Free-access Software Research Articles

Accelerated Polymer Photodegradation

Abstract: This article presents preliminary results of the accelerated degradation of polymers using concentrated solar radiation. For this purpose, a passive solar concentration prototype was designed, which consists of four trapezoidal mirrors placed in the shape of an inverted truncated square pyramid. The mirrors are placed at an angle of 30° respect to the zenith. The prototype has a square base of 46 cm x 46 cm where the polymers to be irradiated are placed and a geometric concentration ratio, CRg, of 1.89. The mass change was determined after 30 days of exposure to solar radiation, and the temperature variation of some samples as a function of irradiance was obtained. In addition, a computer simulation was carried out using the free access software Energy2D. Some polymers maintained their flexible mechanical properties, such as PET (type 1), others were partially embrittled, while type 2, 5 and 7 polymers were completely embrittled. It was possible to reduce the degradation time of different types of commercial polymers, while polymers exposed to non-concentrated radiation and without exposure remains intact. Embrittled polymers can be used as waterproof material in slabs and pre-cast walls, as well in applications where they are not exposed to solar radiation. On the other hand, the polymers that remained intact must be used in applications with permanent radiation exposure, such as in flower pots, plastic parts for automobiles, etc.

A new automatic method for tracking rats in the Morris water maze

Morris water maze (MWM) test is widely used to evaluate the learning and memory deficits in rodents. Image processing and pattern recognition can be used to analyse videos and recognize automatically the tracking in MWM. There are several commercial and free access software that allows analyzing the behavioral tasks although they also have limitations such as automation, cost, user intervention among other things. The aim of this paper was to develop a new image processing technique to automatically analyse the track of the rat in the MWM, which we called RatsTrack. The MWM test was performed with an animal model for Alzheimer, and the videos were recorded to measure the distance, time, and speed. The segmentation method based on the projection of the video frames was made for pool identification, eliminating the rat, while conserving the shape of the pool. Then, the Hough transformation was used to recognize the position and radius of the pool. Finally, the frame in which the rat is released into the pool was established automatically using mathematical morphology techniques and added as a plugin on free access ImageJ software. The new image processing technique, RatsTrack, successfully detected and located the pool and rat without user intervention, significantly decreasing operational time and providing results for distance, time, speed, and acceleration parameters of the MWM test. Alzheimer's rats compared with the control group presented significant data measured with the RatsTrack. RatsTrack is a plugin of ImageJ software and will be made freely available for public use.

Management of hemotherapy services in the context of the COVID-19 pandemic.

This study aimed to analyze the management of hemotherapy services (HS) in the context of the COVID-19 pandemic from the perspective of municipal managers in different regions of Brazil. A qualitative approach with semi-structured interviews was applied to HS managers in the three Brazilian capitals, from different regions of Brazil, during the period between September 2021 and April 2022. The textual content of the interviews was submitted to lexicographic textual analysis using the free access software, Iramuteq. The managers' perceptions resulted from the descending hierarchical classification (DHC) analysis, which generated six classes: availability of resources for the development of work; installed capacity of services; strategies and challenges for attracting blood donors; risks and worker protection; measures for crisis management; and communication strategies for the adhesion of candidates for donation. The analysis highlighted several strategies used by the management, as well as pointed out limits and challenges for HS organization and management, exacerbated in the context of the pandemic.

Gestão dos serviços hemoterápicos no contexto da pandemia de COVID-19

Abstract This study aimed to analyze the management of hemotherapy services (HS) in the context of the COVID-19 pandemic from the perspective of municipal managers in different regions of Brazil. A qualitative approach with semi-structured interviews was applied to HS managers in the three Brazilian capitals, from different regions of Brazil, during the period between September 2021 and April 2022. The textual content of the interviews was submitted to lexicographic textual analysis using the free access software, Iramuteq. The managers’ perceptions resulted from the descending hierarchical classification (DHC) analysis, which generated six classes: availability of resources for the development of work; installed capacity of services; strategies and challenges for attracting blood donors; risks and worker protection; measures for crisis management; and communication strategies for the adhesion of candidates for donation. The analysis highlighted several strategies used by the management, as well as pointed out limits and challenges for HS organization and management, exacerbated in the context of the pandemic.

Evaluation of control strategies applied in small-scale photovoltaic solar tracking systems: a review

This work evaluates the control algorithms applied to decentralized photovoltaic solar tracking systems. For this, the control strategies are divided into three: open loop, closed loop and hybrid loop. Each strategy is screened for its suitability as a suitable technology for small-scale applications, defined by meeting a set of eleven attributes. A specialized literature review process was developed specifically to present the potential of each control algorithm strategy, through an evaluation matrix. The analysis of the algorithms and attributes was carried out using the formal methodology of concept analysis. To facilitate the processing of the information, free access software called “concept Explorer” is used. The analysis carried out shows that open loop control algorithms currently have a greater application in one and two-axis solar tracking systems. Additionally, the on-off control is the one with the greatest application for the three types of control loops evaluated. Finally, the applied methodology has proven to be useful for the evaluation of information and serves as a reference, to carry out analyzes that group and link different alternatives as a model for evaluating a deterministic set of attributes.

A toolbox for the retrodeformation and muscle reconstruction of fossil specimens in Blender.

Accurate muscle reconstructions can offer new information on the anatomy of fossil organisms and are also important for biomechanical analysis (multibody dynamics and finite-element analysis (FEA)). For the sake of simplicity, muscles are often modelled as point-to-point strands or frustra (cut-off cones) in biomechanical models. However, there are cases in which it is useful to model the muscle morphology in three dimensions, to better examine the effects of muscle shape and size. This is especially important for fossil analyses, where muscle force is estimated from the reconstructed muscle morphology (rather than based on data collected in vivo). The two main aims of this paper are as follows. First, we created a new interactive tool in the free open access software Blender to enable interactive three-dimensional modelling of muscles. This approach can be applied to both palaeontological and human biomechanics research to generate muscle force magnitudes and lines of action for FEA. Second, we provide a guide on how to use existing Blender tools to reconstruct distorted or incomplete specimens. This guide is aimed at palaeontologists but can also be used by anatomists working with damaged specimens or to test functional implication of hypothetical morphologies.

Estimation of gender and age through the angulation formed by the pterygoid processes of the sphenoid bone

To obtain angular measurements formed from the junction of the bilateral pterygoid processes of the sphenoid bone through computed tomography scans of the conical beam of the sphenoid bone, in order to correlate them with the estimation of gender and age in a human identification process. 602 computed tomography (CBCT) scans were selected – 301 males and 301 females. The tomographic images were analyzed, in low light conditions, independently the using of the free access software Radiant DICOM Viewer and, within the program, an angle calculation tool was applied on top of the axial cut in the union of the pterygoid processes medial and lateral bilaterally. The collected data were quantified in tables according to their age and gender, in addition to being statistically analyzed. There was no correlation between increasing age and the angles formed by bilateral pterygoid processes. But there is a statistically significant difference between the values of the angles between males and females on the left and right sides, t(600) = 2,6186 (p-value = 0,0091) and t(600) = 3.3593 (p- value = 0,0008), respectively. Based on our results, there are statistically significant differences between genders in relation to the angles formed by the pterygoid processes of the sphenoid bone, with higher descriptive values in men with older ages.

Grain Size Distribution and Head Rice Yield of Some Rice Breeding Lines using Flat-Bed Scanning and Digital Image Analysis

Rice grain quality evaluation is crucial in rice breeding and production of selected varieties. Characterization of rice grain fractions after milling is important; these include brown rice, milled rice, and head rice yield (HRY). The latter is the main determinant for the market price of rice. The present study aims to utilize image analysis as a tool for assessing HRY. Digital image analysis (DIA) was used to quantitatively determine HRY for eight selected rice breeding lines and the results were compared with those obtained by the conventional method of manual inspection (MI). Digital images of the rice grains were taken with a flat-bed scanner (FBS) and analyzed using free-access software (ImageJ). Areas of individual grains were determined, and percent grain area was calculated in terms of the ratio of actual-to-whole grain areas (AWGA). Size grain distribution plots were generated per breeding line, and those grains with values of the AWGA ratio greater than or equal to 75% were classified as head rice. The HRY value was calculated in percent-by-mass basis using the mass of 100 whole rice grains. Values of HRY obtained using DIA showed no significant difference compared to those obtained using the conventional method. This was done according to the paired samples t-test at 95% confidence interval, which showed a high correlation coefficient (R2 = 0.99). The DIA method showed good repeatability and reproducibility based on different precision parameters indicating its potential as a practical, inexpensive, and quantitative method for determining HRY of rice breeding lines.

Optical Performance Assessment of a Handmade Prototype of Linear Fresnel Concentrator

This article aims to evaluate the optical behavior of a small handmade prototype of a linear Fresnel concentrator (LFC). The system was developed and tested as a water heater and steam generator at the Unidades Tecnológicas de Santander university, located in Bucaramanga, Colombia. Optical factors of the thermo-solar system studied were taken into account, such as concentration ratio and optical efficiency relationships. The Monte Carlo ray tracing method (MCRT) was carried out as an optical evaluation tool through the application of the free access software "SolTrace" and "TONATIUH" to later contrast the results obtained with both simulation tools. At the same time, the performance output from the simulations was compared with the optical performance of the experiments previously carried out with the device LFC, with the aim of evaluating the reliability and accuracy of the analysis developed through the MCRT methodology. The results obtained showed that the number of reflective mirrors or area of reflection has a direct impact on the optical efficiency of the prototype, where it is evidenced that there is a higher optical efficiency and a higher CR when the reflection area is larger. Similarly, direct solar radiation (DNI) has the same trend, showing that higher levels of direct solar radiation (DNI) increase optical efficiency. Finally, it was observed that the variation in the number of rays used in the simulations (10,000,000 and 5,000,000) does not influence the optical performance of the device.

Presenter: Werner Paulus, University Hospital Muenster, Muenster. Publishing A High-quality, Non-commercial Neuropathology Journal Without a Publisher: The First Nine Months

Scholarly communication faces increasing economical and ethical challenges, including pricing policies and overbearing behavior of commercial publishing houses. Based on the hypothesis that a diamond open access neuropathology journal of a high scientific and technical quality can be run entirely by neuropathologists, we launched Free Neuropathology (FNP; freeneuropathology.org) in January 2020. Classical publisher activities, such as copyediting, layout, website maintenance, and journal promotion, are undertaken by neuropathologists and neuroscientists using free open access software. The journal is free for both readers and authors, and papers are published under a Creative Commons BY SA licence, where copyright remains with the authors. Based on 26 articles published by August 2020, it takes FNP 11.1 days from submission to first, and 19.9 days to final, decision. High-quality copyediting, layout, and online publishing in the final format is accomplished in only 8 days. Absence of a commercial publisher enables prioritization of democratic and scientifically-driven decisions on editorial structure, website design, journal promotion, paper formatting, special article series, and number of accepted papers. This new model of journal publishing, which returns the control of scholarly communication to scientists, will be of interest to neuropathologists and wider scientific community alike.Learning ObjectivesSummarize the current state and driving forces behind commercial and non-commercial scientific publishing in neuropathology.Describe the advantages and challenges of a non-commercial publishing platform for neuropathology.

Co-culture of Glioblastoma Stem-like Cells on Patterned Neurons to Study Migration and Cellular Interactions.

Glioblastomas (GBMs), grade IV malignant gliomas, are one of the deadliest types of human cancer because of their aggressive characteristics. Despite significant advances in the genetics of these tumors, how GBM cells invade the healthy brain parenchyma is not well understood. Notably, it has been shown that GBM cells invade the peritumoral space via different routes; the main interest of this paper is the route along white matter tracts (WMTs). The interactions of tumor cells with the peritumoral nervous cell components are not well characterized. Herein, a method has been described that evaluates the impact of neurons on GBM cell invasion. This paper presents an advanced co-culture in vitro assay that mimics WMT invasion by analyzing the migration of GBM stem-like cells on neurons. The behavior of GBM cells in the presence of neurons is monitored by using an automated tracking procedure with open-source and free-access software. This method is useful for many applications, in particular, for functional and mechanistic studies as well as for analyzing the effects of pharmacological agents that can block GBM cell migration on neurons.

Providing a simple online toolkit for school libraries in developing countries so that they can become centers of competence in primary and secondary schools

This paper describes a co-operative effort between the ENSIL Foundation and the Royal Tropical Institute, KIT Information and Library Services to provide school libraries, especially those in developing countries, with a simple online toolkit, which will help them to become centres of competence in primary and secondary schools. It is based on a similar toolkit which was designed by the KIT and is being used by university libraries throughout Africa. Although many school libraries have few facilities or funding, the IFLA/FAIFE World Report 2010 reports that approximately 30% of all school libraries worldwide now have Internet access. Using free open access software, the toolkit will provide school libraries with simple (online) training opportunities for library staff in literacy and information literacy skills, an advocacy platform, simple cataloguing tools, and access to online (full-text) resources). In addition it will provide access to online communities which focus on knowledge sharing. The paper will also broach the subject of an international, online, open-access repository for school libraries.

Analysis of apparent amylose content of market milled rice via digital image photometry using a smartphone camera

Apparent amylose content (AC) of market milled rice was analyzed through digital image photometry (DIP) utilizing a smartphone camera and a free-access software (ImageJ). The DIP-AC method was validated using seven test samples and applied to a set of 17 commercially available milled rices varying in AC. A light box was constructed to accommodate a cuvette and a smartphone while ImageJ was used for digital image analysis towards quantifying AC. Smartphone camera settings were also optimized using the red, green, and blue (RGB) values of the digital images of amylose-iodine blue solutions. ISO 100 combined with shutter speed 1/640 was the optimum and most suitable settings combination when B values were used to generate calibration curves yielding a high degree of linearity (r = 0.995–0.998). Validation showed the DIP-AC method to be accurate based on the conventional ultraviolet–visible (UV-vis) spectrophotometric AC assay. It was also found to be repeatable and precise for non-waxy rice samples only, yielding RSD values below 7% among all replications made within one day and across different days. With the optimized DIP-AC assay, limits of detection and quantitation of AC that is capable of iodine binding at alkaline pH and influencing cooked rice texture, were 0.2% and 0.4% (milled rice basis at 12–14% moisture), respectively. The reported DIP-AC method can be a reliable and accurate assay for determining AC of non-waxy milled rice alternative to UV–vis spectrophotometry. Further refinement of the DIP-AC method is warranted to improve precision in measuring AC of milled waxy rice.

Identification of Maillard Based Lactose Adduct in Roflumilast Generated During Incompatibility Studies and its RP-HPLC Method Development, Validation and Impurity Control

Roflumilast is Prescribe as the first line treatment for COPD (Chronic Obstructive Pulmonary Disease). One of the critical starting materials for the synthesis of Roflumilast API is 3,5-dichloro-4-aminopyridine. It is also generated during the degradation of Roflumilast API and termed as degradant product-1(DP-1). The primary amino group of DP-1 reacts with lactose monohydrate (Maillard reaction) in the formulation to form DP-1Lactose Adduct (DPLA) under relatively harsh conditions. This adduct formed, was isolated and characterized by different spectroscopic methods. In-silico toxicological evaluation of characterized adduct was done using online free access software T.E.S.T toxicity estimation tool, Pro-TOX-II and Pre-ADMET, results advocating that the adduct may have Carcinogenicity, Developmental toxicity or Immuno-toxicity. In addition to this, a selective, robust and precise reversed-phase high-performance liquid chromatography (RP-HPLC) method was developed and validated as per ICH Q2(R1) guideline for the determination of Roflumilast, 3, 5-dichloro-4-aminopyridine in presence of DPLA. The chromatographic separation was performed with Phenomenex Luna C 18 column (250 mm × 4.6 mm, 5 μm) using a mobile phase consisting of Acetonitrile - Ammonium formate (10mM) (pH 8.0). pH was adjusted to 8 with triethylamine, in gradient mode 0 min (75:25, v/v), 3.5min (70:30, v/v) and 5 min (85:15, v/v) keeping the flow rate of 0.6 ml/min. Quantification was achieved using UV detection at 254nm. Linearity, accuracy, and precision were found to be under acceptable criteria for the determination of Roflumilast, 3, 5-dichloro-4-aminopyridine and DPLA in the concentration range of 200-1200 µg ml -1 , 1–6 µg ml -1 and 0.2-1.2 µg ml -1 , respectively. Further for rationalization of formation of DPLA, stability studies of DP-1 spiked in-house and marketed formulation were performed at 25°C ± 2°C and 60% RH ± 5% RH and at 40°C ± 2°C and 75% RH ± 5% RH, which conclude that up to the 180 days there was no evidence of the formation of lactose adduct so far. The DPLA should be controlled ≤ 0.3% during formulation development, calculated concerning the ICH M7 guideline to prevent its genotoxic effect. Overall, this study suggests either replacing the lactose monohydrate as an excipient in tablet or avoidance of high moisture and higher temperature during formulation development to avoid the impurity generation.

Interactive machine learning for soybean seed and seedling quality classification

New computer vision solutions combined with artificial intelligence algorithms can help recognize patterns in biological images, reducing subjectivity and optimizing the analysis process. The aim of this study was to propose an approach based on interactive and traditional machine learning methods to classify soybean seeds and seedlings according to their appearance and physiological potential. In addition, we correlated the appearance of seeds to their physiological performance. Images of soybean seeds and seedlings were used to develop models using low-cost approaches and free-access software. The models developed showed high performance, with overall accuracy reaching 0.94 for seeds and seedling classification. The high precision of the models that were developed based on interactive and traditional machine learning demonstrated that the method can easily be used to classify soybean seeds according to their appearance, as well as to classify soybean seedling vigor quickly and non-subjectively. The appearance of soybean seeds is strongly correlated with their physiological performance.

Bark water storage capacity influences epiphytic orchid preference for host trees.

Of all orchid species described, 70% live on phorophytes. Trees offer a vital space with characteristics that influence the successful establishment and life cycle of orchids. Field inventory and distribution analysis suggest that phorophyte selection is biased to certain tree species that would serve as better hosts. Phorophyte bark is known as an important factor that influences this preference, but the chemical and physical properties of bark that contribute to creating a favorable space for orchids are still poorly understood. In this work, the effect of bark physical characteristics on phorophyte preference of tropical orchids was studied. Orchids and their phorophytes were counted and identified along transects inside two natural reserves in Southeast Mexico. A rhytidome classification was used to describe the bark decoration patterns of the phorophytes. To quantify bark fissuring, we developed a new protocol based on image processing of light micrographs using free-access software. Bark topology characterization was complemented with scanning electronic microscopy. Maximum and minimum water content was also determined. Analyses of bark decorations and bark fissuring were not enough to explain the preference found for some tropical trees. In contrast, a positive relationship was found among water-storage capacity, bark porosity, and phorophyte preference. The host trees preferred by most orchids have bark with higher pore density and higher water retention after draining. Unexpectedly, the phorophytes preferred by orchids are not those with more fissured bark but those with a higher ability to retain minimum water content after draining, which is a bark property positively correlated with higher pore density. Our data indicate that the bark microenvironment, determined by topology and water storage capacity, has a pivotal role in phorophyte specificity, a key factor that affects orchid diversity and distribution in the world.

Quantification of the Food Dye Indigo Carmine in Candies Using Digital Image Analysis in a Polyurethane Foam Support

The aim of this present work was to propose an alternative methodology to quantify the food dye indigo carmine in industrialized candies by the innovative technique of digital image analysis. To do so, the candy was solubilized in water and extracted to polyurethane foam, which is capable of selectively adsorbing the dye, removing interferents from the matrix. The foam was dried and glued on a sheet of paper. After that, digital images of the system were taken using a flatbed scanner. A free-access software was used to treat these images in order to obtain the color intensity of the foam, which was related to the concentration of the analyte. The linear range of this proposed method was 0.1 to 5.0 mg L−1. The limits of detection and quantification were respectively 0.20 μg g−1 and 0.68 μg g−1. These limits were adequate to determine indigo carmine in the studied candies. The precision of the method was estimated in 2.16% by the standard deviation of daily replicates and the accuracy in 113 ± 2% by recovery tests. The method was applied in the quantification of the analyte in real samples, and these results were compared with the ones obtained by a previously established chromatographic method, resulting in a statistical conformity at 95% confidence level.

The porous size distribution obtained and analyzed by free access software

Abstract This paper presents the description of methods for using in the analysis of the pore size distribution of complex porous media as, for instance, soils. The sequence of analyses presented here can be implemented in classes of post-graduation in physics applied to earth, soil, and environmental sciences. The objective was to present the use, by students and/or researchers, of free access software to analyze images for obtaining some morphological aspects of porous systems. Two methods of obtaining the pore size distribution are presented: the first one is based on ImageJ internal routines, and the second in the study presented in Yang [1]. The results obtained permitted a detailed analysis of three-dimensional(3D) images of porous systems and also obtaining the pore size distribution of the investigated medium. The procedures here introduced can easily be extended for educational purposes in courses related to the investigation of systems with complex internal structures.

Estudio computacional de la reactividad y propiedades fisicoquímicas del eugenol, 2-metoxi-4-oxiranilmetilfenol y quinona metilada

El eugenol es un fenilpropanoide con potencial farmacológico, este estudio determinó teóricamente las propiedades fisicoquímicas del eugenol y derivados. Se encontró que estos cumplen con las reglas de cinco de Lipinski, lo que los posiciona como posibles fármacos. Asimismo, se estudió la reactividad de estas moléculas frente al citocromo P450 y en microorganismos aeróbicos. Utilizando programas de acceso libre se encontró que estas reacciones se dan, principalmente, en los átomos de carbono 1, 2, 3 y 7. Por último, se encontró una correlación entre el desplazamiento químico del 1H RMN y la energía de activación de los átomos de carbono.

Design and manufacture of a didactic tool through the use of 3D printing technology to teach the capacitor charging and discharging phenomenon

This paper reports the design and manufacture of an easy-to-use and accessible teaching system by using 3D printing as a tool for the teaching of the capacitor charging and discharging phenomenon. The didactic system developed, is structured in modules-built piece by piece with 3D printing technology. They are made in a relatively low-cost polymer that could facilitate both teachers and students to improve the teaching-learning processes. This didactic system is reliable, easy to use and low cost. As a way to improve the functionality, the built system is complemented by the use of a free access software and a simple generator of signals that allows to simulate a virtual oscilloscope. This is an additional strategy that would allow the didactic system to enrich the study of the phenomena and eliminate the use of high cost devices that generally limit the experimentation developed traditionally in the teaching of physics. The practical application and implementation of 3D printing technology can be incorporated into a wide variety university subjects in the development of experiments in circuit theory, electricity and magnetism, among others, for its advantages in facilitating the comprehension and assimilation of difficult theoretical concepts and the learning of the physical tangibility of the phenomena under study.