending on the availability of equivalent datasets for these groups.Rapid Least Concern users can assess a single species or upload a list of species that are assessed in a batch operation. The batch operation can either utilise georeferenced occurrence data from GBIF or occurrence data provided by the user. The output includes a series of CSV files and a point map file that meet the minimum data requirements for a Least Concern Red List assessment (IUCN 2013). The CSV files are compliant with the IUCN Red List SIS Connect system that transfers the data files to the IUCN database and, pending quality control checks and review, publication on the Red List.We outline the knowledge gap this application aims to fill and describe how the application works. We demonstrate a use-case for Rapid Least Concern as part of an ongoing initiative to complete a global Red List assessment of all native species for the United Kingdom Overseas Territory of Bermuda.

La política matrimonial sobre los empleados públicos en Indias y los montepíos oficiales en las postrimerías del período colonial

Uno de los motivos principales de los montepíos oficiales coloniales creados en el siglo XVIII fue asegurar de manera prioritaria a esposas e hijos de los empleados públicos con destino en Ultramar. Son objetivos del presente trabajo analizar las condiciones que establecen los montepíos para el beneficio de las pensiones a viudas y huérfanos, y la normativa relativa a las interdicciones regias que afectaba directamente a los matrimonios de los socios en los montes y al régimen de viudedad. Se han consultado algunos reglamentos generados por aquellas instituciones, así como distintas leyes y reales órdenes, que supusieron más obstáculos que beneficios para los afiliados y las viudas y huérfanos de ministros y otros empleados de rangos inferiores. Se destaca el recurso ampliamente utilizado por el colectivo para obtener una pensión o ayuda por vía de gracia, a través del estudio de una serie de peticiones y expedientes consultados en el Archivo General de Indias.

Determination of the 25th Frame with the Eeg Signals Stored in the Videos

Nowadays, the videos that appear in every part of our lives are a set of images resulting from the sequential addition of a series of image files. One second of the video is the result of the merging of 24 picture frames. The visual subliminal perceives 24 frames per second. It is difficult to see pictures hidden in the frames of videos and called the 25th frame effect. In this study, electroencephalogram (EEG) signals are analyzed and it is aimed to determine whether or not the 25th frame effect is perceived by the brain. In the study, 50 participants were shown 6 different videos. Participants watched videos containing a pure and 25th frame effect and recorded EEG signals. Statistical feature extraction algorithms were applied to EEG signals. In this study, k-nearest neighbor (knn) classifier and Naive Bayes(NB) classifier, are used Training was performed by applying the k-fold cross validation method. The knn classifiers achievement performance is as follows; accuracy %96.60, recall %98.00, F1 score %96.50 precision %95.29. The NB classifiers achievement performance is as follows; accuracy %92.00, recall %92.00, F1 score %92.20 precision %92.00. It is aimed to develop the study by using different classification methods and signal processing methods.

How to Make Educational Lemonade Out of a Didactic Lemon: The Benefits of Listening to Your Students.

When educators develop and introduce new learning approaches or resources, they usually have specific didactic goals in mind that they want to achieve. However, these goals may not always match the needs of their students, who often confound such plans by finding new and different uses for the educational tools that are offered to them. Originating from the author's work as the histology component director at the University of Michigan, the experience described here provides an example of a learning resource being reappropriated by the learning community. In order to encourage dental students to study histological micrographs after faculty-guided laboratory sessions were eliminated, the author prepared and offered them a series of PowerPoint files with histology images and some corresponding questions. However, instead of increasing their motivation to use the online virtual microscopy resources, students adapted this new tool for reviewing the material and for self-evaluation whether they were prepared for upcoming examinations. Although the product did not succeed as originally devised, it turned into a very popular review resource for the author's students. Students' feedback and critical input, as well as their active participation in producing additional, similar learning tools were the deciding factors for this successful change of purpose and the further development and refinement of this new learning resource.

A generic integrity verification algorithm of version files for cloud deduplication data storage

Data owners’ outsourced data on cloud data storage servers by the deduplication technique can reduce not only their own storage cost but also cloud’s. This paradigm also introduces new security issues such as the potential threat of data lost or corrupted. Data integrity verification is utilized to safeguard these data integrity. However, the cloud deduplication storage only focuses on file/chunk level to store one copy of the same data hosted by different data owners, and is not concerned with the same part of different data, e.g., a series of version files. We propose an integrity verification algorithm of different version files. The algorithm establishes the generic storage model of different version control methods to improve the universality of data verification. Then, the methods of verification tags and proofs generating are improved based on the index pointers corresponding to the storage relationship in the version groups and chained keys. Finally, the random diffusion extraction based on the random data sampling in the version group is proposed to improve the verification efficiency. The results of theoretical and experimental analysis indicate that the algorithm can achieve fast and large-scale verification for different version data.

StatsX v2.0: the interactive graphical software for population statistics on X-STR

StatsX (Statistics for X-STR) v2.0 is developed to facilitate the workflow for analysis of population data on X-chromosomal short tandem repeat (X-STR) marker. The interactive graphical and installable software can estimate allele/haplotype frequencies from female, male, and pooled samples and calculate forensic parameters by importing a single file. In addition, it is able to filter out the invalid raw data and export a series of pre-formatted Arlequin input files that are directly used for testing the significance of the Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), and gender differentiation. As expected, all results of frequencies and forensic parameters can be saved as EXCEL workbooks and also plotted as bar or line graphs. Further, full concordance was obtained by recalculating frequencies and forensic parameters with other established software from a published Han Chinese population.

The Novel as the Future Anterior of the Book: Tom McCarthy's Remainder and Ali Smith's The Accidental

This article asks what it means to consider a twenty-first-century novel as a machine able to talk about its own materiality. Is it a series of keystrokes or digital files or marks on a page? If, as Friedrich Kittler presumes, digital technology has boosted the autopoietic qualities of the media system, in what sense do paper books remain active components of this system and in what sense do they appear within it as old media, spoken for by the electronically mediated texts that represent them? Or have novels become comments on this in-between state of being no longer quite materially decipherable as paper sequences, portable objects, material containers of letters arranged on a page and yet not being fully free of this image of the book? Focusing on Tom McCarthy's Remainder (2005) and Ali Smith's The Accidental (2005) as novels that speak from what Jacques Derrida calls the “future anterior” of the page, it argues for the view of the book that opens up once a technology is no longer in use as a primary medium. By this logic, if novels like Remainder and The Accidental perform the space of new media, it is not because they describe or actively cede a role to electronic text but because they deploy a nonnative capacity to look at narrative in its incarnation as paper and print. This also means that they engage with medial form without being strictly self-referential.

An improved representation of geographically isolated wetlands in a watershed‐scale hydrologic model

AbstractGeographically isolated wetlands (GIWs), defined as wetlands surrounded by uplands, provide an array of ecosystem goods and services. Within the United States, federal regulatory protections for GIWs are contingent, in part, on the quantification of their singular or aggregate effects on the hydrological, biological, or chemical integrity of waterways regulated by the Clean Water Act (CWA). However, limited tools are available to assess the downgradient effects of GIWs. We constructed a Soil and Water Assessment Tool (SWAT) model with improved representations of GIW hydrologic processes for the approximately 1700 km2 Pipestem Creek watershed in the Prairie Pothole Region of North Dakota, USA. We then executed a series of novel modifications on the Pipestem Creek SWAT model. We (1) redefined the model's hydrologic response unit spatial boundaries to conform to mapped GIWs and associated watershed boundaries, (2) constructed a series of new model input files to direct the simulation of GIW fill–spill hydrology and upland flows to GIWs, and (3) modified the model source code to facilitate use of the new SWAT input files and improve GIW water balance simulations. We then calibrated and verified our modified SWAT model at a daily time step from 2009 through 2013. Simulation results indicated good predictive power (the maximum Nash–Sutcliffe Efficiency statistic was 0.86) and an acceptable range of uncertainty (measured using the Sequential Uncertainty Fitting v.2 uncertainty statistics). Simulation results additionally indicated good model performance with respect to GIW water balance simulations based on literature‐based descriptions of regional GIW hydrologic behaviour. Our modified SWAT model represents a critical step in advancing scientific understandings of the watershed‐scale hydrologic effects of GIWs and provides a novel method for future assessments in different watersheds and physiographic regions. Copyright © 2016 John Wiley &amp; Sons, Ltd.

Impacts on cooling energy consumption due to the UHI and vegetation changes in Manchester, UK

Climate change projections estimate a rise of approximately 3°C by the 2080s for most of the UK (medium emissions scenario at 50% probability level, 1961–1990 baseline). Warming is a particular concern for urban areas due to urban densification and the Urban Heat Island (UHI) effect.To counteract the UHI, one adaptation strategy for urban areas is increasing the proportion of greenspace, such as parks, street tree plantings, and green roofs. This research employed an interdisciplinary approach to measure and model fine-scale microclimate changes due to greenspace and explore the implications for building energy demand in Manchester, UK. Both the modelled and measured microclimate data informed development of a series of weather files for building energy modelling of three commercial building types.For a scenario adding 5% mature trees to the urban case study, the combination of microclimate modelling and data analysis estimated a maximum hourly air temperature reduction of nearly 1.0°C under peak UHI conditions and wind speed reductions up to 1.0m/s. These results were used to change the weather files in the building energy modelling, which estimated a reduction of 2.7% in July chiller energy due to the combination of reduced UHI peak hours and eight additional trees shading a three-storey shallow plan building. Energy savings increased to 4.8% under a three-day period of peak UHI conditions.

Taking a SecondLook™ at a Time-Efficient Self-Review Resource

Interactive review tools are highly valued by today’s students. The SecondLook™ Histology resource was developed for students at the University of Michigan to test their knowledge and skills in analyzing micrographic histology images. Originally conceived as a series of PowerPoint files, it has also been converted to mobile applications.

Automated DICOM metadata and volumetric anatomical information extraction for radiation dosimetry

Patient-specific dosimetry calculations based on simulation techniques have as a prerequisite the modeling of the modality system and the creation of voxelized phantoms. This procedure requires the knowledge of scanning parameters and patients’ information included in a DICOM file as well as image segmentation. However, the extraction of this information is complicated and time-consuming. The objective of this study was to develop a simple graphical user interface (GUI) to (i) automatically extract metadata from every slice image of a DICOM file in a single query and (ii) interactively specify the regions of interest (ROI) without explicit access to the radiology information system. The user-friendly application developed in Matlab environment. The user can select a series of DICOM files and manage their text and graphical data. The metadata are automatically formatted and presented to the user as a Microsoft Excel file. The volumetric maps are formed by interactively specifying the ROIs and by assigning a specific value in every ROI. The result is stored in DICOM format, for data and trend analysis. The developed GUI is easy, fast and and constitutes a very useful tool for individualized dosimetry. One of the future goals is to incorporate a remote access to a PACS server functionality.