ResearchPad - computational-science https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Comparison of mobile and clinical EEG sensors through resting state simultaneous data collection]]> https://www.researchpad.co/article/Na9ad671e-9020-41e5-9873-c25142c66f31 Development of mobile sensors brings new opportunities to medical research. In particular, mobile electroencephalography (EEG) devices can be potentially used in low cost screening for epilepsy and other neurological and psychiatric disorders. The necessary condition for such applications is thoughtful validation in the specific medical context. As part of validation and quality assurance, we developed a computer-based analysis pipeline, which aims to compare the EEG signal acquired by a mobile EEG device to the one collected by a medically approved clinical-grade EEG device. Both signals are recorded simultaneously during 30 min long sessions in resting state. The data are collected from 22 patients with epileptiform abnormalities in EEG. In order to compare two multichannel EEG signals with differently placed references and electrodes, a novel data processing pipeline is proposed. It allows deriving matching pairs of time series which are suitable for similarity assessment through Pearson correlation. The average correlation of 0.64 is achieved on a test dataset, which can be considered a promising result, taking the positions shift due to the simultaneous electrode placement into account.

]]>
<![CDATA[Estimation of nitrogen leaching load from agricultural fields in the Puck Commune with an interactive calculator]]> https://www.researchpad.co/article/Na6c604bb-8649-4c15-a748-d3f79bf681dc

Background

Nutrient leaching from agricultural fields is one of the main causes of pollution and eutrophication of the Baltic Sea. The quantity of nitrogen (N) leached from a particular field can be very different from the amount of N leached from other fields in a given region or even within a single farm. Therefore, it is necessary to estimate the quantity of N leached for each field separately.

Methods

An opinion poll has been conducted on 31 farms within the Puck Commune, which is approximately 3.6% of all farms located in this commune. Farmers provided data on the manner of fertilizing and cultivating crops on all their farms. For each field individually, on the basis of collected data, an estimated amount of the N leaching from the field has been determined.

Results

An interactive calculator to assist farmers in determining the quantity of N leaching from the agricultural field has been developed. The influence of factors shaping the amount of N leaching from a single field has been analyzed, and it has been determined that autumn plowing (specifically its absence) and the type of cultivated soil had the greatest average influence on this value in the studied sample.

Discussion

Due to the possible ways of reducing N leaching from agricultural fields, most of the studied fields were fertilized in an appropriate manner. However, in the studied sample there were fields for which the fertilization intensity significantly exceeded the recommended doses. In this context, a tool in the form of an interactive, easy-to-use N leaching calculator should help farmers to select appropriate doses and optimal fertilization practices.

]]>
<![CDATA[Speeding up training of automated bird recognizers by data reduction of audio features]]> https://www.researchpad.co/article/N40f36632-3f00-4944-a631-cf570fa0d134

Automated acoustic recognition of birds is considered an important technology in support of biodiversity monitoring and biodiversity conservation activities. These activities require processing large amounts of soundscape recordings. Typically, recordings are transformed to a number of acoustic features, and a machine learning method is used to build models and recognize the sound events of interest. The main problem is the scalability of data processing, either for developing models or for processing recordings made over long time periods. In those cases, the processing time and resources required might become prohibitive for the average user. To address this problem, we evaluated the applicability of three data reduction methods. These methods were applied to a series of acoustic feature vectors as an additional postprocessing step, which aims to reduce the computational demand during training. The experimental results obtained using Mel-frequency cepstral coefficients (MFCCs) and hidden Markov models (HMMs) support the finding that a reduction in training data by a factor of 10 does not significantly affect the recognition performance.

]]>
<![CDATA[Integrated bioinformatics analysis of potential pathway biomarkers using abnormal proteins in clubfoot]]> https://www.researchpad.co/article/N281503c4-030c-45ad-a2bb-9a1a2cd47d9c

Background

As one of the most common major congenital distal skeletal abnormalities, congenital talipes equinovarus (clubfoot) affects approximately one in one thousandth newborns. Although several etiologies of clubfoot have been proposed and several genes have been identified as susceptible genes, previous studies did not further explore signaling pathways and potential upstream and downstream regulatory networks. Therefore, the aim of the present investigation is to explore abnormal pathways and their interactions in clubfoot using integrated bioinformatics analyses.

Methods

KEGG, gene ontology (GO), Reactome (REAC), WikiPathways (WP) or human phenotype ontology (HP) enrichment analysis were performed using WebGestalt, g:Profiler and NetworkAnalyst.

Results

A large number of signaling pathways were enriched e.g. signal transduction, disease, metabolism, gene expression (transcription), immune system, developmental biology, cell cycle, and ECM. Protein-protein interactions (PPIs) and gene regulatory networks (GRNs) analysis results indicated that extensive and complex interactions occur in these proteins, enrichment pathways, and TF-miRNA coregulatory networks. Transcription factors such as SOX9, CTNNB1, GLI3, FHL2, TGFBI and HOXD13, regulated these candidate proteins.

Conclusion

The results of the present study supported previously proposed hypotheses, such as ECM, genetic, muscle, neurological, skeletal, and vascular abnormalities. More importantly, the enrichment results also indicated cellular or immune responses to external stimuli, and abnormal molecular transport or metabolism may be new potential etiological mechanisms of clubfoot.

]]>
<![CDATA[Differentially expressed genes and key molecules of BRCA1/2-mutant breast cancer: evidence from bioinformatics analyses]]> https://www.researchpad.co/article/N73edecdb-f021-45e4-8424-5855f8b14663

Background

BRCA1 and BRCA2 genes are currently proven to be closely related to high lifetime risks of breast cancer. To date, the closely related genes to BRCA1/2 mutations in breast cancer remains to be fully elucidated. This study aims to identify the gene expression profiles and interaction networks influenced by BRCA1/2 mutations, so as to reflect underlying disease mechanisms and provide new biomarkers for breast cancer diagnosis or prognosis.

Methods

Gene expression profiles from The Cancer Genome Atlas (TCGA) database were downloaded and combined with cBioPortal website to identify exact breast cancer patients with BRCA1/2 mutations. Gene set enrichment analysis (GSEA) was used to analyze some enriched pathways and biological processes associated BRCA mutations. For BRCA1/2-mutant breast cancer, wild-type breast cancer and corresponding normal tissues, three independent differentially expressed genes (DEGs) analysis were performed to validate potential hub genes with each other. Protein–protein interaction (PPI) networks, survival analysis and diagnostic value assessment helped identify key genes associated with BRCA1/2 mutations.

Results

The regulation process of cell cycle was significantly enriched in mutant group compared with wild-type group. A total of 294 genes were identified after analysis of DEGs between mutant patients and wild-type patients. Interestingly, by the other two comparisons, we identified 43 overlapping genes that not only significantly expressed in wild-type breast cancer patients relative to normal tissues, but more significantly expressed in BRCA1/2-mutant breast patients. Based on the STRING database and cytoscape software, we constructed a PPI network using 294 DEGs. Through topological analysis scores of the PPI network and 43 overlapping genes, we sought to select some genes, thereby using survival analysis and diagnostic value assessment to identify key genes pertaining to BRCA1/2-mutant breast cancer. CCNE1, NPBWR1, A2ML1, EXO1 and TTK displayed good prognostic/diagnostic value for breast cancer and BRCA1/2-mutant breast cancer.

Conclusion

Our research provides comprehensive and new insights for the identification of biomarkers connected with BRCA mutations, availing diagnosis and treatment of breast cancer and BRCA1/2-mutant breast cancer patients.

]]>
<![CDATA[From command-line bioinformatics to bioGUI]]> https://www.researchpad.co/article/N6907988f-0003-4d82-90f3-5cffef06aa7f

Bioinformatics is a highly interdisciplinary field providing (bioinformatics) applications for scientists from many disciplines. Installing and starting applications on the command-line (CL) is inconvenient and/or inefficient for many scientists. Nonetheless, most methods are implemented with a command-line interface only. Providing a graphical user interface (GUI) for bioinformatics applications is one step toward routinely making CL-only applications available to more scientists and, thus, toward a more effective interdisciplinary work. With our bioGUI framework we address two main problems of using CL bioinformatics applications: First, many tools work on UNIX-systems only, while many scientists use Microsoft Windows. Second, scientists refrain from using CL tools which, however, could well support them in their research. With bioGUI install modules and templates, installing and using CL tools is made possible for most scientists—even on Windows, due to bioGUI’s support for Windows Subsystem for Linux. In addition, bioGUI templates can easily be created, making the bioGUI framework highly rewarding for developers. From the bioGUI repository it is possible to download, install and use bioinformatics tools with just a few clicks.

]]>
<![CDATA[Low expression or hypermethylation of PLK2 might predict favorable prognosis for patients with glioblastoma multiforme]]> https://www.researchpad.co/article/Na7b85ab5-e17c-4fa8-8fbd-b40babb896f2

Background

As the most aggressive brain tumor, patients with glioblastoma multiforme (GBM) have a poor prognosis. Our purpose was to explore prognostic value of Polo-like kinase 2 (PLK2) in GBM, a member of the PLKs family.

Methods

The expression profile of PLK2 in GBM was obtained from The Cancer Genome Atlas database. The PLK2 expression in GBM was tested. Kaplan–Meier curves were generated to assess the association between PLK2 expression and overall survival (OS) in patients with GBM. Furthermore, to assess its prognostic significance in patients with primary GBM, we constructed univariate and multivariate Cox regression models. The association between PLK2 expression and its methylation was then performed. Differentially expressed genes correlated with PLK2 were identified by Pearson test and functional enrichment analysis was performed.

Results

Overall survival results showed that low PLK2 expression had a favorable prognosis of patients with GBM (P-value = 0.0022). Furthermore, PLK2 (HR = 0.449, 95% CI [0.243–0.830], P-value = 0.011) was positively associated with OS by multivariate Cox regression analysis. In cluster 5, DNA methylated PLK2 had the lowest expression, which implied that PLK2 expression might be affected by its DNA methylation status in GBM. PLK2 in CpG island methylation phenotype (G-CIMP) had lower expression than non G-CIMP group (P = 0.0077). Regression analysis showed that PLK2 expression was negatively correlated with its DNA methylation (P = 0.0062, Pearson r = −0.3855). Among all differentially expressed genes of GBM, CYGB (r = 0.5551; P < 0.0001), ISLR2 (r = 0.5126; P < 0.0001), RPP25 (r = 0.5333; P < 0.0001) and SOX2 (r = −0.4838; P < 0.0001) were strongly correlated with PLK2. Functional enrichment analysis results showed that these genes were enriched several biological processes or pathways that were associated with GBM.

Conclusion

Polo-like kinase 2 expression is regulated by DNA methylation in GBM, and its low expression or hypermethylation could be considered to predict a favorable prognosis for patients with GBM.

]]>
<![CDATA[DCEMRI.jl: a fast, validated, open source toolkit for dynamic contrast enhanced MRI analysis]]> https://www.researchpad.co/article/5989da4fab0ee8fa60b8d75c

We present a fast, validated, open-source toolkit for processing dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data. We validate it against the Quantitative Imaging Biomarkers Alliance (QIBA) Standard and Extended Tofts-Kety phantoms and find near perfect recovery in the absence of noise, with an estimated 10–20× speedup in run time compared to existing tools. To explain the observed trends in the fitting errors, we present an argument about the conditioning of the Jacobian in the limit of small and large parameter values. We also demonstrate its use on an in vivo data set to measure performance on a realistic application. For a 192 × 192 breast image, we achieved run times of <1 s. Finally, we analyze run times scaling with problem size and find that the run time per voxel scales as O(N1.9), where N is the number of time points in the tissue concentration curve. DCEMRI.jl was much faster than any other analysis package tested and produced comparable accuracy, even in the presence of noise.

]]>
<![CDATA[Beyond xMOOCs in healthcare education: study of the feasibility in integrating virtual patient systems and MOOC platforms]]> https://www.researchpad.co/article/5989d9ddab0ee8fa60b685d6

Background. Massive Open Online Courses (MOOCs) are an emerging trend in online learning. However, their technology is not yet completely adjusted to the needs of healthcare education. Integration of Virtual Patients within MOOCs to increase interactivity and foster clinical reasoning skills training, has been discussed in the past, but not verified by a practical implementation.

Objective. To investigate the technical feasibility of integrating MOOCs with Virtual Patients for the purpose of enabling further research into the potential pedagogical benefits of this approach.

Methods. We selected OpenEdx and Open Labyrinth as representative constituents of a MOOC platform and Virtual Patient system integration. Based upon our prior experience we selected the most fundamental technical requirement to address. Grounded in the available literature we identified an e-learning standard to guide the integration. We attempted to demonstrate the feasibility of the integration by designing a “proof-of-concept” prototype. The resulting pilot implementation was subject of verification by two test cases.

Results. A Single Sign-On mechanism connecting Open Labyrinth with OpenEdx and based on the IMS LTI standard was successfully implemented and verified.

Conclusion. We investigated the technical perspective of integrating Virtual Patients with MOOCs. By addressing this crucial technical requirement we set a base for future research on the educational benefits of using virtual patients in MOOCs. This provides new opportunities for integrating specialized software in healthcare education at massive scale.

]]>
<![CDATA[A simple and efficient method to enhance audiovisual binding tendencies]]> https://www.researchpad.co/article/5989db59ab0ee8fa60bdefd1

Individuals vary in their tendency to bind signals from multiple senses. For the same set of sights and sounds, one individual may frequently integrate multisensory signals and experience a unified percept, whereas another individual may rarely bind them and often experience two distinct sensations. Thus, while this binding/integration tendency is specific to each individual, it is not clear how plastic this tendency is in adulthood, and how sensory experiences may cause it to change. Here, we conducted an exploratory investigation which provides evidence that (1) the brain’s tendency to bind in spatial perception is plastic, (2) that it can change following brief exposure to simple audiovisual stimuli, and (3) that exposure to temporally synchronous, spatially discrepant stimuli provides the most effective method to modify it. These results can inform current theories about how the brain updates its internal model of the surrounding sensory world, as well as future investigations seeking to increase integration tendencies.

]]>
<![CDATA[Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology]]> https://www.researchpad.co/article/5989db2dab0ee8fa60bd1b22

Orthology inference and other sequence analyses across multiple genomes typically start by performing exhaustive pairwise sequence comparisons, a process referred to as “all-against-all”. As this process scales quadratically in terms of the number of sequences analysed, this step can become a bottleneck, thus limiting the number of genomes that can be simultaneously analysed. Here, we explored ways of speeding-up the all-against-all step while maintaining its sensitivity. By exploiting the transitivity of homology and, crucially, ensuring that homology is defined in terms of consistent protein subsequences, our proof-of-concept resulted in a 4× speedup while recovering >99.6% of all homologs identified by the full all-against-all procedure on empirical sequences sets. In comparison, state-of-the-art k-mer approaches are orders of magnitude faster but only recover 3–14% of all homologous pairs. We also outline ideas to further improve the speed and recall of the new approach. An open source implementation is provided as part of the OMA standalone software at http://omabrowser.org/standalone.

]]>
<![CDATA[Visual analytics in healthcare education: exploring novel ways to analyze and represent big data in undergraduate medical education]]> https://www.researchpad.co/article/5989da4fab0ee8fa60b8d8b8

Introduction. The big data present in the medical curriculum that informs undergraduate medical education is beyond human abilities to perceive and analyze. The medical curriculum is the main tool used by teachers and directors to plan, design, and deliver teaching and assessment activities and student evaluations in medical education in a continuous effort to improve it. Big data remains largely unexploited for medical education improvement purposes. The emerging research field of visual analytics has the advantage of combining data analysis and manipulation techniques, information and knowledge representation, and human cognitive strength to perceive and recognize visual patterns. Nevertheless, there is a lack of research on the use and benefits of visual analytics in medical education.

Methods. The present study is based on analyzing the data in the medical curriculum of an undergraduate medical program as it concerns teaching activities, assessment methods and learning outcomes in order to explore visual analytics as a tool for finding ways of representing big data from undergraduate medical education for improvement purposes. Cytoscape software was employed to build networks of the identified aspects and visualize them.

Results. After the analysis of the curriculum data, eleven aspects were identified. Further analysis and visualization of the identified aspects with Cytoscape resulted in building an abstract model of the examined data that presented three different approaches; (i) learning outcomes and teaching methods, (ii) examination and learning outcomes, and (iii) teaching methods, learning outcomes, examination results, and gap analysis.

Discussion. This study identified aspects of medical curriculum that play an important role in how medical education is conducted. The implementation of visual analytics revealed three novel ways of representing big data in the undergraduate medical education context. It appears to be a useful tool to explore such data with possible future implications on healthcare education. It also opens a new direction in medical education informatics research.

]]>
<![CDATA[Contribution of temporal data to predictive performance in 30-day readmission of morbidly obese patients]]> https://www.researchpad.co/article/5989db59ab0ee8fa60bdf076

Background

Reduction of readmissions after discharge represents an important challenge for many hospitals and has attracted the interest of many researchers in the past few years. Most of the studies in this field focus on building cross-sectional predictive models that aim to predict the occurrence of readmission within 30-days based on information from the current hospitalization. The aim of this study is demonstration of predictive performance gain obtained by inclusion of information from historical hospitalization records among morbidly obese patients.

Methods

The California Statewide inpatient database was used to build regularized logistic regression models for prediction of readmission in morbidly obese patients (n = 18,881). Temporal features were extracted from historical patient hospitalization records in a one-year timeframe. Five different datasets of patients were prepared based on the number of available hospitalizations per patient. Sample size of the five datasets ranged from 4,787 patients with more than five hospitalizations to 20,521 patients with at least two hospitalization records in one year. A 10-fold cross validation was repeted 100 times to assess the variability of the results. Additionally, random forest and extreme gradient boosting were used to confirm the results.

Results

Area under the ROC curve increased significantly when including information from up to three historical records on all datasets. The inclusion of more than three historical records was not efficient. Similar results can be observed for Brier score and PPV value. The number of selected predictors corresponded to the complexity of the dataset ranging from an average of 29.50 selected features on the smallest dataset to 184.96 on the largest dataset based on 100 repetitions of 10-fold cross-validation.

Discussion

The results show positive influence of adding information from historical hospitalization records on predictive performance using all predictive modeling techniques used in this study. We can conclude that it is advantageous to build separate readmission prediction models in subgroups of patients with more hospital admissions by aggregating information from up to three previous hospitalizations.

]]>
<![CDATA[An elaborate data set on human gait and the effect of mechanical perturbations]]> https://www.researchpad.co/article/5989db4bab0ee8fa60bda210

Here we share a rich gait data set collected from fifteen subjects walking at three speeds on an instrumented treadmill. Each trial consists of 120 s of normal walking and 480 s of walking while being longitudinally perturbed during each stance phase with pseudo-random fluctuations in the speed of the treadmill belt. A total of approximately 1.5 h of normal walking (>5000 gait cycles) and 6 h of perturbed walking (>20,000 gait cycles) is included in the data set. We provide full body marker trajectories and ground reaction loads in addition to a presentation of processed data that includes gait events, 2D joint angles, angular rates, and joint torques along with the open source software used for the computations. The protocol is described in detail and supported with additional elaborate meta data for each trial. This data can likely be useful for validating or generating mathematical models that are capable of simulating normal periodic gait and non-periodic, perturbed gaits.

]]>
<![CDATA[How word-beginnings constrain the pronunciations of word-ends in the reading aloud of English: the phenomena of head- and onset-conditioning]]> https://www.researchpad.co/article/5989db0fab0ee8fa60bcba5c

Background. A word whose body is pronounced in different ways in different words is body-inconsistent. When we take the unit that precedes the vowel into account for the calculation of body-consistency, the proportion of English words that are body-inconsistent is considerably reduced at the level of corpus analysis, prompting the question of whether humans actually use such head/onset-conditioning when they read.

Methods. Four metrics for head/onset-constrained body-consistency were calculated: by the last grapheme of the head, by the last phoneme of the onset, by place and manner of articulation of the last phoneme of the onset, and by manner of articulation of the last phoneme of the onset. Since these were highly correlated, principal component analysis was performed on them.

Results. Two out of four resulting principal components explained significant variance in the reading-aloud reaction times, beyond regularity and body-consistency.

Discussion. Humans read head/onset-conditioned words faster than would be predicted based on their body-consistency and regularity only. We conclude that humans are sensitive to the dependency between word-beginnings and word-ends when they read aloud, and that this dependency is phonological in nature, rather than orthographic.

]]>
<![CDATA[Language workbench user interfaces for data analysis]]> https://www.researchpad.co/article/5989dab5ab0ee8fa60baca63

Biological data analysis is frequently performed with command line software. While this practice provides considerable flexibility for computationally savy individuals, such as investigators trained in bioinformatics, this also creates a barrier to the widespread use of data analysis software by investigators trained as biologists and/or clinicians. Workflow systems such as Galaxy and Taverna have been developed to try and provide generic user interfaces that can wrap command line analysis software. These solutions are useful for problems that can be solved with workflows, and that do not require specialized user interfaces. However, some types of analyses can benefit from custom user interfaces. For instance, developing biomarker models from high-throughput data is a type of analysis that can be expressed more succinctly with specialized user interfaces. Here, we show how Language Workbench (LW) technology can be used to model the biomarker development and validation process. We developed a language that models the concepts of Dataset, Endpoint, Feature Selection Method and Classifier. These high-level language concepts map directly to abstractions that analysts who develop biomarker models are familiar with. We found that user interfaces developed in the Meta-Programming System (MPS) LW provide convenient means to configure a biomarker development project, to train models and view the validation statistics. We discuss several advantages of developing user interfaces for data analysis with a LW, including increased interface consistency, portability and extension by language composition. The language developed during this experiment is distributed as an MPS plugin (available at http://campagnelab.org/software/bdval-for-mps/).

]]>
<![CDATA[Dramatyping: a generic algorithm for detecting reasonable temporal correlations between drug administration and lab value alterations]]> https://www.researchpad.co/article/5989da95ab0ee8fa60ba1829

According to the World Health Organization, one of the criteria for the standardized assessment of case causality in adverse drug reactions is the temporal relationship between the intake of a drug and the occurrence of a reaction or a laboratory test abnormality. This article presents and describes an algorithm for the detection of a reasonable temporal correlation between the administration of a drug and the alteration of a laboratory value course. The algorithm is designed to process normalized lab values and is therefore universally applicable. It has a sensitivity of 0.932 for the detection of lab value courses that show changes in temporal correlation with the administration of a drug and it has a specificity of 0.967 for the detection of lab value courses that show no changes. Therefore, the algorithm is appropriate to screen the data of electronic health records and to support human experts in revealing adverse drug reactions. A reference implementation in Python programming language is available.

]]>
<![CDATA[DrugOn: a fully integrated pharmacophore modeling and structure optimization toolkit]]> https://www.researchpad.co/article/5989daceab0ee8fa60bb5306

During the past few years, pharmacophore modeling has become one of the key components in computer-aided drug design and in modern drug discovery. DrugOn is a fully interactive pipeline designed to exploit the advantages of modern programming and overcome the command line barrier with two friendly environments for the user (either novice or experienced in the field of Computer Aided Drug Design) to perform pharmacophore modeling through an efficient combination of the PharmACOphore, Gromacs, Ligbuilder and PDB2PQR suites. Our platform features a novel workflow that guides the user through each logical step of the iterative 3D structural optimization setup and drug design process. For the pharmacophore modeling we are focusing on either the characteristics of the receptor or the full molecular system, including a set of selected ligands. DrugOn can be freely downloaded from our dedicated server system at www.bioacademy.gr/bioinformatics/drugon/.

]]>
<![CDATA[An experimental search strategy retrieves more precise results than PubMed and Google for questions about medical interventions]]> https://www.researchpad.co/article/5989dac0ab0ee8fa60bb07f5

Objective. We compared the precision of a search strategy designed specifically to retrieve randomized controlled trials (RCTs) and systematic reviews of RCTs with search strategies designed for broader purposes.

Methods. We designed an experimental search strategy that automatically revised searches up to five times by using increasingly restrictive queries as long at least 50 citations were retrieved. We compared the ability of the experimental and alternative strategies to retrieve studies relevant to 312 test questions. The primary outcome, search precision, was defined for each strategy as the proportion of relevant, high quality citations among the first 50 citations retrieved.

Results. The experimental strategy had the highest median precision (5.5%; interquartile range [IQR]: 0%–12%) followed by the narrow strategy of the PubMed Clinical Queries (4.0%; IQR: 0%–10%). The experimental strategy found the most high quality citations (median 2; IQR: 0–6) and was the strategy most likely to find at least one high quality citation (73% of searches; 95% confidence interval 68%–78%). All comparisons were statistically significant.

Conclusions. The experimental strategy performed the best in all outcomes although all strategies had low precision.

]]>
<![CDATA[Low relative error in consumer-grade GPS units make them ideal for measuring small-scale animal movement patterns]]> https://www.researchpad.co/article/5989daadab0ee8fa60baa2b2

Consumer-grade GPS units are a staple of modern field ecology, but the relatively large error radii reported by manufacturers (up to 10 m) ostensibly precludes their utility in measuring fine-scale movement of small animals such as insects. Here we demonstrate that for data collected at fine spatio-temporal scales, these devices can produce exceptionally accurate data on step-length and movement patterns of small animals. With an understanding of the properties of GPS error and how it arises, it is possible, using a simple field protocol, to use consumer grade GPS units to collect step-length data for the movement of small animals that introduces a median error as small as 11 cm. These small error rates were measured in controlled observations of real butterfly movement. Similar conclusions were reached using a ground-truth test track prepared with a field tape and compass and subsequently measured 20 times using the same methodology as the butterfly tracking. Median error in the ground-truth track was slightly higher than the field data, mostly between 20 and 30 cm, but even for the smallest ground-truth step (70 cm), this is still a signal-to-noise ratio of 3:1, and for steps of 3 m or more, the ratio is greater than 10:1. Such small errors relative to the movements being measured make these inexpensive units useful for measuring insect and other small animal movements on small to intermediate scales with budgets orders of magnitude lower than survey-grade units used in past studies. As an additional advantage, these units are simpler to operate, and insect or other small animal trackways can be collected more quickly than either survey-grade units or more traditional ruler/gird approaches.

]]>