Special issue on analysis and mining of social media data.

This Editorial introduces the PeerJ Computer Science Special Issue on Analysis and Mining of Social Media Data. The special issue called for submissions with a primary focus on the use of social media data, for a variety of fields including natural language processing, computational social science, data mining, information retrieval and recommender systems. Of the 48 abstract submissions that were deemed within the scope of the special issue and were invited to submit a full article, 17 were ultimately accepted.

Human Papilloma Virus DNA Detection in Clinical Samples Using Fluorogenic Probes Based on Oligonucleotide Gated Nanoporous Anodic Alumina Films.

In this work, fluorogenic probes based on oligonucleotide capped nanoporous anodic alumina films are developed for specific and sensitive detection of human papilloma virus (HPV) DNA. The probe consists of anodic alumina nanoporous films loaded with the fluorophore rhodamine B (RhB) and capped with oligonucleotides bearing specific base sequences complementary to genetic material of different high-risk (hr) HPV types. Synthesis protocol is optimized for scale up production of sensors with high reproducibility.

No metabolic effects of mustard allyl-isothiocyanate compared with placebo in men.

Induction of nonshivering thermogenesis can be used to influence energy balance to prevent or even treat obesity. The pungent component of mustard, allyl-isothiocyanate (AITC), activates the extreme cold receptor transient receptor potential channel, subfamily A, member 1 and may thus induce energy expenditure and metabolic changes. The objective of our study was to evaluate the potential of mustard AITC to induce thermogenesis (primary outcome) and alter body temperature, cold and hunger sensations, plasma metabolic parameters, and energy intake (secondary outcomes).

Performance of surface and subsurface flow constructed wetlands treating eutrophic waters.

Three medium size constructed wetlands (CWs) with a total surface of 90ha are working since 2009 in the Albufera de Valencia Natural Park (Spain). Two of them are fed with eutrophic waters from l'Albufera Lake. Their objectives are both reduce the phytoplankton biomass and increase the biodiversity; consequently, improved water quality is returned to the lake.

Strontium folate loaded biohybrid scaffolds seeded with dental pulp stem cells induce in vivo bone regeneration in critical sized defects.

Strontium folate (SrFO) is a recently developed bone promoting agent with interest in medical and pharmaceutical fields due to its improved features in comparison to current strontium based therapies for osteoporosis and other bone diseases. In this work SrFO derivative was synthesized and loaded into biohybrid scaffolds obtained through lyophilisation of semi-interpenetrating networks of chitosan polyethylene glycol dimethacrylate and beta tri-calcium phosphate (βTCP) fabricated using free radical polymerization. The scaffolds were seeded with pluripotent stem cells obtained from human dental pulp and their potential to regenerate bone tissues were assessed using a critical sized defect model of calvaria in rats and compared with those obtained without SrFO.

Simulated and Real Sheet-of-Light 3D Object Scanning Using a-Si:H Thin Film PSD Arrays.

A MATLAB/SIMULINK software simulation model (structure and component blocks) has been constructed in order to view and analyze the potential of the PSD (Position Sensitive Detector) array concept technology before it is further expanded or developed. This simulation allows changing most of its parameters, such as the number of elements in the PSD array, the direction of vision, the viewing/scanning angle, the object rotation, translation, sample/scan/simulation time, etc. In addition, results show for the first time the possibility of scanning an object in 3D when using an a-Si:H thin film 128 PSD array sensor and hardware/software system.

Bandwidth resource management for neural signal telemetry.

Recent advances in modern neurocomputing have shown the utmost necessity of wireless communication systems that allow real-time (RT) monitoring of neural signals meeting several requirements such as source compression and high fidelity of the received signal. Neural recordings require multielectrode probes with up to hundreds of electrodes and transmission of signals wirelessly over a limited bandwidth (BW). In this paper, a RT resource management algorithm is proposed so that adequate source compression is applied to each channel in order to fit them into the available BW.

Porous silicon for photosensitized formation of singlet oxygen in water and in simulated body fluid: two methods of modification by undecylenic acid.

Initially H-terminated and therefore hydrophobic surface of electrochemically prepared luminescent porous silicon (PSi) powder was transformed to the hydrophilic one by means of surface modification by undecylenic acid. Physical adsorption of undecylenic acid as a non-ionic surfactant and its chemical binding through C[triple bond]C bond opening and Si-C bond formation were applied as two different methods of PSi surface modification, physical and chemical modification, respectively. Luminescence of aqueous suspensions of the both types of modified PSi powders in merely water and in simulated body fluid physiological electrolyte was measured as a function of time.

Ultra wideband for wireless real-time monitoring of neural signals.

Performance of an ultra wideband (UWB) wireless system for real-time neural signal monitoring is evaluated by comparing spiking characteristics between transmitted and received signals for different experimental set-ups. Spike detection quality is selected as the main spiking characteristic of evaluated signals. Results are presented in receiver-operating characteristics and area-under-the-curve (AUC).

Standardization of discharge reports with the ISO 13606 norm.

The International Organization for Standardization (ISO) has recently approved a new standard for the communication and semantic interoperability of electronic health record extracts. This standard is based on a dual model architecture, where a simple and generic reference model is defined for the representation of data and an archetype model is used for the representation of complex domain concepts of the electronic health record. By using this standard and a tool called LinkEHR-Ed, we have defined different types of hospital discharge reports in the form of archetypes and then we have normalized automatically discharge reports instances in a real environment following those archetype definitions.

Semantic upgrade and normalization of existing EHR extracts.

We present the mapping and data transformation capabilities of LinkEHR-Ed, a visual tool to construct formal definitions of medical concepts in the form of archetypes which can be defined on the basis on multiple electronic health record architecture such as ISO 13606. With LinkEHR-Ed, users can enrich archetypes with mapping information which captures the relationship between relational or XML data sources and archetype structures. This mapping information is then analyzed and compiled into an XQuery expression that transforms source instances into an XML document.

Deformable brain atlas validation of the location of subthalamic nucleus using T1-weighted MR images of patients operated on for Parkinson's.

Parkinson's disease is a degenerative disease of the central nervous system. One of the most effective treatments is deep brain stimulation. This technique requires the localization of an objective structure: the subthalamic nucleus.

Microwave disinfestation of bulk timber.

In this paper a complete microwave system for bulk timber disinfestation is developed and tested. A commercial FEM simulator has been used to design the applicator, looking for structures providing uniform field distributions, which is a factor of capital relevance for a successful treatment. Special attention has also been given to the reduction of electromagnetic energy leakage.

Stoichiometric modelling of cell metabolism.

There are several methodologies based on representations of cell metabolism that share two characteristics: the use of a metabolic network and the assumption of pseudosteady state. These methodologies have different purposes, employ different mathematical tools and are based on different assumptions; however, they all exploit the properties of a similar mathematical description. In this article we use the term stoichiometric modelling to encompass all these methodologies and to describe them within a common framework.

The importance of the intensity and frequency of perturbations on the germination delay.

An iterative model is developed to evaluate the reproductive strategies of plants in environments with different frequencies and intensities of disturbance. Two extreme reproductive strategies are compared: the "homocarpic" strategy, in which all the seeds germinate the following spring, without dormancy, and the "heterocarpic" strategy, whereby, each year, half of the existing seeds germinate. It is observed that this sort of heterocarpy is beneficial in environments with strong perturbations, in which a high percentage of the population dies.

A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient.

Background: An indirect approach is usually used to estimate the metabolic fluxes of an organism: couple the available measurements with known biological constraints (e.g. stoichiometry).

Framework for clinical data standardization based on archetypes.

Standardization of data is a prerequisite to achieve semantic interoperability in any domain. This is even more important in the healthcare sector where the need for exchanging health related data among professional and institutions is not an exception but the rule. Currently, there are several international organizations working on the definition of electronic health record architectures, some of them based on a dual-model approach.

The sense of smell: molecular basis of odorant recognition.

Most animal species rely on odorant compounds to locate food, predators, or toxins. The sense of smell is also involved in animal communication, and revealing the underlying mechanisms will therefore facilitate a deeper understanding of animal behaviour. Since the 1940s different theories have speculated on the fundamental basis of olfaction.

Non-invasive lightweight integration engine for building EHR from autonomous distributed systems.

In this paper we describe Pangea-LE, a message-oriented lightweight data integration engine that allows homogeneous and concurrent access to clinical information from disperse and heterogeneous data sources. The engine extracts the information and passes it to the requesting client applications in a flexible XML format. The XML response message can be formatted on demand by appropriate Extensible Stylesheet Language (XSL) transformations in order to meet the needs of client applications.

Directive sources in acoustic discrete-time domain simulations based on directivity diagrams.

Discrete-time domain methods provide a simple and flexible way to solve initial boundary value problems. With regard to the sources in such methods, only monopoles or dipoles can be considered. However, in many problems such as room acoustics, the radiation of realistic sources is directional-dependent and their directivity patterns have a clear influence on the total sound field.

An interval approach for dealing with flux distributions and elementary modes activity patterns.

This work introduces the use of an interval representation of fluxes. This representation can be useful in two common situations: (a) when fluxes are uncertain due to the lack of accurate measurements and (b) when the flux distribution is partially unknown. In addition, the interval representation can be used for other purposes such as dealing with inconsistency or representing a range of behaviour.

Radiofrequency heating of the cornea: an engineering review of electrodes and applicators.

This paper reviews the different applicators and electrodes employed to create localized heating in the cornea by means of the application of radiofrequency (RF) currents. Thermokeratoplasty (TKP) is probably the best known of these techniques and is based on the principle that heating corneal tissue (particularly the central part of the corneal tissue, i.e.

Non-invasive light-weight integration engine for building EHR from autonomous distributed systems.

Pangea-LE is a message oriented light-weight integration engine, allowing concurrent access to clinical information from disperse and heterogeneous data sources. The engine extracts the information and serves it to the requester client applications in a flexible XML format. This XML response message can be formatted on demand by the appropriate XSL (Extensible Stylesheet Language) transformation in order to fit client application needs.

A review and numerical assessment of the random walk particle tracking method.

We review the basic mathematical concepts of random walk particle tracking (RWPT) and its advantages and limitations. Three different numerical approaches to overcome the local mass conservation problem of the random walk methodology are examined: (i) the interpolation method, (ii) the reflection principle, and (iii) the generalized stochastic differential equations (GSDE). Analytical solutions of the spatial moments for a two-layer system are compared to model predictions using the different techniques and results demonstrate that the interpolation method reproduces correctly average velocity, but fails to reproduce macrodispersion at higher hydraulic conductivity contrasts between the two layers.

Comprehensive pharmacokinetic model of insulin Glargine and other insulin formulations.

In this paper, a comprehensive pharmacokinetic model for different insulin formulations including insulin Glargine is developed based on the model proposed by Trajanoski et al. (1993). Current models show limitations for insulin Glargine due to the appearance of an uncharacteristic peak in the concentration-time evolution of plasma insulin that does not coincide with real experimental data.