This article describes the R package DEoptim, which implements the differential evolution algorithm for global optimization of a real-valued function of a real-valued parameter vector. The ...implementation of differential evolution in DEoptim interfaces with C code for efficiency. The utility of the package is illustrated by case studies in fitting a Parratt model for X-ray reflectometry data and a Markov-switching generalized autoregressive conditional heteroskedasticity model for the returns of the Swiss Market Index.
User-generated content about brands is an important source of big data that can be transformed into valuable information. A huge number of items are reviewed and rated by consumers on a daily basis, ...and managers have a keen interest in real-time monitoring of this information to improve decision-making. The main challenge is to mine reliable textual consumer opinions, and automatically use them to rate the best products or brands. We propose a framework to automatically analyse these reviews, transforming negative and positive user opinions in a quantitative score. Sentiment analysis was employed to analyse online reviews on Amazon. The Fake Review Detection Framework—FRDF— detects and removes fake reviews using Natural Language Processing technology. The FRDF was tested on reviews of products from high-tech industries. Brands were rated according to consumer sentiment. The findings demonstrate that brand managers and consumers would find this tool useful, in combination with the 5-Star score, for more comprehensive decision-making. For instance, the FRDF ranks the best products by price alongside their respective sentiment value and the 5-Star score.
•A novel modular framework that deals with textual information mining included in users’ reviews is proposed.•The framework uses NLP techniques including Sentiment Analysis and Fake Review Detectors tools.•Fake reviews are detected and removed because they influence negatively in the obtained results.•The application of the framework with a case study using a corpus of reviews of tech products is included in order to validate the proposal.•Dashboards generated assist managers to improve the decision-making process.
The Internet of Things (IoT) has made it possible for devices around the world to acquire information and store it, in order to be able to use it at a later stage. However, this potential opportunity ...is often not exploited because of the excessively big interval between the data collection and the capability to process and analyse it. In this paper, we review the current IoT technologies, approaches and models in order to discover what challenges need to be met to make more sense of data. The main goal of this paper is to review the surveys related to IoT in order to provide well integrated and context aware intelligent services for IoT. Moreover, we present a state-of-the-art of IoT from the context aware perspective that allows the integration of IoT and social networks in the emerging Social Internet of Things (SIoT) term.
The formation of condensed (compacted) protein phases is associated with a wide range of human disorders, such as eye cataracts, amyotrophic lateral sclerosis, sickle cell anaemia and Alzheimer's ...disease. However, condensed protein phases have their uses: as crystals, they are harnessed by structural biologists to elucidate protein structures, or are used as delivery vehicles for pharmaceutical applications. The physiochemical properties of crystals can vary substantially between different forms or structures ('polymorphs') of the same macromolecule, and dictate their usability in a scientific or industrial context. To gain control over an emerging polymorph, one needs a molecular-level understanding of the pathways that lead to the various macroscopic states and of the mechanisms that govern pathway selection. However, it is still not clear how the embryonic seeds of a macromolecular phase are formed, or how these nuclei affect polymorph selection. Here we use time-resolved cryo-transmission electron microscopy to image the nucleation of crystals of the protein glucose isomerase, and to uncover at molecular resolution the nucleation pathways that lead to two crystalline states and one gelled state. We show that polymorph selection takes place at the earliest stages of structure formation and is based on specific building blocks for each space group. Moreover, we demonstrate control over the system by selectively forming desired polymorphs through site-directed mutagenesis, specifically tuning intermolecular bonding or gel seeding. Our results differ from the present picture of protein nucleation, in that we do not identify a metastable dense liquid as the precursor to the crystalline state. Rather, we observe nucleation events that are driven by oriented attachments between subcritical clusters that already exhibit a degree of crystallinity. These insights suggest ways of controlling macromolecular phase transitions, aiding the development of protein-based drug-delivery systems and macromolecular crystallography.
Abstract
This article presents a discussion of the emerging ethical issue of geodata privacy in geographical research. The paper highlights the importance of considering challenges to privacy when ...working with geographically explicit data and explores explicit ways in which researchers and practitioners can be conscious of these issues. Through summarising the key problems in this area and presenting outstanding open research areas and questions from a seminar series on geodata privacy, we highlight important considerations for future research in this field. We focus on the specific topics of appropriate anonymization, responsible data dissemination, the balance between data sharing and privacy, and the challenges posed by working across international contexts. We conclude by recommending approaches to manage various legal and ethical frameworks, raise the importance of the international context, and inspire future research to address the challenges of safeguarding sensitive geodata while promoting openness and transparency.
We present CGeNArate, a new model for molecular dynamics simulations of very long segments of B-DNA in the context of biotechnological or chromatin studies. The developed method uses a coarse-grained ...Hamiltonian with trajectories that are back-mapped to the atomistic resolution level with extreme accuracy by means of Machine Learning Approaches. The method is sequence-dependent and reproduces very well not only local, but also global physical properties of DNA. The efficiency of the method allows us to recover with a reduced computational effort high-quality atomic-resolution ensembles of segments containing many kilobases of DNA, entering into the gene range or even the entire DNA of certain cellular organelles.
Cellular proteins begin to fold as they emerge from the ribosome. The folding landscape of nascent chains is not only shaped by their amino acid sequence but also by the interactions with the ...ribosome. Here, we combine biophysical methods with cryo‐EM structure determination to show that folding of a β‐barrel protein begins with formation of a dynamic α‐helix inside the ribosome. As the growing peptide reaches the end of the tunnel, the N‐terminal part of the nascent chain refolds to a β‐hairpin structure that remains dynamic until its release from the ribosome. Contacts with the ribosome and structure of the peptidyl transferase center depend on nascent chain conformation. These results indicate that proteins may start out as α‐helices inside the tunnel and switch into their native folds only as they emerge from the ribosome. Moreover, the correlation of nascent chain conformations with reorientation of key residues of the ribosomal peptidyl‐transferase center suggest that protein folding could modulate ribosome activity.
SYNOPSIS
Folding of nascent peptide chains is defined not only by their amino acid sequence but also by their interaction with the ribosome. Here, cotranslational folding of a small β‐structured protein is found to involve formation of a highly dynamic α‐helix inside the ribosome exit tunnel.
Cotranslational folding of a small β‐structured protein is described in real time using a combination of biophysical, biochemical, and structural methods.
Inside the exit tunnel, the β‐structured protein forms a highly dynamic α‐helix.
The helical module transitions toward the β conformation as the nascent chain reaches the exit port.
Different conformations of the nascent chain correlate with reorientation of key residues at the peptidyl‐transferase center of the ribosome.
Co‐translational folding of a small β‐structured protein involves formation of a highly dynamic α‐helix inside the ribosome exit tunnel.
The new Internet of Things paradigm allows for small devices with sensing, processing and communication capabilities to be designed, which enable the development of sensors, embedded devices and ...other 'things' ready to understand the environment. In this paper, a distributed framework based on the internet of things paradigm is proposed for monitoring human biomedical signals in activities involving physical exertion. The main advantages and novelties of the proposed system is the flexibility in computing the health application by using resources from available devices inside the body area network of the user. This proposed framework can be applied to other mobile environments, especially those where intensive data acquisition and high processing needs take place. Finally, we present a case study in order to validate our proposal that consists in monitoring footballers' heart rates during a football match. The real-time data acquired by these devices presents a clear social objective of being able to predict not only situations of sudden death but also possible injuries.
Cycling power meters enable monitoring external loads and performance changes. We aimed to determine the concurrent validity of the novel Favero Assioma Duo (FAD) pedal power meter compared with the ...crank-based SRM system (considered as gold standard). Thirty-three well-trained male cyclists were assessed at different power output (PO) levels (100-500 W and all-out 15-s sprints), pedaling cadences (75-100 rpm) and cycling positions (seating and standing) to compare the FAD device vs. SRM. No significant differences were found between devices for cadence nor for PO during all-out efforts (
> 0.05), although significant but small differences were found for efforts at lower PO values (
< 0.05 for 100-500 W, mean bias 3-8 W). A strong agreement was observed between both devices for mean cadence (ICC > 0.87) and PO values (ICC > 0.81) recorded in essentially all conditions and for peak cadence (ICC > 0.98) and peak PO (ICC > 0.99) during all-out efforts. The coefficient of variation for PO values was consistently lower than 3%. In conclusion, the FAD pedal-based power meter can be considered an overall valid system to record PO and cadence during cycling, although it might present a small bias compared with power meters placed on other locations such as SRM.
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