A thorough analysis of continuous adventitious sounds (CAS) can provide distinct and complementary information about bronchodilator response (BDR), beyond that provided by spirometry. Nevertheless, previous approaches to CAS analysis were limited by certain methodology issues. The aim of this study is to propose a new integrated approach to CAS analysis that contributes to improving the assessment of BDR in clinical practice for asthma patients.
Respiratory sounds and flow were recorded in 25 subjects, including 7 asthma patients with positive BDR (BDR+), assessed by spirometry, 13 asthma patients with negative BDR (BDR-), and 5 controls. A total of 5149 acoustic components were characterized using the Hilbert spectrum, and used to train and validate a support vector machine classifier, which distinguished acoustic components corresponding to CAS from those corresponding to other sounds. Once the method was validated, BDR was assessed in all participants by CAS analysis, and compared to BDR assessed by spirometry.
BDR+ patients had a homogenous high change in the number of CAS after bronchodilation, which agreed with the positive BDR by spirometry, indicating high reversibility of airway obstruction. Nevertheless, we also found an appreciable change in the number of CAS in many BDR- patients, revealing alterations in airway obstruction that were not detected by spirometry. We propose a categorization for the change in the number of CAS, which allowed us to stratify BDR- patients into three consistent groups. From the 13 BDR- patients, 6 had a high response, similar to BDR+ patients, 4 had a noteworthy medium response, and 1 had a low response.
In this study, a new non-invasive and integrated approach to CAS analysis is proposed as a high-sensitive tool for assessing BDR in terms of acoustic parameters which, together with spirometry parameters, contribute to improving the stratification of BDR levels in patients with obstructive pulmonary diseases.
Among Parkinson’s disease (PD) symptoms, freezing of gait (FoG) is one of the most debilitating. To assess FoG, current clinical practice mostly employs repeated evaluations over weeks and months based on questionnaires, which may not accurately map the severity of this symptom. The use of a non-invasive system to monitor the activities of daily living (ADL) and the PD symptoms experienced by patients throughout the day could provide a more accurate and objective evaluation of FoG in order to better understand the evolution of the disease and allow for a more informed decision-making process in making adjustments to the patient’s treatment plan. This paper presents a new algorithm to detect FoG with a machine learning approach based on Support Vector Machines (SVM) and a single tri-axial accelerometer worn at the waist. The method is evaluated through the acceleration signals in an outpatient setting gathered from 21 PD patients at their home and evaluated under two different conditions: first, a generic model is tested by using a leave-one-out approach and, second, a personalised model that also uses part of the dataset from each patient. Results show a significant improvement in the accuracy of the personalised model compared to the generic model, showing enhancement in the specificity and sensitivity geometric mean (GM) of 7.2%. Furthermore, the SVM approach adopted has been compared to the most comprehensive FoG detection method currently in use (referred to as MBFA in this paper). Results of our novel generic method provide an enhancement of 11.2% in the GM compared to the MBFA generic model and, in the case of the personalised model, a 10% of improvement with respect to the MBFA personalised model. Thus, our results show that a machine learning approach can be used to monitor FoG during the daily life of PD patients and, furthermore, personalised models for FoG detection can be used to improve monitoring accuracy.
In this article we present the development of a set of opto-mechanical components (a kinematic mount, a translation stage and an integrating sphere) that can be easily built using a 3D printer based on Fused Filament Fabrication (FFF) and parts that can be found in any hardware store. Here we provide a brief description of the 3D models used and some details on the fabrication process. Moreover, with the help of three simple experimental setups, we evaluate the performance of the opto-mechanical components developed by doing a quantitative comparison with its commercial counterparts. Our results indicate that the components fabricated are highly customizable, low-cost, require a short time to be fabricated and surprisingly, offer a performance that compares favorably with respect to low-end commercial alternatives.
Incipient Alzheimer’s Disease (AD) is characterized by a slow onset of clinical symptoms, with pathological brain changes starting several years earlier. Consequently, it is necessary to first understand and differentiate age-related changes in brain regions in the absence of disease, and then to support early and accurate AD diagnosis. However, there is poor understanding of the initial stage of AD; seemingly healthy elderly brains lose matter in regions related to AD, but similar changes can also be found in non-demented subjects having mild cognitive impairment (MCI). By using a Linear Mixed Effects approach, we modelled the change of 166 Magnetic Resonance Imaging (MRI)-based biomarkers available at a 5-year follow up on healthy elderly control (HC, n = 46) subjects. We hypothesized that, by identifying their significant variant (vr) and quasi-variant (qvr) brain regions over time, it would be possible to obtain an age-based null model, which would characterize their normal atrophy and growth patterns as well as the correlation between these two regions. By using the null model on those subjects who had been clinically diagnosed as HC (n = 161), MCI (n = 209) and AD (n = 331), normal age-related changes were estimated and deviation scores (residuals) from the observed MRI-based biomarkers were computed. Subject classification, as well as the early prediction of conversion to MCI and AD, were addressed through residual-based Support Vector Machines (SVM) modelling. We found reductions in most cortical volumes and thicknesses (with evident gender differences) as well as in sub-cortical regions, including greater atrophy in the hippocampus. The average accuracies (ACC) recorded for men and women were: AD-HC: 94.11%, MCI-HC: 83.77% and MCI converted to AD (cAD)-MCI non-converter (sMCI): 76.72%. Likewise, as compared to standard clinical diagnosis methods, SVM classifiers predicted the conversion of cAD to be 1.9 years earlier for females (ACC:72.5%) and 1.4 years earlier for males (ACC:69.0%).
In recent years, many researchers have addressed the issue of making Unmanned Aerial Vehicles (UAVs) more and more autonomous. In this context, the state estimation of the vehicle position is a fundamental necessity for any application involving autonomy. However, the problem of position estimation could not be solved in some scenarios, even when a GPS signal is available, for instance, an application requiring performing precision manoeuvres in a complex environment. Therefore, some additional sensory information should be integrated into the system in order to improve accuracy and robustness. In this work, a novel vision-based simultaneous localization and mapping (SLAM) method with application to unmanned aerial vehicles is proposed. One of the contributions of this work is to design and develop a novel technique for estimating features depth which is based on a stochastic technique of triangulation. In the proposed method the camera is mounted over a servo-controlled gimbal that counteracts the changes in attitude of the quadcopter. Due to the above assumption, the overall problem is simplified and it is focused on the position estimation of the aerial vehicle. Also, the tracking process of visual features is made easier due to the stabilized video. Another contribution of this work is to demonstrate that the integration of very noisy GPS measurements into the system for an initial short period of time is enough to initialize the metric scale. The performance of this proposed method is validated by means of experiments with real data carried out in unstructured outdoor environments. A comparative study shows that, when compared with related methods, the proposed approach performs better in terms of accuracy and computational time.
Brunel, H.; Massanet, R.; Martinez, A.; Ziyatdinov, A.; Martin-Fernandez, L.; Souto, J.; Perera, A.; Soria, J. PLoS one Vol. 11, num. 12, p. 1-14 DOI: 10.1371/journal.pone.0167187 Data de publicació: 2016-12-22 Article en revista
Traditional genetic studies of single traits may be unable to detect the pleiotropic effects involved in complex diseases. To detect the correlation that exists between several phenotypes involved in the same biological process, we introduce an original methodology to analyze sets of correlated phenotypes involved in the coagulation cascade in genome-wide association studies. The methodology consists of a two-stage process. First, we define new phenotypic meta-variables (linear combinations of the original phenotypes), named metaphenotypes, by applying Independent Component Analysis for the multivariate analysis of correlated phenotypes (i.e. the levels of coagulation pathway–related proteins). The resulting
metaphenotypes integrate the information regarding the underlying biological process (i.e. thrombus/clot formation). Secondly, we take advantage of a family based Genome Wide Association Study to identify genetic elements influencing these metaphenotypes and consequently thrombosis risk. Our study utilized data from the GAIT Project (Genetic Analysis of Idiopathic Thrombophilia). We obtained 15 metaphenotypes, which showed significant heritabilities, ranging from 0.2 to 0.7. These results indicate the importance of genetic factors in the variability of these traits. We found 4 metaphenotypes that showed significant associations with SNPs. The most relevant were those mapped in a region near the HRG, FETUB and KNG1 genes. Our results are provocative since they show that the KNG1 locus plays a central role as a genetic determinant of the entire coagulation pathway and thrombus/clot formation. Integrating data from multiple correlated measurements through metaphenotypes is a promising approach to elucidate the hidden genetic mechanisms underlying complex diseases.
Knowledge of the location of muscle Innervation Zones (IZs) is important in many applications, e.g. for minimizing the quantity of injected botulinum toxin for the treatment of spasticity or for deciding on the type of episiotomy during child delivery. Surface EMG (sEMG) can be noninvasively recorded to assess physiological and morphological characteristics of contracting muscles. However, it is not often possible to record signals of high quality. Moreover, muscles could have multiple IZs, which should all be identified. We designed a fully-automatic algorithm based on the enhanced image Graph-Cut segmentation and morphological image processing methods to identify up to five IZs in 60-ms intervals of very-low to moderate quality sEMG signal detected with multi-channel electrodes (20 bipolar channels with Inter Electrode Distance (IED) of 5 mm). An anisotropic multilayered cylinder model was used to simulate 750 sEMG signals with signal-to-noise ratio ranging from -5 to 15 dB (using Gaussian noise) and in each 60-ms signal frame, 1 to 5 IZs were included. The micro- and macro- averaged performance indices were then reported for the proposed IZ detection algorithm. In the micro-averaging procedure, the number of True Positives, False Positives and False Negatives in each frame were summed up to generate cumulative measures. In the macro-averaging, on the other hand, precision and recall were calculated for each frame and their averages are used to determine F1-score. Overall, the micro (macro)-averaged sensitivity, precision and F1-score of the algorithm for IZ channel identification were 82.7% (87.5%), 92.9% (94.0%) and 87.5% (90.6%), respectively. For the correctly identified IZ locations, the average bias error was of 0.02±0.10 IED ratio. Also, the average absolute conduction velocity estimation error was 0.41±0.40 m/s for such frames. The sensitivity analysis including increasing IED and reducing interpolation coefficient for time samples was performed. Meanwhile, the effect of adding power-line interference and using other image interpolation methods on the deterioration of the performance of the proposed algorithm was investigated. The average running time of the proposed algorithm on each 60-ms sEMG frame was 25.5±8.9 (s) on an Intel dual-core 1.83 GHz CPU with 2 GB of RAM. The proposed algorithm correctly and precisely identified multiple IZs in each signal epoch in a wide range of signal quality and is thus a promising new offline tool for electrophysiological studies.
In the present study, we report the discovery of a novel allosteric inhibitory site for p38a, a subclass of the mitogen-activated protein kinases (MAPK) family. The putative site was discovered after inspection of the crystallographic structure of the p38a-MK2 complex. MK2 (MAPK-activated protein kinase 2) is an interesting protein playing a dual role as modulator and substrate of p38a. This intriguing behavior is due to the ability of the two proteins to form distinctive heterodimers when p38a is phosphorylated or not. We hypothesized that the regulatory action of MK2 is due to its capability to keep p38a in an inactive conformation and consequently, we investigated the atomic structure of the p38a-MK2 complex to understand such regulatory behavior at the molecular level. After inspection of the complex structure, two peptides designed from the MK2 regulatory loop in contact with p38a with sequences Tyr1-Ser2-Asn3-His4-Gly5-Leu6 (peptide-1) and [Phe0]-peptide-1 (peptide-2) in their zwitterionic form were investigated for their phosphorylation inhibitory capability in vitro. Since both peptides exhibited inhibitory capability of the p38a kinase mediated phosphorylation of MEF2A, in a subsequent step we pursued the discovery of small molecule peptidomimetics. For this purpose we characterized in detail the peptide-p38a interaction using molecular dynamics simulations, leading to the definition of a pharmacophore for the peptide-protein interaction. This hypothesis was used as query for a in silico screening, leading to the discovery of a fused ring compound with micromolar inhibitory activity. Site-directed mutagenesis studies support that the compound binds to the putative novel allosteric site in p38a.
Arrhythmias in cardiac tissue are generally associated with irregular electrical wave propagation in the heart. Cardiac tissue is formed by a discrete cell network, which is often heterogeneous. Recently, it was shown in simulations of two-dimensional (2D) discrete models of cardiac tissue that a wave crossing a fibrotic, heterogeneous region may produce reentry and transient or persistent ectopic activity provided the fraction of conducting connections is just above the percolation threshold. Here, we investigate the occurrence of these phenomena in three-dimensions by simulations of a discrete model representing a thin slab of cardiac tissue. This is motivated (i) by the necessity to study the relevance and properties of the percolation-related mechanism for the emergence of microreentries in three dimensions and (ii) by the fact that atrial tissue is quite thin in comparison with ventricular tissue. Here, we simplify the model by neglecting details of tissue anatomy, e. g. geometries of atria or ventricles and the anisotropy in the conductivity. Hence, our modeling study is confined to the investigation of the effect of the tissue thickness as well as to the comparison of the dynamics of electrical excitation in a 2D layer with the one in a 3D slab. Our results indicate a strong and non-trivial effect of the thickness even for thin tissue slabs on the probability of microreentries and ectopic beat generation. The strong correlation of the occurrence of microreentry with the percolation threshold reported earlier in 2D layers persists in 3D slabs. Finally, a qualitative agreement of 3D simulated electrograms in the fibrotic region with the experimentally observed complex fractional atrial electrograms (CFAE) as well as strong difference between simulated electrograms in 2D and 3D were found for the cases where reentry and ectopic activity were triggered by the micro-fibrotic region.
Pérez, L.; Inzitari, M.; Quinn, T.; Montaner, J.; Gavaldà, R.; Duarte, E.; Coll, L.; Cerdá, M.; Santaeugenia, S.; Closa, C.; Gallofre, M. PLoS one Vol. 11, num. 11, p. 1-13 DOI: 10.1371/journal.pone.0166304 Data de publicació: 2016-11-09 Article en revista
Stroke is a major cause of disability in older adults, but the evidence around post-acute treatment is limited and heterogeneous. We aimed to identify profiles of older adult stroke survivors admitted to intermediate care geriatric rehabilitation units.
We performed a cohort study, enrolling stroke survivors aged 65 years or older, admitted to 9 intermediate care units in Catalonia-Spain. To identify potential profiles, we included age, caregiver presence, comorbidity, pre-stroke and post-stroke disability, cognitive impairment and stroke severity in a cluster analysis. We also proposed a practical decision tree for patient’s classification in clinical practice. We analyzed differences between profiles in functional improvement (Barthel index), relative functional gain (Montebello index), length of hospital stay (LOS), rehabilitation efficiency (functional improvement by LOS), and new institutionalization using multivariable regression models (for continuous and dichotomous outcomes).
Among 384 patients (79.1±7.9 years, 50.8% women), we identified 3 complexity profiles: a) Lower Complexity with Caregiver (LCC), b) Moderate Complexity without Caregiver (MCN), and c) Higher Complexity with Caregiver (HCC). The decision tree showed high agreement with cluster analysis (96.6%). Using either linear (continuous outcomes) or logistic regression, both LCC and MCN, compared to HCC, showed statistically significant higher chances of functional improvement (OR = 4.68, 95%CI = 2.54–8.63 and OR = 3.0, 95%CI = 1.52–5.87, respectively, for Barthel index improvement =20), relative functional gain (OR = 4.41, 95%CI = 1.81–10.75 and OR = 3.45, 95%CI = 1.31–9.04, respectively, for top Vs lower tertiles), and rehabilitation efficiency (OR = 7.88, 95%CI = 3.65–17.03 and OR = 3.87, 95%CI = 1.69–8.89, respectively, for top Vs lower tertiles). In relation to LOS, MCN cluster had lower chance of shorter LOS than LCC (OR = 0.41, 95%CI = 0.23–0.75) and HCC (OR = 0.37, 95%CI = 0.19–0.73), for LOS lower Vs higher tertiles.
Our data suggest that post-stroke rehabilitation profiles could be identified using routine assessment tools and showed differential recovery. If confirmed, these findings might help to develop tailored interventions to optimize recovery of older stroke patients.
The thalamus is a key brain element in the processing of sensory information. During the sleep and awake states, this brain area is characterized by the presence of two distinct dynamical regimes: in the sleep state activity is dominated by spindle oscillations (7 - 15 Hz) weakly affected by external stimuli, while in the awake state the activity is primarily driven by external stimuli. Here we develop a simple and computationally efficient model of the thalamus that exhibits two dynamical regimes with different information-processing capabilities, and study the transition between them. The network model includes glutamatergic thalamocortical (TC) relay neurons and GABAergic reticular (RE) neurons described by adaptive integrate-and-fire models in which spikes are induced by either depolarization or hyperpolarization rebound. We found a range of connectivity conditions under which the thalamic network composed by these neurons displays the two aforementioned dynamical regimes. Our results show that TC-RE loops generate spindle-like oscillations and that a minimum level of clustering (i.e. local connectivity density) in the RE-RE connections is necessary for the coexistence of the two regimes. We also observe that the transition between the two regimes occurs when the external excitatory input on TC neurons (mimicking sensory stimulation) is large enough to cause a significant fraction of them to switch from hyperpolarization-rebound-driven firing to depolarization-driven firing. Overall, our model gives a novel and clear description of the role that the two types of neurons and their connectivity play in the dynamical regimes observed in the thalamus, and in the transition between them. These results pave the way for the development of efficient models of the transmission of sensory information from periphery to cortex.
Marzano, M.; Fosso, B.; Manzari, C.; Grieco, F.; Intranuovo, M.; Cozzi, G.; Mule, G.; Scoscia, G.; Valiente, G.; Tullo, A.; Sbisa, E.; Pesole, G.; Santamaria, M. PLoS one Vol. 11, num. 6, p. 1-19 DOI: 10.1371/journal.pone.0157383 Data de publicació: 2016-06-14 Article en revista
Currently, there is very little information available regarding the microbiome associated with the wine production chain. Here, we used an amplicon sequencing approach based on high-throughput sequencing (HTS) to obtain a comprehensive assessment of the bacterial community associated with the production of three Apulian red wines, from grape to final product. The relationships among grape variety, the microbial community, and fermentation was investigated. Moreover, the winery microbiota was evaluated compared to the autochthonous species in vineyards that persist until the end of the winemaking process. The analysis highlighted the remarkable dynamics within the microbial communities during fermentation. A common microbial core shared among the examined wine varieties was observed, and the unique taxonomic signature of each wine appellation was revealed. New species belonging to the genus Halomonas were also reported. This study demonstrates the potential of this metagenomic approach, supported by optimized protocols, for identifying the biodiversity of the wine supply chain. The developed experimental pipeline offers new prospects for other research fields in which a comprehensive view of microbial community complexity and dynamics is desirable.
Although heavy-tailed fluctuations are ubiquitous in complex systems, a good understanding of the mechanisms that generate them is still lacking. Optical complex systems are ideal candidates for investigating heavy-tailed fluctuations, as they allow recording large datasets under controllable experimental conditions. A dynamical regime that has attracted a lot of attention over the years is the so-called low-frequency fluctuations (LFFs) of semiconductor lasers with optical feedback. In this regime, the laser output intensity is characterized by abrupt and apparently random dropouts. The statistical analysis of the inter-dropout-intervals (IDIs) has provided many useful insights into the underlying dynamics. However, the presence of large temporal fluctuations in the IDI sequence has not yet been investigated. Here, by applying fluctuation analysis we show that the experimental distribution of IDI fluctuations is heavy-tailed, and specifically, is well-modeled by a non-Gaussian stable distribution. We find a good qualitative agreement with simulations of the Lang-Kobayashi model. Moreover, we uncover a transition from a less-heavy-tailed state at low pump current to a more-heavy-tailed state at higher pump current. Our results indicate that fluctuation analysis can be a useful tool for investigating the output signals of complex optical systems; it can be used for detecting underlying regime shifts, for model validation and parameter estimation.
Sanromà, G.; Peñate, A.; Alquezar, R.; Serratosa, F.; Moreno-Noguer, F.; Andrade-Cetto, J.; Gonzalez-Ballester, M.A. PLoS one Vol. 11, num. 1 DOI: 10.1371/journal.pone.0145846 Data de publicació: 2016-01-01 Article en revista
We present a novel approach for feature correspondence and multiple structure discovery in computer vision. In contrast to existing methods, we exploit the fact that point-sets on the same structure usually lie close to each other, thus forming clusters in the image. Given a pair of input images, we initially extract points of interest and extract hierarchical representations by agglomerative clustering. We use the maximum weighted clique problem to find the set of corresponding clusters with maximum number of inliers representing the multiple structures at the correct scales. Our method is parameter-free and only needs two sets of points along with their tentative correspondences, thus being extremely easy to use. We demonstrate the effectiveness of our method in multiple-structure fitting experiments in both publicly available and in-house datasets. As shown in the experiments, our approach finds a higher number of structures containing fewer outliers compared to state-of-the-art methods.
Pastor, A.; Fernández-Aranda, F.; Fitó, M.; Jiménez-Murcia, S.; Botella, C.; Fernández-Real, J.; Frühbeck, G.; Tinahones, F.; Fagundo, A.; Rodriguez, J.; Agüera, Z.; Langohr, K.; Casanueva, F.; de la Torre, R. PLoS one Vol. 11, num. 2, p. 1-15 DOI: 10.1371/journal.pone.0148734 Data de publicació: 2016 Article en revista
The endocannabinoid (eCB) system can promote food intake by increasing odor detection in mice. The eCB system is over-active in human obesity. Our aim is to measure circulating eCB concentrations and olfactory capacity in a human sample that includes people with obesity and explore the possible interaction between olfaction, obesity and the eCB system. The study sample was made up of 161 females with five groups of body mass index sub-categories ranging from under-weight to morbidly obese. We assessed olfactory capacity with the “Sniffin´Sticks” test, which measures olfactory threshold-discrimination-identification (TDI) capacity. We measured plasma concentrations of the eCBs 2-arachidonoylglycerol (2-AG) and N-arachidonoylethanolamine or anandamide (AEA), and several eCB-related compounds, 2-acylglycerols and N-acylethanolamines. 2-AG and other 2-acylglycerols fasting plasma circulating plasma concentrations were higher in obese and morbidly obese subjects. AEA and other N-acylethanolamine circulating concentrations were lower in under-weight subjects. Olfactory TDI scores were lower in obese and morbidly obese subjects. Lower TDI scores were independently associated with higher 2-AG fasting plasma circulating concentrations, higher %body fat, and higher body mass index, after controlling for age, smoking, menstruation, and use of contraceptives. Our results show that obese subjects have a lower olfactory capacity than non-obese ones and that elevated fasting plasma circulating 2-AG concentrations in obesity are linked to a lower olfactory capacity. In agreement with previous studies we show that eCBs AEA and 2-AG, and their respective congeners have a distinct profile in relation to body mass index. The present report is the first study in humans in which olfactory capacity and circulating eCB concentrations have been measured in the same subjects.
The robustness of large scale critical infrastructures, which can be modeled as complex networks, is of great significance. One of the most important means to enhance robustness is to optimize the allocation of resources. Traditional allocation of resources is mainly based on the topology information, which is neither realistic nor systematic. In this paper, we try to build a framework for searching for the most favorable pattern of node capacity allocation to reduce the vulnerability to cascading failures at a low cost. A nonlinear and multi-objective optimization model is proposed and tackled using a particle swarm optimization algorithm (PSO). It is found that the network becomes more robust and economical when less capacity is left on the heavily loaded nodes and the optimized network performs better resisting noise. Our work is helpful in designing a robust economical network.
Lopez, M.; Escartín, J.A.; Martinez, S.; Fernandez, R.; Querol, L.; Romero, S.; Mañanas, M.A.; Riba, J. PLoS one Vol. 10, num. 8 DOI: 10.1371/journal.pone.0136786 Data de publicació: 2015-08-31 Article en revista
Multiple sclerosis (MS) is a chronic central nervous system disorder characterized by white matter inflammation, demyelination and neurodegeneration. Although cognitive dysfunction is a common manifestation, it may go unnoticed in recently-diagnosed patients. Prior studies suggest MS patients develop compensatory mechanisms potentially involving enhanced performance monitoring. Here we assessed the performance monitoring system in early-stage MS patients using the error-related negativity (ERN), an event-related brain potential (ERP) observed following behavioral errors. Twenty-seven early-stage MS patients and 31 controls were neuropsychologically assessed. Electroencephalography recordings were obtained while participants performed: a) a stop task and b) an auditory oddball task. Behavior and ERP measures were assessed. No differences in performance were found between groups in most neuropsychological tests or in behavior or ERP components in the auditory oddball task. However, the amplitude of the ERN associated with stop errors in the stop task was significantly higher in patients. ERN amplitude correlated positively with scores on the Expanded Disability Status Scale and the Multiple Sclerosis Severity Score, and negatively with the time since last relapse. Patients showed higher neuronal recruitment in tasks involving performance monitoring. Results suggest the development of compensatory brain mechanisms in early-stage MS and reflect the sensitivity of the ERN to detect these changes.
We report the preparation of novel magnetic field-responsive tissue substitutes based on biocompatible multi-domain magnetic particles dispersed in a fibrin–agarose biopolymer scaffold. We characterized our biomaterials with several experimental techniques. First we analyzed their microstructure and found that it was strongly affected by the presence of magnetic particles, especially when a magnetic field was applied at the start of polymer gelation. In these samples we observed parallel stripes consisting of closely packed fibers, separated by more isotropic net-like spaces. We then studied the viability of oral mucosa fibroblasts in the magnetic scaffolds and found no significant differences compared to positive control samples. Finally, we analyzed the magnetic and mechanical properties of the tissue substitutes. Differences in microstructural patterns of the tissue substitutes correlated with their macroscopic mechanical properties. We also found that the mechanical properties of our magnetic tissue substitutes could be reversibly tuned by noncontact magnetic forces. This unique advantage with respect to other biomaterials could be used to match the mechanical properties of the tissue substitutes to those of potential target tissues in tissue engineering application
Zipf's law is a fundamental paradigm in the statistics of written and spoken natural language as well as in other communication systems. We raise the question of the elementary units for which Zipf's law should hold in the most natural way, studying its validity for plain word forms and for the corresponding lemma forms. We analyze several long literary texts comprising four languages, with different levels of morphological complexity. In all cases Zipf's law is fulfilled, in the sense that a power-law distribution of word or lemma frequencies is valid for several orders of magnitude. We investigate the extent to which the word-lemma transformation preserves two parameters of Zipf's law: the exponent and the low-frequency cut-off. We are not able to demonstrate a strict invariance of the tail, as for a few texts both exponents deviate significantly, but we conclude that the exponents are very similar, despite the remarkavble transformation that going from words to lemmas represents, considerably affecting all ranges of frequencies. In contrast, the low-frequency cut-offs are less stable, tending to increase substantially after the transformation.
The osteogenic capacity of biomimetic calcium deficient hydroxyapatite microspheres with and without collagen obtained by emulsification of a calcium phosphate cement paste has been evaluated in an in vivo model, and compared with an injectable calcium phosphate cement with the same composition. The materials were implanted into a 5 mm defect in the femur condyle of rabbits, and bone formation was assessed after 1 and 3 months. The histological analysis revealed that the cements presented cellular activity only in the margins of the material, whereas each one of the individual microspheres was covered with osteogenic cells. Consequently, bone ingrowth was enhanced by the microspheres, with a tenfold increase compared to the cement, which was associated to the higher accessibility for the cells provided by the macroporous network between the microspheres, and the larger surface area available for osteoconduction. No significant differences were found in terms of bone formation associated with the presence of collagen in the materials, although a more extensive erosion of the collagen-containing microspheres was observed.
Marcé-Nogué, J.; Fortuny, J.; Sanchez, M.; Esteban-Trivigno, S.; Gil, L.; Galobart, À. PLoS one Vol. 10, num. 6, p. 1-23 DOI: 10.1371/journal.pone.0131320 Data de publicació: 2015-06-24 Article en revista
For the first time in vertebrate palaeontology, the potential of joining Finite Element Analysis (FEA) and Parametrical Analysis (PA) is used to shed new light on two different cranial parameters from the orbits to evaluate their biomechanical role and evolutionary patterns. The early tetrapod group of Stereospondyls, one of the largest groups of Temnospondyls is used as a case study because its orbits position and size vary hugely within the members of this group. An adult skull of Edingerella madagascariensis was analysed using two different cases of boundary and loading conditions in order to quantify stress and deformation response under a bilateral bite and during skull raising. Firstly, the variation of the original geometry of its orbits was introduced in the models producing new FEA results, allowing the exploration of the ecomorphology, feeding strategy and evolutionary patterns of these top predators. Secondly, the quantitative results were analysed in order to check if the orbit size and position were correlated with different stress patterns. These results revealed that in most of the cases the stress distribution is not affected by changes in the size and position of the orbit. This finding supports the high mechanical plasticity of this group during the Triassic period. The absence of mechanical constraints regarding the orbit probably promoted the ecomorphological diversity acknowledged for this group, as well as its ecological niche differentiation in the terrestrial Triassic ecosystems in clades as lydekkerinids, trematosaurs, capitosaurs or metoposaurs.
Finite element analyses (FEA) were applied to assess the lower jaw biomechanics of cingulate xenarthrans: 14 species of armadillos as well as one Pleistocene pampathere (11 extant taxa and the extinct forms Vassallia, Eutatus and Macroeuphractus). The principal goal of this work is to comparatively assess the biomechanical capabilities of the mandible based on FEA and to relate the obtained stress patterns with diet preferences and variability, in extant and extinct species through an ecomorphology approach. The results of FEA showed that omnivorous species have stronger mandibles than insectivorous species. Moreover, this latter group of species showed high variability, including some similar biomechanical features of the insectivorous Tolypeutes matacus and Chlamyphorus truncatus to those of omnivorous species, in agreement with reported diets that include items other than insects. It remains unclear the reasons behind the stronger than expected lower jaw of Dasypus kappleri. On the other hand, the very strong mandible of the fossil taxon Vassallia maxima agrees well with the proposed herbivorous diet. Moreover, Eutatus seguini yielded a stress pattern similar to Vassalia in the posterior part of the lower jaw, but resembling that of the stoutly built Macroeuphractus outesi in the anterior part. The results highlight the need for more detailed studies on the natural history of extant armadillos. FEA proved a powerful tool for biomechanical studies in a comparative framework.
Melia, U.; Vallverdu, M.; Borrat, X.; Jospin, M.; Valencia, J.F.; Jensen, E.W; Gambus, P.; Caminal, P. PLoS one Vol. 10, num. 4 DOI: 10.1371/journal.pone.0123464 Data de publicació: 2015-04-22 Article en revista
The level of sedation in patients undergoing medical procedures evolves continuously, affected by the interaction between the effect of the anesthetic and analgesic agents and the pain stimuli. The monitors of depth of anesthesia, based on the analysis of the electroencephalogram (EEG), have been progressively introduced into the daily practice to provide additional information about the state of the patient. However, the quantification of analgesia still remains an open problem. The purpose of this work is to improve the prediction of nociceptive responses with linear and non-linear measures calculated from EEG signal filtered in frequency bands higher than the traditional bands. Power spectral density and auto-mutual information function was applied in order to predict the presence or absence of the nociceptive responses to different stimuli during sedation in endoscopy procedure. The proposed measures exhibit better performances than the bispectral index (BIS). Values of prediction probability of P-k above 0.75 and percentages of sensitivity and specificity above 70% were achieved combining EEG measures from the traditional frequency bands and higher frequency bands.
Unconscious mental processes have recently started gaining attention in a number of scientific disciplines. One of the theoretical frameworks for describing unconscious processes was introduced by Jung as a part of his model of the psyche. This framework uses the concept of archetypes that represent prototypical experiences associated with objects, people, and situations. Although the validity of Jungian model remains an open question, this framework is convenient from the practical point of view. Moreover, archetypes found numerous applications in the areas of psychology and marketing. Therefore, observation of both conscious and unconscious traces related to archetypal experiences seems to be an interesting research endeavor. In a study with 36 subjects, we examined the effects of experiencing conglomerations of unconscious emotions associated with various archetypes on the participants' introspective reports and patterns of physiological activations. Our hypothesis for this experiment was that physiological data may predict archetypes more precisely than introspective reports due to the implicit nature of archetypal experiences. Introspective reports were collected using the Self-Assessment Manikin (SAM) technique. Physiological measures included cardiovascular, electrodermal, respiratory responses and skin temperature of the subjects. The subjects were stimulated to feel four archetypal experiences and four explicit emotions by means of film clips. The data related to the explicit emotions served as a reference in analysis of archetypal experiences. Our findings indicated that while prediction models trained on the collected physiological data could recognize the archetypal experiences with accuracy of 55 percent, similar models built based on the SAM data demonstrated performance of only 33 percent. Statistical tests enabled us to confirm that physiological observations are better suited for observation of implicit psychological constructs like archetypes than introspective reports.
Guaita, M.; Melia, U.; Vallverdu, M.; Caminal, P.; Vilaseca, L.; Montserrat, J.; Gaig, C.; Salamero, M.; Santamaria, J. PLoS one DOI: 10.1371/journal.pone.0122645 Data de publicació: 2015-04-10 Article en revista
Biting is an integral feature of the feeding mechanism for aquatic and terrestrial salamanders to capture, fix or immobilize elusive or struggling prey. However, little information is available on how it works and the functional implications of this biting system in amphibians although such approaches might be essential to understand feeding systems performed by early tetrapods. Herein, the skull biomechanics of the Chinese giant salamander, Andrias davidianus is investigated using 3D finite element analysis. The results reveal that the prey contact position is crucial for the structural performance of the skull, which is probably related to the lack of a bony bridge between the posterior end of the maxilla and the anterior quadrato-squamosal region. Giant salamanders perform asymmetrical strikes. These strikes are unusual and specialized behavior but might indeed be beneficial in such sit-and-wait or ambush-predators to capture laterally approaching prey. However, once captured by an asymmetrical strike, large, elusive and struggling prey have to be brought to the anterior jaw region to be subdued by a strong bite. Given their basal position within extant salamanders and their "conservative" morphology, cryptobranchids may be useful models to reconstruct the feeding ecology and biomechanics of different members of early tetrapods and amphibians, with similar osteological and myological constraints.
Biting is an integral feature of the feeding mechanism for aquatic and terrestrial salamanders to capture, fix or immobilize elusive or struggling prey. However, little information is available on how it works and the functional implications of this biting system in amphibians although such approaches might be essential to understand feeding systems performed by early tetrapods. Herein, the skull biomechanics of the Chinese giant salamander, Andrias davidianus is investigated using 3D finite element analysis. The results reveal that the prey contact position is crucial for the structural performance of the skull, which is probably related to the lack of a bony bridge between the posterior end of the maxilla and the anterior quadrato-squamosal region. Giant salamanders perform asymmetrical strikes. These strikes are unusual and specialized behavior but might indeed be beneficial in such sit-and-wait or ambush-predators to capture laterally approaching prey. However, once captured by an asymmetrical strike, large, elusive and struggling prey have to be brought to the anterior jaw region to be subdued by a strong bite. Given their basal position within extant salamanders and their
The proliferation and activation of leukocytes upon contact with a biomaterial play a crucial role in the degree of inflammatory response, which may then determine the clinical failure or success of an implanted biomaterial. The aim of this study was to evaluate whether nano-and microstructured biomimetic hydroxyapatite substrates can influence the growth and activation of macrophage-like cells. Hydroxyapatite substrates with different crystal morphologies consisting of an entangled network of plate-like and needle-like crystals were evaluated. Macrophage proliferation was evaluated on the material surface (direct contact) and also in extracts i.e. media modified by the material (indirect contact). Additionally, the effect of supplementing the extracts with calcium ions and/or proteins was investigated. Macrophage activation on the substrates was evaluated by quantifying the release of reactive oxygen species and by morphological observations. The results showed that differences in the substrate's microstructure play a major role in the activation of macrophages as there was a higher release of reactive oxygen species after culturing the macrophages on plate-like crystals substrates compared to the almost non-existent release on needle-like substrates. However, the difference in macrophage proliferation was ascribed to different ionic exchanges and protein adsorption/retention from the substrates rather than to the texture of materials.
The traditional Watson-Crick base pairs in DNA may occasionally adopt a Hoogsteen conformation, with a different organization of hydrogen bonds. Previous crystal structures have shown that the Hoogsteen conformation is favored in alternating AT sequences of DNA. Here we present new data for a different sequence, d(ATTAAT)(2), which is also found in the Hoogsteen conformation. Thus we demonstrate that other all-AT sequences of DNA with a different sequence may be found in the Hoogsteen conformation. We conclude that any all-AT sequence might acquire this conformation under appropriate conditions. We also compare the detailed features of DNA in either the Hoogsteen or Watson-Crick conformations.
Melia, U.; Burgos, F.; Vallverdu, M.; Velickovski , F.; LLuch-Ariet, M.; Roca, J.; Caminal, P. PLoS one Vol. 9, num. 12 DOI: 10.1371/journal.pone.0116238 Data de publicació: 2014-12-31 Article en revista
We hypothesized that the implementation of automatic real-time assessment of quality of forced spirometry (FS) may significantly enhance the potential for extensive deployment of a FS program in the community. Recent studies have demonstrated that the application of quality criteria defined by the ATS/ERS (American Thoracic Society/European Respiratory Society) in commercially available equipment with automatic quality assessment can be markedly improved. To this end, an algorithm for assessing quality of FS automatically was reported. The current research describes the mathematical developments of the algorithm. An innovative analysis of the shape of the spirometric curve, adding 23 new metrics to the traditional 4 recommended by ATS/ERS, was done. The algorithm was created through a two-step iterative process including: (1) an initial version using the standard FS curves recommended by the ATS; and, (2) a refined version using curves from patients. In each of these steps the results were assessed against one expert's opinion. Finally, an independent set of FS curves from 291 patients was used for validation purposes. The novel mathematical approach to characterize the FS curves led to appropriate FS classification with high specificity (95%) and sensitivity (96%). The results constitute the basis for a successful transfer of FS testing to non-specialized professionals in the community.
The bacterial mechanosensitive channel MscL, a small protein mainly activated by membrane tension, is a central model system to study the transduction of mechanical stimuli into chemical signals. Mutagenic studies suggest that MscL gating strongly depends on both intra-protein and interfacial lipid-protein interactions. However, there is a gap between this detailed chemical information and current mechanical models of MscL gating. Here, we investigate the MscL bilayer-protein interface through molecular dynamics simulations, and take a combined continuum-molecular approach to connect chemistry and mechanics. We quantify the effect of membrane tension on the forces acting on the surface of the channel, and identify interactions that may be critical in the force transduction between the membrane and MscL. We find that the local stress distribution on the protein surface is largely asymmetric, particularly under tension, with the cytoplasmic side showing significantly larger and more localized forces, which pull the protein radially outward. The molecular interactions that mediate this behavior arise from hydrogen bonds between the electronegative oxygens in the lipid headgroup and a cluster of positively charged lysine residues on the amphipathic S1 domain and the C-terminal end of the second trans-membrane helix. We take advantage of this strong interaction (estimated to be 10-13 kT per lipid) to actuate the channel (by applying forces on protein-bound lipids) and explore its sensitivity to the pulling magnitude and direction. We conclude by highlighting the simple motif that confers MscL with strong anchoring to the bilayer, and its presence in various integral membrane proteins including the human mechanosensitive channel K2P1 and bovine rhodopsin.
Dupuytren's disease is a fibro-proliferative disease characterized by a disorder of the extracellular matrix (ECM) and high myofibroblast proliferation. However, studies failed to determine if the whole palm fascia is affected by the disease. The objective of this study was to analyze several components of the extracellular matrix of three types of tissues—Dupuytren's diseased contracture cords (DDC), palmar fascia clinically unaffected by Dupuytren's disease contracture (NPF), and normal forehand fascia (NFF). Histological analysis, quantification of cells recultured from each type of tissue, mRNA microarrays and immunohistochemistry for smooth muscle actin (SMA), fibrillar ECM components and non-fibrillar ECM components were carried out. The results showed that DDC samples had abundant fibrosis with reticular fibers and few elastic fibers, high cell proliferation and myofibroblasts, laminin and glycoproteins, whereas NFF did not show any of these findings. Interestingly, NPF tissues had more cells showing myofibroblasts differentiation and more collagen and reticular fibers, laminin and glycoproteins than NFF, although at lower level than DDC, with similar elastic fibers than DDC. Immunohistochemical expression of decorin was high in DDC, whereas versican was highly expressed NFF, with no differences for aggrecan. Cluster analysis revealed that the global expression profile of NPF was very similar to DDC, and reculturing methods showed that cells corresponding to DDC tissues proliferated more actively than NPF, and NPF more actively than NFF. All these results suggest that NPF tissues may be affected, and that a modification of the therapeutic approach used for the treatment of Dupuytren's disease should be considered
The surface waters of the Mediterranean Sea are extremely poor in the nutrients necessary for plankton growth. At the same time, the Mediterranean Sea borders with the largest and most active desert areas in the world and the atmosphere over the basin is subject to frequent injections of mineral dust particles. We describe statistical correlations between dust deposition over the Mediterranean Sea and surface chlorophyll concentrations at ecological time scales. Aerosol deposition of Saharan origin may explain 1 to 10% (average 5%) of seasonally detrended chlorophyll variability in the low nutrient-low chlorophyll Mediterranean. Most of the statistically significant correlations are positive with main effects in spring over the Eastern and Central Mediterranean, conforming to a view of dust events fueling needed nutrients to the planktonic community. Some areas show negative effects of dust deposition on chlorophyll, coinciding with regions under a large influence of aerosols from European origin. The influence of dust deposition on chlorophyll dynamics may become larger in future scenarios of increased aridity and shallowing of the mixed layer
Muñoz-Moreno, J.A.; Perez, N.; Muñoz, A.; Prats, A.; Garolera, M.; Jurado, M.; Fumaz, C.R.; Negredo, E.; Ferrer, M.; Clotet, B. PLoS one Vol. 9, num. 9, p. e107625-1-e107625-7 DOI: 10.1371/journal.pone.0107625 Data de publicació: 2014-09-19 Article en revista
Objective: We used demographic and clinical data to design practical classification models for prediction of neurocognitive impairment (NCI) in people with HIV infection.; Methods: The study population comprised 331 HIV-infected patients with available demographic, clinical, and neurocognitive data collected using a comprehensive battery of neuropsychological tests. Classification and regression trees (CART) were developed to obtain detailed and reliable models to predict NCI. Following a practical clinical approach, NCI was considered the main variable for study outcomes, and analyses were performed separately in treatment-naive and treatment-experienced patients.; Results: The study sample comprised 52 treatment-naive and 279 experienced patients. In the first group, the variables identified as better predictors of NCI were CD4 cell count and age (correct classification [CC]: 79.6%, 3 final nodes). In treatment-experienced patients, the variables most closely related to NCI were years of education, nadir CD4 cell count, central nervous system penetration-effectiveness score, age, employment status, and confounding comorbidities (CC: 82.1%, 7 final nodes). In patients with an undetectable viral load and no comorbidities, we obtained a fairly accurate model in which the main variables were nadir CD4 cell count, current CD4 cell count, time on current treatment, and past highest viral load (CC: 88%, 6 final nodes).; Conclusion: Practical classification models to predict NCI in HIV infection can be obtained using demographic and clinical variables. An approach based on CART analyses may facilitate screening for HIV-associated neurocognitive disorders and complement clinical information about risk and protective factors for NCI in HIV-infected patients.
Plana, O.; Olsen, J.; Andersen, P.; Gomez, G.; Cnattingius, S.; Li, J. PLoS one Vol. 9, num. 7, p. e103353-1-e103353-8 DOI: 10.1371/journal.pone.0103353 Data de publicació: 2014-07-28 Article en revista
Introduction: The decline in birth rates is a concern in public health. Fertility is partly determined before birth by the intrauterine environment and prenatal exposure to maternal stress could, through hormonal disturbance, play a role. There has been such evidence from animal studies but not from humans. We aimed to examine the association between prenatal stress due to maternal bereavement following the death of a relative and childbirths in the offspring. Materials and Methods: This population-based cohort study included all subjects born in Denmark after 1968 and in Sweden after 1973 and follow-up started at the age of 12 years. Subjects were categorized as exposed if their mothers lost a close relative during pregnancy or the year before and unexposed otherwise. The main outcomes were age at first child and age-specific mean numbers of childbirths. Data was analyzed using Cox Proportional Hazards models stratified by gender and adjusted for several covariates. Subanalyses were performed considering the type of relative deceased and timing of bereavement. Results: A total of 4,121,596 subjects were followed-up until up to 41 years of age. Of these subjects, 93,635 (2.3%) were exposed and 981,989 (23.8%) had at least one child during follow-up time. Compared to unexposed, the hazard ratio (HR) [95% confidence interval] of having at least one child for exposed males and females were 0.98 [0.96-1.01] and 1.01 [0.98-1.03], respectively. We found a slightly reduced probability of having children in females born to mothers who lost a parent with HR = 0.97 [0.94-0.99] and increased probability in females born to mothers who lost another child (HR = 1.09 [1.04-1.14]), the spouse (HR = 1.29 [1.12-1.48]) or a sibling (HR = 1.13 [1.01-1.27]). Conclusions: Our results suggested no overall association between prenatal exposure to maternal stress and having a child in early adulthood but a longer time of follow-up is necessary in order to reach a firmer conclusion.
Vilaplana, C.; Prats, C.; Marzo, E.; Barril, C.; Vegué, M.; Jorge, D.; Valls, J.; Lopez, D.; Cardona, P.J. PLoS one Vol. 9, num. 6, p. e100830- DOI: 10.1371/journal.pone.0100830 Data de publicació: 2014-06-24 Article en revista
The temporo-spatial relationship between the three organs (lung, spleen and lymph node) involved during the initial stages
of Mycobacterium tuberculosis infection has been poorly studied. As such, we performed an experimental study to evaluate
the bacillary load in each organ after aerosol or intravenous infection and developed a mathematical approach using the
data obtained in order to extract conclusions. The results showed that higher bacillary doses result in an earlier IFN-c
response, that a certain bacillary load (BL) needs to be reached to trigger the IFN-c response, and that control of the BL is
not immediate after onset of the IFN-c response, which might be a consequence of the spatial dimension. This study may
have an important impact when it comes to designing new vaccine candidates as it suggests that triggering an earlier IFN-c
response might not guarantee good infection control, and therefore that additional properties should be considered for
The consequences of phrenic nerve paralysis vary from a considerable reduction in respiratory function to an apparently normal state. Acoustic analysis of lung sound intensity (LSI) could be an indirect non-invasive measurement of respiratory muscle function, comparing activity on the two sides of the thoracic cage. Lung sounds and airflow were recorded in ten males with unilateral phrenic paralysis and ten healthy subjects (5 men/5 women), during progressive increasing airflow maneuvers. Subjects were in sitting position and two acoustic sensors were placed on their back, on the left and right sides. LSI was determined from 1.2 to 2.4 L/s between 70 and 2000 Hz. LSI was significantly greater on the normal (19.3±4.0 dB) than the affected (5.7±3.5 dB) side in all patients (p = 0.0002), differences ranging from 9.9 to 21.3 dB (13.5±3.5 dB). In the healthy subjects, the LSI was similar on both left (15.1±6.3 dB) and right (17.4±5.7 dB) sides (p = 0.2730), differences ranging from 0.4 to 4.6 dB (2.3±1.6 dB). There was a positive linear relationship between the LSI and the airflow, with clear differences between the slope of patients (about 5 dB/L/s) and healthy subjects (about 10 dB/L/s). Furthermore, the LSI from the affected side of patients was close to the background noise level, at low airflows. As the airflow increases, the LSI from the affected side did also increase, but never reached the levels seen in healthy subjects. Moreover, the difference in LSI between healthy and paralyzed sides was higher in patients with lower FEV1 (%). The acoustic analysis of LSI is a relevant non-invasive technique to assess respiratory function. This method could reinforce the reliability of the diagnosis of unilateral phrenic paralysis, as well as the monitoring of these patients.
The study assesses complexity of the cardiac control directed to the sinus node and to ventricles in long QT syndrome type 1 (LQT1) patients with KCNQ1-A341V mutation. Complexity was assessed via refined multiscale entropy (RMSE) computed over the beat-to-beat variability series of heart period (HP) and QT interval. HP and QT interval were approximated respectively as the temporal distance between two consecutive R-wave peaks and between the R-wave apex and T-wave end. Both measures were automatically taken from 24-hour electrocardiographic Holter traces recorded during daily activities in non mutation carriers (NMCs, n = 14) and mutation carriers (MCs, n = 34) belonging to a South African LQT1 founder population. The MC group was divided into asymptomatic (ASYMP, n = 11) and symptomatic (SYMP, n = 23) patients according to the symptom severity. Analyses were carried out during daytime (DAY, from 2PM to 6PM) and nighttime (NIGHT, from 12PM to 4AM) off and on beta-adrenergic blockade (BBoff and BBon). We found that the complexity of the HP variability at short time scale was under vagal control, being significantly increased during NIGHT and BBon both in ASYMP and SYMP groups, while the complexity of both HP and QT variability at long time scales was under sympathetic control, being smaller during NIGHT and BBon in SYMP subjects. Complexity indexes at long time scales in ASYMP individuals were smaller than those in SYMP ones regardless of therapy (i.e. BBoff or BBon), thus suggesting that a reduced complexity of the sympathetic regulation is protective in ASYMP individuals. RMSE analysis of HP and QT interval variability derived from routine 24-hour electrocardiographic Holter recordings might provide additional insights into the physiology of the cardiac control and might be fruitfully exploited to improve risk stratification in LQT1 population.
Del Valle, J.; Silva, W.; Tinco, C.; Pons, M.; del Valle, LJ.; Casabona, V.; Champin, D.; Bazan, J.; Zavalea, V.; Vargas, M.; Ruiz, J. PLoS one Vol. 9, num. 3, p. e92283- DOI: 10.1371/journal.pone.0092283 Data de publicació: 2014-03-20 Article en revista
Bartonella bacilliformis is the etiologic agent of Carrion’s disease. This disease has two well established phases, the most relevant being the so called Oroya Fever, in which B. bacilliformis infect the erythrocytes resulting in severe anemia and transient immunosuppression, with a high lethality in the absence of adequate antibiotic treatment. The presence of B. bacilliformis was studied in 113 blood samples suspected of Carrion’s disease based on clinical criteria, despite the absence of a positive thin blood smear, by two different PCR techniques (using Bartonella-specific and universal 16S rRNA gene primers), and by bacterial culture. The specific 16S rRNA gene primers revealed the presence of 21 B. bacilliformis and 1 Bartonella elizabethae, while universal primers showed both the presence of 3 coinfections in which a concomitant pathogen was detected plus Bartonella, in addition to the presence of infections by other microorganisms such as Agrobacterium or Bacillus firmus. These data support the need to implement molecular tools to diagnose Carrion’s disease.
The analysis of amplitude parameters of the diaphragm mechanomyographic (MMGdi) signal is a non-invasive technique to assess respiratory muscle effort and to detect and quantify the severity of respiratory muscle weakness. The amplitude of the MMGdi signal is usually evaluated using the average rectified value or the root mean square of the signal. However, these estimations are greatly affected by the presence of cardiac vibration or mechanocardiographic (MCG) noise. In this study, we present a method for improving the estimation of the respiratory muscle effort from MMGdi signals that is robust to the presence of MCG. This method is based on the calculation of the sample entropy using fixed tolerance values (fSampEn), that is, with tolerance values that are not normalized by the local standard deviation of the window analyzed. The behavior of the fSampEn parameter was tested in synthesized mechanomyographic signals, with different ratios between the amplitude of the MCG and clean mechanomyographic components. As an example of application of this technique, the use of fSampEn was explored also in recorded MMGdi signals, with different inspiratory loads. The results with both synthetic and recorded signals indicate that the entropy parameter is less affected by the MCG noise, especially at low signal-to-noise ratios. Therefore, we believe that the proposed fSampEn parameter could improve estimates of respiratory muscle effort from MMGdi signals with the presence of MCG interference.
Background: Etravirine (ETR) was approved for patients with virological failure and antiretroviral resistance mutations. It has also shown antiviral efficacy in antiretroviral-naive patients. However, data on the switching from protease inhibitors (PI) to ETR are lacking.; Methods: HIV-1-infected patients with suppressed viral load (VL) during a PI-containing regimen (>12 months) and no previous virological failure were randomized to switch from the PI to ETR (400 mg/day, dissolved in water) (ETR group, n = 22) or to continue with the same regimen (control group, n = 21). Percentage of patients with VL <= 50 copies/mL were assessed at week 48, as well as changes in CD4 T-cell counts and metabolic profile.; Results: We included 43 patients [72.9% male, 46.3 (42.2; 50.6) years]. Two patients receiving ETR (grade-1 diarrhea and voluntary discontinuation) and another in the control group (simplification) discontinued therapy early. No patients presented virological failure (two consecutive VL>50 copies/mL); treatment was successful in 95.2% of the control group and 90.9% of the ETR group (intention-to-treat analysis, missing = failure) (p = 0.58). CD4+ T-cell counts did not significantly vary [+49 cells/mu L in the ETR group (p = 0.25) and -4 cells/mu L in the control group (p = 0.71)]. The ETR group showed significant reductions in cholesterol (p<0.001), triglycerides (p=<0.001), and glycemia (p = 0.03) and higher satisfaction (0-10 scale) (p = 0.04). Trough plasma concentrations of ETR were similar to observed in studies using ETR twice daily.; Conclusion: Switch from a PI-based regimen to a once-daily combination based on ETR maintained undetectable VL during 48 weeks in virologically suppressed HIV-infected patients while lipid profile and patient satisfaction improved significantly.
In machine olfaction, the design of applications based on gas sensor arrays is highly dependent on the robustness of the signal and data processing algorithms. While the practice of testing the algorithms on public benchmarks is not common in the field, we propose software for performing data simulations in the machine olfaction field by generating parameterized sensor array data. The software is implemented as an R language package chemosensors which is open-access, platform-independent and self-contained. We introduce the concept of a virtual sensor array which can be used as a data generation tool. In this work, we describe the data simulation workflow which basically consists of scenario definition, virtual array parameterization and the generation of sensor array data. We also give examples of the processing of the simulated data as proof of concept for the parameterized sensor array data: the benchmarking of classification algorithms, the evaluation of linear- and non-linear regression algorithms, and the biologically inspired processing of sensor array data. All the results presented were obtained under version 0.7.6 of the chemosensors package whose home page is chemosensors.r-forge.r-project.org.
At least ten species of beaked whales inhabit the North Pacific, but little is known about their abundance, ecology, and behavior, as they are elusive and difficult to distinguish visually at sea. Six of these species produce known species-specific frequency modulated (FM) echolocation pulses: Baird’s, Blainville’s, Cuvier’s, Deraniyagala’s, Longman’s, and Stejneger’s beaked whales. Additionally, one described FM pulse (BWC) from Cross Seamount, Hawai’i, and three unknown FM pulse types (BW40, BW43, BW70) have been identified from almost 11 cumulative years of autonomous recordings at 24 sites throughout the North Pacific. Most sites had a dominant FM pulse type with other types being either absent or limited. There was not a strong seasonal influence on the occurrence of these signals at any site, but longer time series may reveal smaller, consistent fluctuations. Only the species producing BWC signals, detected throughout the Pacific Islands region, consistently showed a diel cycle with nocturnal foraging. By comparing stranding and sighting information with acoustic findings, we hypothesize that BWC signals are produced by ginkgo-toothed beaked whales. BW43 signal encounters were restricted to Southern California and may be produced by Perrin’s beaked whale, known only from Californian waters. BW70 signals were detected in the southern Gulf of California, which is prime habitat for Pygmy beaked whales. Hubb’s beaked whale may have produced the BW40 signals encountered off central and southern California; however, these signals were also recorded off Pearl and Hermes Reef and Wake Atoll, which are well south of their known range.
In genetic association studies, tests for Hardy-Weinberg proportions are often employed as a quality control checking procedure. Missing genotypes are typically discarded prior to testing. In this paper we show that inference for Hardy-Weinberg proportions can be biased when missing values are discarded. We propose to use multiple imputation of missing values in order to improve inference for Hardy-Weinberg proportions. For imputation we employ a multinomial logit model that uses information from allele intensities and/or neighbouring markers. Analysis of an empirical data set of single nucleotide polymorphisms possibly related to colon cancer reveals that missing genotypes are not missing completely at random. Deviation from Hardy-Weinberg proportions is mostly due to a lack of heterozygotes. Inbreeding coefficients estimated by multiple imputation of the missings are typically lowered with respect to inbreeding coefficients estimated by discarding the missings. Accounting for missings by multiple imputation qualitatively changed the results of 10 to 17% of
the statistical tests performed. Estimates of inbreeding coefficients obtained by multiple imputation showed high correlation with estimates obtained by single imputation using an external reference panel. Our conclusion is that imputation of missing data leads to improved statistical inference for Hardy-Weinberg proportions.
In genetic association studies, tests for Hardy-Weinberg proportions are often employed as a quality control checking
procedure. Missing genotypes are typically discarded prior to testing. In this paper we show that inference for Hardy-
Weinberg proportions can be biased when missing values are discarded. We propose to use multiple imputation of missing
values in order to improve inference for Hardy-Weinberg proportions. For imputation we employ a multinomial logit model
that uses information from allele intensities and/or neighbouring markers. Analysis of an empirical data set of single
nucleotide polymorphisms possibly related to colon cancer reveals that missing genotypes are not missing completely at
random. Deviation from Hardy-Weinberg proportions is mostly due to a lack of heterozygotes. Inbreeding coefficients
estimated by multiple imputation of the missings are typically lowered with respect to inbreeding coefficients estimated by
discarding the missings. Accounting for missings by multiple imputation qualitatively changed the results of 10 to 17% of
the statistical tests performed. Estimates of inbreeding coefficients obtained by multiple imputation showed high
correlation with estimates obtained by single imputation using an external reference panel. Our conclusion is that
imputation of missing data leads to improved statistical inference for Hardy-Weinberg proportions
Ortega, S.; Ruiz, H.; Vellido, A.; Olier, I.; Romero, E.; Julia, M.; Martin, J.; Jarman, I.; Arus, C.; Lisboa, P. PLoS one Vol. 8, num. 12, p. e83773-1-e83773-14 DOI: 10.1371/journal.pone.0083773 Data de publicació: 2013-12-23 Article en revista
Background: The clinical investigation of human brain tumors often starts with a non-invasive imaging study, providing information about the tumor extent and location, but little insight into the biochemistry of the analyzed tissue. Magnetic Resonance Spectroscopy can complement imaging by supplying a metabolic fingerprint of the tissue. This study analyzes single-voxel magnetic resonance spectra, which represent signal information in the frequency domain. Given that a single voxel may contain a heterogeneous mix of tissues, signal source identification is a relevant challenge for the problem of tumor type classification from the spectroscopic signal.
Methodology/Principal Findings: Non-negative matrix factorization techniques have recently shown their potential for the identification of meaningful sources from brain tissue spectroscopy data. In this study, we use a convex variant of these methods that is capable of handling negatively-valued data and generating sources that can be interpreted as tumor class prototypes. A novel approach to convex non-negative matrix factorization is proposed, in which prior knowledge about class information is utilized in model optimization. Class-specific information is integrated into this semi-supervised process by setting the metric of a latent variable space where the matrix factorization is carried out. The reported experimental study comprises 196 cases from different tumor types drawn from two international, multi-center databases. The results indicate that the proposed approach outperforms a purely unsupervised process by achieving near perfect correlation of the extracted sources with the mean spectra of the tumor types. It also improves tissue type classification...
The Facioscapulohumeral Muscular Dystrophy (FSHD) is an autosomal dominant neuromuscular disorder whose incidence is estimated in about one in 400,000 to one in 20,000. No effective therapeutic strategies are known to halt progression or reverse muscle weakness and atrophy. It is known that the FSHD is caused by modifications located within a D4ZA repeat array in the chromosome 4q, while recent advances have linked these modifications to the DUX4 gene. Unfortunately, the complete mechanisms responsible for the molecular pathogenesis and progressive muscle weakness still remain unknown. Although there are many studies addressing cancer databases from a machine learning perspective, there is no such precedent in the analysis of the FSHD. This study aims to fill this gap by analyzing two specific FSHD databases. A feature selection algorithm is used as the main engine to select genes promoting the highest possible classification capacity. The combination of feature selection and classification aims at obtaining simple models (in terms of very low numbers of genes) capable of good generalization, that may be associated with the disease. We show that the reported method is highly efficient in finding genes to discern between healthy cases (not affected by the FSHD) and FSHD cases, allowing the discovery of very parsimonious models that yield negligible repeated cross-validation error. These models in turn give rise to very simple decision procedures in the form of a decision tree. Current biological evidence regarding these genes shows that they are linked to skeletal muscle processes concerning specific human conditions.
Sole, M.; Lenoir, M.; Durfort, M.; López-Béjar, M.; Lombarte, A.; Andre, M. PLoS one Vol. 8, num. 10, p. e78825-1-e78825-12 DOI: 10.1371/journal.pone.0078825 Data de publicació: 2013-10-15 Article en revista
There is a considerable lack of information concerning marine invertebrate sensitivity to sound exposure. However, recent findings on cuttlefish and octopi showed that exposure to artificial noise had a direct consequence on the functionality and physiology of the statocysts, sensory organs, which are responsible for their equilibrium and movements in the water column. Owing to a lack of available data on deep diving cephalopod species, we conducted a noise exposure comparative experiment on one Mediterranean squid, Illex coindetii, and on the European squid Loligo vulgaris. Scanning electron microscopy (SEM) revealed similar injuries in the inner structure of the statocysts, as those found in cuttlefish and octopi. In addition to the ultrastructural description of the lesions, we publish here the first images of the crista-cupula system and inner statocyst cavity of I. coindetii.
Tamburini, C.; Canals, M.; Durrieu de Madron, X.; Houpert; Lefèvre, D.; Andre, M.; Aguilar, J.; Bigongiari, C.; Emanuele, U.; Dornic, D. PLoS one Vol. 8, num. 7 DOI: 10.1371/journal.pone.0067523 Data de publicació: 2013-07-10 Article en revista
The deep ocean is the largest and least known ecosystem on Earth. It hosts numerous pelagic organisms, most of which are able to emit light. Here we present a unique data set consisting of a 2.5-year long record of light emission by deep-sea pelagic organisms, measured from December 2007 to June 2010 at the ANTARES underwater neutrino telescope in the deep NW Mediterranean Sea, jointly with synchronous hydrological records. This is the longest continuous time-series of deep-sea bioluminescence ever recorded. Our record reveals several weeks long, seasonal bioluminescence blooms with light intensity up to two orders of magnitude higher than background values, which correlate to changes in the properties of deep waters. Such changes are triggered by the winter cooling and evaporation experienced by the upper ocean layer in the Gulf of Lion that leads to the formation and subsequent sinking of dense water through a process known as ‘‘open-sea convection’’. It episodically renews the deep water of the study area and conveys fresh organic matter that fuels the deep ecosystems. Luminous bacteria most likely are the main contributors to the observed deep-sea bioluminescence blooms.
Our observations demonstrate a consistent and rapid connection between deep open-sea convection and bathypelagic
biological activity, as expressed by bioluminescence. In a setting where dense water formation events are likely to decline under global warming scenarios enhancing ocean stratification, in situ observatories become essential as environmental sentinels for the monitoring and understanding of deep-sea ecosystem shifts
The deep ocean is the largest and least known ecosystem on Earth. It hosts numerous pelagic organisms, most of which are able to emit light. Here we present a unique data set consisting of a 2.5-year long record of light emission by deep-sea pelagic organisms, measured from December 2007 to June 2010 at the ANTARES underwater neutrino telescope in the deep NW Mediterranean Sea, jointly with synchronous hydrological records. This is the longest continuous time-series of deep-sea bioluminescence ever recorded. Our record reveals several weeks long, seasonal bioluminescence blooms with light intensity up to two orders of magnitude higher than background values, which correlate to changes in the properties of deep waters. Such changes are triggered by the winter cooling and evaporation experienced by the upper ocean layer in the Gulf of Lion that leads to the formation and subsequent sinking of dense water through a process known as “open-sea convection”. It episodically renews the deep water of the study area and conveys fresh organic matter that fuels the deep ecosystems. Luminous bacteria most likely are the main contributors to the observed deep-sea bioluminescence blooms. Our observations demonstrate a consistent and rapid connection between deep open-sea convection and bathypelagic biological activity, as expressed by bioluminescence. In a setting where dense water formation events are likely to decline under global warming scenarios enhancing ocean stratification, in situ observatories become essential as environmental sentinels for the monitoring and understanding of deep-sea ecosystem shifts
We present GStream, a method that combines genome-wide SNP and CNV genotyping in the Illumina microarray platform with unprecedented accuracy. This new method outperforms previous well-established SNP genotyping software. More importantly, the CNV calling algorithm of GStream dramatically improves the results obtained by previous state-of-the-art methods and yields an accuracy that is close to that obtained by purely CNV-oriented technologies like Comparative Genomic Hybridization (CGH). We demonstrate the superior performance of GStream using microarray data generated from HapMap samples. Using the reference CNV calls generated by the 1000 Genomes Project (1KGP) and well-known studies on whole genome CNV characterization based either on CGH or genotyping microarray technologies, we show that GStream can increase the number of reliably detected variants up to 25% compared to previously developed methods. Furthermore, the increased genome coverage provided by GStream allows the discovery of CNVs in close linkage disequilibrium with SNPs, previously associated with disease risk in published Genome-Wide Association Studies (GWAS). These results could provide important insights into the biological mechanism underlying the detected disease risk association. With GStream, large-scale GWAS will not only benefit from the combined genotyping of SNPs and CNVs at an unprecedented accuracy, but will also take advantage of the computational efficiency of the method.
We present GStream, a method that combines genome-wide SNP and CNV genotyping in the Illumina microarray platform with unprecedented accuracy. This new method outperforms previous well-established SNP genotyping software. More importantly, the CNV calling algorithm of GStream dramatically improves the results obtained by previous state-of-the-art methods and yields an accuracy that is close to that obtained by purely CNV-oriented technologies like Comparative Genomic Hybridization (CGH). We demonstrate the superior performance of GStream using microarray data generated from HapMap samples. Using the reference CNV calls generated by the 1000 Genomes Project (1KGP) and well-known studies on whole genome CNV characterization based either on CGH or genotyping microarray technologies, we show that GStream can increase the number of reliably detected variants up to 25% compared to previously developed methods. Furthermore, the increased genome coverage provided by GStream allows the discovery of CNVs in close linkage disequilibrium with SNPs, previously associated with disease risk in published Genome-Wide Association Studies (GWAS). These results could provide important insights into the biological mechanism underlying the detected disease risk association. With GStream,
large-scale GWAS will not only benefit from the combined genotyping of SNPs and CNVs at an unprecedented accuracy, but will also take advantage of the computational efficiency of the method.
A variety of cardiac arrhythmias are initiated by a focal excitation that disrupts the regular beating of the heart. In some
cases it is known that these excitations are due to calcium (Ca) release from the sarcoplasmic reticulum (SR) via propagating
subcellular Ca waves. However, it is not understood what are the physiological factors that determine the timing of these
excitations at both the subcellular and tissue level. In this paper we apply analytic and numerical approaches to determine
the timing statistics of spontaneous Ca release (SCR) in a simplified model of a cardiac myocyte. In particular, we compute
the mean first passage time (MFPT) to SCR, in the case where SCR is initiated by spontaneous Ca sparks, and demonstrate
that this quantity exhibits either an algebraic or exponential dependence on system parameters. Based on this analysis we
identify the necessary requirements so that SCR occurs on a time scale comparable to the cardiac cycle. Finally, we study
how SCR is synchronized across many cells in cardiac tissue, and identify a quantitative measure that determines the relative
timing of SCR in an ensemble of cells. Using this approach we identify the physiological conditions so that cell-to-cell
variations in the timing of SCR is small compared to the typical duration of an SCR event. We argue further that under these
conditions inward currents due to SCR can summate and generate arrhythmogenic triggered excitations in cardiac tissue.
Centromere sequences in the genome are associated with the formation of kinetochores, where spindle microtubules grow in mitosis. Centromere sequences usually have long tandem repeats (satellites). In holocentric nematodes it is not clear how kinetochores are formed during mitosis; they are distributed throughout the chromosomes. For this reason it appeared of interest to study the satellites in nematodes in order to determine if they offer any clue on how kinetochores are assembled in these species. We have studied the satellites in the genome of six nematode species. We found that the presence of satellites depends on whether the nematode chromosomes are holocentric or monocentric. It turns out that holocentric nematodes are unique because they have a large number of satellites scattered throughout their genome. Their number, length and composition are different in each species: they apparently have very little evolutionary conservation. In contrast, no scattered satellites are found in the monocentric nematode Trichinella spiralis. It appears that the absence/presence of scattered satellites in the genome distinguishes monocentric from holocentric nematodes. We conclude that the presence of satellites is related to the holocentric nature of the chromosomes of most nematodes. Satellites may stabilize a higher order structure of chromatin and facilitate the formation of kinetochores. We also present a new program, SATFIND, which is suited to find satellite sequences.