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This study aims to present a combination of methods and propose robust theoretical and conceptual frameworks for solving socio-environmental issues. This proposal included the Problem, Intervention, Context, and Outcome (PICO) framework and Protocol and Reporting result with Search, Appraisal, Synthesis, and Analysis framework, and develop (PSALSAR) method through SODIP steps: (i) Systematic review and meta-analysis defining the study from guiding questions; (ii) Open-source related to software and data; (iii) Data visualization and design information; (iv) Identification of gaps, challenges and trends through automation and lexicometric analysis; and (v) Proposal of theoretical and conceptual frameworks. This proposal defines the steps as support to combine and systematize information necessary to facilitate the production of this type of document using open-access software in the visualization and design of information. All these steps are replicable and essential to propose a conceptual and theoretical framework to contribute to the construction of knowledge in socio-environmental research and to propose solutions by filling in the gaps. In summary, this combination of methods shows:â¢The use of SODIP steps provides robustness and efficiency in carrying out review studies, facilitating the way to propose theoretical or conceptual frameworks.â¢Choosing to use open-source tools is essential for better evaluation and visualization of qualitative and quantitative data in review studies.â¢The combination of methods and data in the systematic review (scientific, political documents. and databases) supports the proposal of robust theoretical and conceptual frameworks.
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BACKGROUND: Uroflowmetry is useful to screen for and manage many voiding disorders. Home-based uroflowmetry might better represent the patient's true voiding pattern and be more widely adopted if an accurate low-cost portable device was available. OBJECTIVE: Development and initial evaluation of an open-platform, open-source low-cost portable uroflowmeter. MATERIALS AND METHODS: We designed and built an uroflowmeter comprising of a load cell and digital memory card unit connected to a programmable microcontroller board mounted upon a 3D printed frame. It generated date-stamped tables which were processed and plotted. Twenty urologists were recruited to assess the device. Each participant received the equipment that was returned, along with a bladder diary, after at least 24 consecutive hours of homemade uroflowmetry recording. Additionally, were assessed with the International Prostatic Symptom Score (I-PSS) and Peeling diagram, whereas the device's ease of use, robustness, and portability were evaluated with a Likert-type questionnaire. Two experienced urodynamicists independently evaluated the tracings' quality rated with a 3° ordinal scale: (1) Interpretable without artifacts; (2) Interpretable with artifacts; (3) Uninterpretable. RESULTS: Participants' median age was 36.6 years old, none having an I-PSS > 5 or Peeling > 2. Overall 138 voidings were recorded (77 daytime, 61 nightly episodes). The device's ease of use, robustness, and portability obtained maximum score in 80% of evaluations. Most (98%) of the tracings were considered interpretable. Limitations included its small study population and short monitoring times. CONCLUSION: The construction of a cheap (<50 USD), accurate user-friendly portable uroflowmeter proved feasible, which could facilitate access to portable uroflowmetry.
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Transtornos Urinários , Micção , Humanos , Adulto , Artefatos , Urodinâmica , ReologiaRESUMO
The Analytic Hierarchy Process (AHP) is a multi-criteria decision support method and is widely applied in many areas. The original AHP method proposed by Thomas L. Saaty in the 1970s requires (n²-n)/2 comparisons. The number of required comparisons can make using this method challenging for maintaining consistent judgments in problems involving many criteria and/or alternatives. Furthermore, the available software is platform-dependent and generally does not support group decision-making. In this paper, we present software for AHP that demands n-1 comparisons. Additionally, the software supports group decision-making using individual aggregation of priorities with arithmetic and geometric means. The system is available at http://ahpweb.net/ and is accessible from any internet-connected device. It currently has more than 100 users and dozens of decision problems in various areas.â¢The original AHP formulation requires (n²-n)/2 comparisons per cluster which makes it difficult to make consistent judgments.â¢AHP avaliable software does not enable group decision making.â¢The proposed system AHP-WEB fills these gaps. The method demands n-1 comparisons per cluster without any inconsistency and allows group decision making on a web system.
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Currently, remote laboratories have gained relevance in engineering education as tools to support active learning, experimentation, and motivation of students. Nonetheless, the costs and issues regarding their implementation and deployment limit the access of the students and educators to their advantages and features such as technical and educational. In this line, this study describes a fully open-source remote laboratory in hardware and software for education in automatic control systems employing Raspberry Pi and Python language with an approximate cost of USD 461. Even, by changing some components, the cost can be reduced to USD 420 or less. To illustrate the functionalities of the laboratory, we proposed a low-cost tank control system with its respective instrumentation, signal conditioning, identification, and control, which are exposed in this document. However, other experiments can be easily scalable and adaptable to the remote laboratory. Concerning the interface of the laboratory, we designed a complete user-friendly web interface with real-time video for the users to perform the different activities in automatic control such as identification or controller implementation through the programming language Python. The instructions to build and replicate the hardware and software are indicated in the open repositories provided for the project as well as in this paper. Our intention with this project is to offer a complete low-cost and open-source remote laboratory that can be adapted and used for the students, educators, and stakeholders to learn, experiment, and teach in the field of automatic control systems.
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Visualizing nerve cells has been fundamental for the systematic description of brain structure and function in humans and other species. Different approaches aimed to unravel the morphological features of neuron types and diversity. The inherent complexity of the human nervous tissue and the need for proper histological processing have made studying human dendrites and spines challenging in postmortem samples. In this study, we used Golgi data and open-source software for 3D image reconstruction of human neurons from the cortical amygdaloid nucleus to show different dendrites and pleomorphic spines at different angles. Procedures required minimal equipment and generated high-quality images for differently shaped cells. We used the "single-section" Golgi method adapted for the human brain to engender 3D reconstructed images of the neuronal cell body and the dendritic ramification by adopting a neuronal tracing procedure. In addition, we elaborated 3D reconstructions to visualize heterogeneous dendritic spines using a supervised machine learning-based algorithm for image segmentation. These tools provided an additional upgrade and enhanced visual display of information related to the spatial orientation of dendritic branches and for dendritic spines of varied sizes and shapes in these human subcortical neurons. This same approach can be adapted for other techniques, areas of the central or peripheral nervous system, and comparative analysis between species.
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Dendritos , Córtex Olfatório , Humanos , Dendritos/fisiologia , Imageamento Tridimensional , Neurônios , Software , Espinhas Dendríticas/fisiologiaRESUMO
Bicycling has grown significantly in the past ten years. In some regions, the implementation of large-scale bike-sharing systems and improved cycling infrastructure are two of the factors enabling this growth. An increase in non-motorized modes of transportation makes our cities more human, decreases pollution, traffic, and improves quality of life. In many cities around the world, urban planners and policymakers are looking at cycling as a sustainable way of improving urban mobility. Although bike-sharing systems generate abundant data about their users' travel habits, most cities still rely on traditional tools and methods for planning and policy-making. Recent technological advances enable the collection and analysis of large amounts of data about urban mobility, which can serve as a solid basis for evidence-based policy-making. In this paper, we introduce a novel analytical method that can be used to process millions of bike-sharing trips and analyze bike-sharing mobility, abstracting relevant mobility flows across specific urban areas. Backed by a visualization platform, this method provides a comprehensive set of analytical tools to support public authorities in making data-driven policy and planning decisions. This paper illustrates the use of the method with a case study of the Greater Boston bike-sharing system and, as a result, presents new findings about that particular system. Finally, an assessment with expert users showed that this method and tool were considered very useful, relatively easy to use and that they intend to adopt the tool in the near future.
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Computational tools can transform the manner by which neuroscientists perform their experiments. More than helping researchers to manage the complexity of experimental data, these tools can increase the value of experiments by enabling reproducibility and supporting the sharing and reuse of data. Despite the remarkable advances made in the Neuroinformatics field in recent years, there is still a lack of open-source computational tools to cope with the heterogeneity and volume of neuroscientific data and the related metadata that needs to be collected during an experiment and stored for posterior analysis. In this work, we present the Neuroscience Experiments System (NES), a free software to assist researchers in data collecting routines of clinical, electrophysiological, and behavioral experiments. NES enables researchers to efficiently perform the management of their experimental data in a secure and user-friendly environment, providing a unified repository for the experimental data of an entire research group. Furthermore, its modular software architecture is aligned with several initiatives of the neuroscience community and promotes standardized data formats for experiments and analysis reporting.
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Resumen Este artículo tiene como objetivo presentar la metodología y resultados de la investigación realizada sobre la adaptación e implementación de un software de código abierto para la descripción documental acorde a las normas internacionales de descripción, en la Fundación Universitaria para el Desarrollo Humano-UNINPAHU. Motivó la investigación el cumplimiento de la normatividad archivística que obliga a las entidades a realizar la descripción de los documentos para un mejor acceso a la información, por tanto, el alcance de este estudio describe los actos administrativos institucionales, en este caso una muestra de la serie documental simple, resoluciones rectorales. La metodología de investigación utilizada fue descriptiva, aplicada y exploratoria, ya que se emplearon teorías, normas y herramientas tecnológicas para la descripción documental, con el fin de contribuir a la institución con un sistema de información que le permita a nivel administrativo describir y controlar su producción documental, y a nivel académico fortalecer las prácticas archivísticas de sus estudiantes. Finalmente se concluye que el sistema de información implementado permitió el registro de metadatos de las resoluciones y su recuperación por los distintos puntos de acceso, lo cual beneficia a la institución al tener un sistema que le permita conservar y acceder a su memoria institucional. El resultado fue la implementación y personalización del sistema de información ICA-AtoM en ambientes administrativo y académico para la Universidad UNINPHAU.
Abstract This article presents the methodology and results of the research carried out about the adaptation and implementation of a software with an open source for the documentary description according to the international standards of description in the University Foundation-UNINPAHU. The research was motivated by compliance of the archival regulations that oblige the entities to make the description of the documents for a better to the access to information; therefore, the scope of this study was to describe the institutional administrative acts, in this case a sample of the simple documentary series, rectoral resolutions. The research was applied and exploratory, since theories, norms, and technological tools were used for the documentary description, in order to contribute with an information system that allows the administrative level to describe and control its documentary production, since academic level strengthen the archival practice of their students. Finally, it is concluded that the implemented information system allowed the registration of metadata of the regulations and their recovery by the different points of access, which benefits the institution by having a system that allows it to conserve and access to institutional memory. The result was the implementation and personalization of the ICA-AtoM information system in administrative and academic environments for the university -UNINPAHU.
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Indexação e Redação de Resumos , Análise Documental , História , Software , ColômbiaRESUMO
Brain-computer interfaces (BCIs) are technologies that provide the user with an alternative way of communication. A BCI measures brain activity (e.g. EEG) and converts it into output commands. Motor imagery (MI), the mental simulation of movements, can be used as a BCI paradigm, where the movement intention of the user can be translated into a real movement, helping patients in motor recovery rehabilitation. One of the main limitations for the broad use of such devices is the high cost associated with the high-quality equipment used for capturing the biomedical signals. Different low-cost consumer-grade alternatives have emerged with the objective of bringing these systems closer to the final users. The quality of the signals obtained with such equipments has already been evaluated and found to be competitive with those obtained with well-known clinical-grade devices. However, how these consumer-grade technologies can be integrated and used for practical MI-BCIs has not yet been explored. In this work, we provide a detailed description of the advantages and disadvantages of using OpenBCI boards, low-cost sensors and open-source software for constructing an entirely consumer-grade MI-BCI system. An analysis of the quality of the signals acquired and the MI detection ability is performed. Even though communication between the computer and the OpenBCI board is not always stable and the signal quality is sometimes affected by ambient noise, we find that by means of a filter-bank based method, similar classification performances can be achieved with an MI-BCI built under low-cost consumer-grade devices as compared to when clinical-grade systems are used. By means of this work we share with the BCI community our experience on working with emerging low-cost technologies, providing evidence that an entirely low-cost MI-BCI can be built. We believe that if communication stability and artifact rejection are improved, these technologies will become a valuable alternative to clinical-grade devices.
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Deep sequencing of viral genomes is a powerful tool to study RNA virus complexity. However, the analysis of next-generation sequencing data might be challenging for researchers who have never approached the study of viral quasispecies by this methodology. In this work we present a suitable and affordable guide to explore the sub-consensus variability and to reconstruct viral quasispecies from Illumina sequencing data. The guide includes a complete analysis pipeline along with user-friendly descriptions of software and file formats. In addition, we assessed the feasibility of the workflow proposed by analyzing a set of foot-and-mouth disease viruses (FMDV) with different degrees of variability. This guide introduces the analysis of quasispecies of FMDV and other viruses through this kind of approach.
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Vírus da Febre Aftosa/genética , Haplótipos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Quase-Espécies , Animais , Vírus da Febre Aftosa/classificação , Genes ViraisRESUMO
The analysis of behavior in animal models is an important objective in many research fields, including neuroscience, psychology, toxicology, and neuropsychopharmacology. Animal models have been used for many years, and several behavioral paradigms, such as locomotor activity, social interactions, and cognitive behavior, have been studied in animal models to correlate the behaviors with pharmacological or environmental interventions and with molecular, biochemical, and physiological findings. We reviewed the literature looking for open-source, freely available software to analyze animal behavior and found 12 freely available programs: ToxTrack, EthoWatcher, Mouse Behavior Tracker, Mouse Move, JAABA, wrMTrck, AnimalTracker, idTracker, Ctrax, Mousetracker, VideoHacking, and Cowlog, which were developed with different programs, work on different platforms, and have particular types of inputs and outputs and analysis capabilities. We reviewed some examples of their use, tested some of them, and provided several recommendations for the future development of programs for the automated analysis of behavior in animal models. In conclusion, we show freely available software for the automated analysis of behavior in animal models such as adult zebrafish and provide information for researchers and students looking for quick, easy-to-implement, and inexpensive behavior analysis alternatives.
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Comportamento Animal , Etologia/métodos , Ciência dos Animais de Laboratório/métodos , Software , Peixe-Zebra , Animais , Etologia/instrumentação , Ciência dos Animais de Laboratório/instrumentaçãoRESUMO
Tracking eye movements is being increasingly recognized as a valuable source of information about stimulus control. So far, however, eye-tracking research has suffered from accessibility issues, with expensive hardware and closed-source software. In this article we review Pupil©, an eye-tracking platform developed by Pupil Labs and that combines open-source software with low-cost hardware components. We offer concrete recommendations about Pupil use in stimulus-control research and we show how the software can be extended to automatize the analysis of gaze data. Finally, we present the results of a study of visual discrimination and conditioned reinforcement conducted with Pupil, establishing the usefulness of this platform as a research tool in behavior analysis.
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Medições dos Movimentos Oculares , Medições dos Movimentos Oculares/economia , Medições dos Movimentos Oculares/instrumentação , Movimentos Oculares , Humanos , Estimulação Luminosa , SoftwareRESUMO
BACKGROUND: Preoperative recognition of the anatomic individualities of each patient can help to achieve more precise and less invasive approaches. It also may help to anticipate potential complications and intraoperative difficulties. Here we describe the use, accuracy, and precision of a free tool for planning microsurgical approaches using 3-dimensional (3D) reconstructions from magnetic resonance imaging (MRI). METHODS: We used the 3D volume rendering tool of a free open-source software program for 3D reconstruction of images of surgical sites obtained by MRI volumetric acquisition. We recorded anatomic reference points, such as the sulcus and gyrus, and vascularization patterns for intraoperative localization of lesions. Lesion locations were confirmed during surgery by intraoperative ultrasound and/or electrocorticography and later by postoperative MRI. RESULTS: Between August 2015 and September 2016, a total of 23 surgeries were performed using this technique for 9 low-grade gliomas, 7 high-grade gliomas, 4 cortical dysplasias, and 3 arteriovenous malformations. The technique helped delineate lesions with an overall accuracy of 2.6 ± 1.0 mm. 3D reconstructions were successfully performed in all patients, and images showed sulcus, gyrus, and venous patterns corresponding to the intraoperative images. All lesion areas were confirmed both intraoperatively and at the postoperative evaluation. CONCLUSIONS: With the technique described herein, it was possible to successfully perform 3D reconstruction of the cortical surface. This reconstruction tool may serve as an adjunct to neuronavigation systems or may be used alone when such a system is unavailable.
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Imageamento Tridimensional , Neuronavegação , Software , Adulto , Neoplasias Encefálicas/diagnóstico por imagem , Neoplasias Encefálicas/cirurgia , Angiografia Cerebral , Córtex Cerebral/irrigação sanguínea , Córtex Cerebral/diagnóstico por imagem , Córtex Cerebral/cirurgia , Feminino , Glioma/diagnóstico por imagem , Glioma/cirurgia , Humanos , Imageamento Tridimensional/métodos , Malformações Arteriovenosas Intracranianas/diagnóstico por imagem , Malformações Arteriovenosas Intracranianas/cirurgia , Imageamento por Ressonância Magnética , Masculino , Malformações do Desenvolvimento Cortical/diagnóstico por imagem , Malformações do Desenvolvimento Cortical/cirurgia , Neuronavegação/métodos , Cirurgia Assistida por Computador/métodos , Tomografia Computadorizada por Raios XRESUMO
Graph derivative indices (GDIs) have recently been defined over N-atoms (N = 2, 3 and 4) simultaneously, which are based on the concept of derivatives in discrete mathematics (finite difference), metaphorical to the derivative concept in classical mathematical analysis. These molecular descriptors (MDs) codify topo-chemical and topo-structural information based on the concept of the derivative of a molecular graph with respect to a given event (S) over duplex, triplex and quadruplex relations of atoms (vertices). These GDIs have been successfully applied in the description of physicochemical properties like reactivity, solubility and chemical shift, among others, and in several comparative quantitative structure activity/property relationship (QSAR/QSPR) studies. Although satisfactory results have been obtained in previous modelling studies with the aforementioned indices, it is necessary to develop new, more rigorous analysis to assess the true predictive performance of the novel structure codification. So, in the present paper, an assessment and statistical validation of the performance of these novel approaches in QSAR studies are executed, as well as a comparison with those of other QSAR procedures reported in the literature. To achieve the main aim of this research, QSARs were developed on eight chemical datasets widely used as benchmarks in the evaluation/validation of several QSAR methods and/or many different MDs (fundamentally 3D MDs). Three to seven variable QSAR models were built for each chemical dataset, according to the original dissection into training/test sets. The models were developed by using multiple linear regression (MLR) coupled with a genetic algorithm as the feature wrapper selection technique in the MobyDigs software. Each family of GDIs (for duplex, triplex and quadruplex) behaves similarly in all modelling, although there were some exceptions. However, when all families were used in combination, the results achieved were quantitatively higher than those reported by other authors in similar experiments. Comparisons with respect to external correlation coefficients (q2ext) revealed that the models based on GDIs possess superior predictive ability in seven of the eight datasets analysed, outperforming methodologies based on similar or more complex techniques and confirming the good predictive power of the obtained models. For the q2ext values, the non-parametric comparison revealed significantly different results to those reported so far, which demonstrated that the models based on DIVATI's indices presented the best global performance and yielded significantly better predictions than the 12 0-3D QSAR procedures used in the comparison. Therefore, GDIs are suitable for structure codification of the molecules and constitute a good alternative to build QSARs for the prediction of physicochemical, biological and environmental endpoints.
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Desenho de Fármacos , Compostos Orgânicos/química , Relação Quantitativa Estrutura-Atividade , Benchmarking , Simulação por Computador , Matemática , Modelos Químicos , Compostos Orgânicos/farmacologiaRESUMO
Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.