Peer-reviewed Articles

128 downloads
102 views

Background Leaching of nutrients from agricultural areas is the main cause of water pollution and eutrophication of the Baltic Sea. A variety of remedial actions to reduce nitrogen and phosphorus losses from agricultural holdings and cultivated fields have been...

["Agricultural Science","Computational Science","Environmental Impacts"]
doi:10.7717/peerj.6478
50 downloads
156 views

Protocols for preparing RNA sequencing (RNA-seq) libraries, most prominently “Smart-seq” variations, introduce global biases that can have a significant impact on the quantification of gene expression levels. This global bias can lead to drastic over- or under-representation...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.6222
56 downloads
363 views

In a previous report, we explored the serverless OpenHealth approach to the Web as a Global Compute space. That approach relies on the modern browser full stack, and, in particular, its configuration for application assembly by code injection. The opportunity,...

["Bioinformatics","Epidemiology","Public Health","Computational Science","Data Science"]
doi:10.7717/peerj.6230
65 downloads
348 views

The co-occurrence of plant species is a fundamental aspect of plant ecology that contributes to understanding ecological processes, including the establishment of ecological communities and its applications in biological conservation. A priori algorithms can be...

["Bioinformatics","Ecology","Computational Science","Data Mining and Machine Learning","Spatial and Geographic Information Science"]
doi:10.7717/peerj.6193
90 downloads
600 views

Background Rhamnolipids, biosurfactants with a wide range of biomedical applications, are amphiphilic molecules produced on the surfaces of or excreted extracellularly by bacteria including Pseudomonas aeruginosa. However, Pseudomonas putida is a non-pathogenic...

["Bioinformatics","Computational Biology","Synthetic Biology","Computational Science","Data Mining and Machine Learning"]
doi:10.7717/peerj.6046
72 downloads
410 views

Background The human hand can perform a range of manipulation tasks, from holding a pen to holding a hammer. The central nervous system (CNS) uses different strategies in different manipulation tasks based on task requirements. Attempts to compare postures of the...

["Bioengineering","Computational Biology","Neuroscience","Kinesiology","Computational Science"]
doi:10.7717/peerj.6078
64 downloads
440 views

Reverse engineering metabolome data to infer metabolic interactions is a challenging research topic. Here we introduce JacLy, a Jacobian-based method to infer metabolic interactions of small networks (<20 metabolites) from the covariance of steady-state metabolome...

["Bioengineering","Bioinformatics","Biotechnology","Computational Biology","Computational Science"]
doi:10.7717/peerj.6034
83 downloads
356 views

Background Remote photoplethysmography (rPPG) is a promising optical method for non-contact assessment of pulse rate (PR) from video recordings. In order to implement the method in real-time applications, it is necessary for the rPPG algorithms to be capable of...

["Biophysics","Anatomy and Physiology","Computational Science"]
doi:10.7717/peerj.5859
69 downloads
278 views

The Bertalanffy–Pütter growth model describes mass m at age t by means of the differential equation dm/dt = p * ma − q * mb. The special case using the von Bertalanffy exponent-pair a = 2/3 and b = 1 is most common (it corresponds to the von Bertalanffy growth...

["Aquaculture, Fisheries and Fish Science","Computational Biology","Mathematical Biology","Computational Science","Natural Resource Management"]
doi:10.7717/peerj.5973
60 downloads
265 views

Multiplex bead assays are an extension of the commonly used sandwich ELISA. The advantage over ELISA is that they make simultaneous evaluation of several analytes possible. Several commercial assay systems, where the beads are acquired on a standard flow cytometer,...

["Immunology","Computational Science"]
doi:10.7717/peerj.5794
80 downloads
419 views

Segmentation of the retinal blood vessels using filtering techniques is a widely used step in the development of an automated system for diagnostic retinal image analysis. This paper optimized the blood vessel segmentation, by extending the trainable B-COSFIRE...

["Ophthalmology","Radiology and Medical Imaging","Human-Computer Interaction","Computational Science"]
doi:10.7717/peerj.5855
121 downloads
688 views

Transcription factors (TFs) and microRNAs (miRNAs) are well-characterized trans-acting essential players in gene expression regulation. Growing evidence indicates that TFs and miRNAs can work cooperatively, and their dysregulation has been associated with many...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.5951
50 downloads
285 views

The ability of vertebrates to generate rhythm within their spinal neural networks is essential for walking, running, and other rhythmic behaviors. The central pattern generator (CPG) network responsible for these behaviors is well-characterized with experimental...

["Animal Behavior","Bioinformatics","Computational Biology","Neuroscience","Computational Science"]
doi:10.7717/peerj.5849
185 downloads
1,265 views

We aimed to investigate the detection of idiopathic macular holes (MHs) using ultra-wide-field fundus images (Optos) with deep learning, which is a machine learning technology. The study included 910 Optos color images (715 normal images, 195 MH images). Of these...

["Ophthalmology","Computational Science"]
doi:10.7717/peerj.5696
1,267 downloads
351 views

Background Material presented at conferences is meant to provide exposure to ongoing research that could affect medical decision making based on future outcomes. It is important then to evaluate the rates of publication from conference presentations as a measure...

["Radiology and Medical Imaging","Science and Medical Education","Statistics","Computational Science"]
doi:10.7717/peerj.5817

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