Biased diffusion in confined media: Test of the Fick-Jacobs approximation and validity criteria

We study biased, diffusive transport of Brownian particles through narrow, spatially periodic structures in which the motion is constrained in lateral directions. The problem is analyzed under the perspective of the Fick-Jacobs equation, which accounts for the effect of the lateral confinement by introducing an entropic barrier in a one-dimensional diffusion. The validity of this approximation, based on the assumption of an instantaneous equilibration of the particle distribution in the cross section of the structure, is analyzed by comparing the different time scales that characterize the problem. A validity criterion is established in terms of the shape of the structure and of the applied force. It is analytically corroborated and verified by numerical simulations that the critical value of the force up to which this description holds true scales as the square of the periodicity of the structure. The criterion can be visualized by means of a diagram representing the regions where the Fick-Jacobs description becomes inaccurate in terms of the scaled force versus the periodicity of the structure.

Study of OSEM with different subsets in grating-based X-ray differential phase-contrast imaging.

Impressive developments in X-ray imaging are associated with X-ray phase contrast computed tomography based on grating interferometry, a technique that provides increased contrast compared with conventional absorption-based imaging. A new "single-step" method capable of separating phase information from other contributions has been recently proposed. This approach not only simplifies data-acquisition procedures, but, compared with the existing phase step approach, significantly reduces the dose delivered to a sample. However, the image reconstruction procedure is more demanding than for traditional methods and new algorithms have to be developed to take advantage of the "single-step" method. In the work discussed in this paper, a fast iterative image reconstruction method named OSEM (ordered subsets expectation maximization) was applied to experimental data to evaluate its performance and range of applicability. The OSEM algorithm with different subsets was also characterized by comparison of reconstruction image quality and convergence speed. Computer simulations and experimental results confirm the reliability of this new algorithm for phase-contrast computed tomography applications. Compared with the traditional filtered back projection algorithm, in particular in the presence of a noisy acquisition, it furnishes better images at a higher spatial resolution and with lower noise. We emphasize that the method is highly compatible with future X-ray phase contrast imaging clinical applications.

Detection of metabolite induction in fungal co-cultures on solid media by high-throughput differential ultra-high pressure liquid chromatography-time-of-flight mass spectrometry fingerprinting.

Access to new biological sources is a key element of natural product research. A particularly large number of biologically active molecules have been found to originate from microorganisms. Very recently, the use of fungal co-culture to activate the silent genes involved in metabolite biosynthesis was found to be a successful method for the induction of new compounds. However, the detection and identification of the induced metabolites in the confrontation zone where fungi interact remain very challenging. To tackle this issue, a high-throughput UHPLC-TOF-MS-based metabolomic approach has been developed for the screening of fungal co-cultures in solid media at the petri dish level. The metabolites that were overexpressed because of fungal interactions were highlighted by comparing the LC-MS data obtained from the co-cultures and their corresponding mono-cultures. This comparison was achieved by subjecting automatically generated peak lists to statistical treatments. This strategy has been applied to more than 600 co-culture experiments that mainly involved fungal strains from the Fusarium genera, although experiments were also completed with a selection of several other filamentous fungi. This strategy was found to provide satisfactory repeatability and was used to detect the biomarkers of fungal induction in a large panel of filamentous fungi. This study demonstrates that co-culture results in consistent induction of potentially new metabolites.

Entropic transport in confined media: a challenge for computational studies in biological and soft-matter systems

Transport in small-scale biological and soft-matter systems typically occurs under confinement conditions in which particles proceed through obstacles and irregularities of the boundaries that may significantly alter their trajectories. A transport model that assimilates the confinement to the presence of entropic barriers provides an efficient approach to quantify its effect on the particle current and the diffusion coefficient. We review the main peculiarities of entropic transport and treat two cases in which confinement effects play a crucial role, with the appearance of emergent properties. The presence of entropic barriers modifies the mean first-passage time distribution and therefore plays a very important role in ion transport through micro- and nano-channels. The functionality of molecular motors, modeled as Brownian ratchets, is strongly affected when the motor proceeds in a confined medium that may constitute another source of rectification. The interplay between ratchet and entropic rectification gives rise to a wide variety of dynamical behaviors, not observed when the Brownian motor proceeds in an unbounded medium. Entropic transport offers new venues of transport control and particle manipulation and new ways to engineer more efficient devices for transport at the nanoscale.

Image quality assessment in digital mammography: part II. NPWE as a validated alternative for contrast detail analysis.

Assessment of image quality for digital x-ray mammography systems used in European screening programs relies mainly on contrast-detail CDMAM phantom scoring and requires the acquisition and analysis of many images in order to reduce variability in threshold detectability. Part II of this study proposes an alternative method based on the detectability index (d') calculated for a non-prewhitened model observer with an eye filter (NPWE). The detectability index was calculated from the normalized noise power spectrum and image contrast, both measured from an image of a 5 cm poly(methyl methacrylate) phantom containing a 0.2 mm thick aluminium square, and the pre-sampling modulation transfer function. This was performed as a function of air kerma at the detector for 11 different digital mammography systems. These calculated d' values were compared against threshold gold thickness (T) results measured with the CDMAM test object and against derived theoretical relationships. A simple relationship was found between T and d', as a function of detector air kerma; a linear relationship was found between d' and contrast-to-noise ratio. The values of threshold thickness used to specify acceptable performance in the European Guidelines for 0.10 and 0.25 mm diameter discs were equivalent to threshold calculated detectability indices of 1.05 and 6.30, respectively. The NPWE method is a validated alternative to CDMAM scoring for use in the image quality specification, quality control and optimization of digital x-ray systems for screening mammography.

Simulation of surface waves in porous media

We present a novel numerical algorithm for the simulation of seismic wave propagation in porous media, which is particularly suitable for the accurate modelling of surface wave-type phenomena. The differential equations of motion are based on Biot's theory of poro-elasticity and solved with a pseudospectral approach using Fourier and Chebyshev methods to compute the spatial derivatives along the horizontal and vertical directions, respectively. The time solver is a splitting algorithm that accounts for the stiffness of the differential equations. Due to the Chebyshev operator the grid spacing in the vertical direction is non-uniform and characterized by a denser spatial sampling in the vicinity of interfaces, which allows for a numerically stable and accurate evaluation of higher order surface wave modes. We stretch the grid in the vertical direction to increase the minimum grid spacing and reduce the computational cost. The free-surface boundary conditions are implemented with a characteristics approach, where the characteristic variables are evaluated at zero viscosity. The same procedure is used to model seismic wave propagation at the interface between a fluid and porous medium. In this case, each medium is represented by a different grid and the two grids are combined through a domain-decomposition method. This wavefield decomposition method accounts for the discontinuity of variables and is crucial for an accurate interface treatment. We simulate seismic wave propagation with open-pore and sealed-pore boundary conditions and verify the validity and accuracy of the algorithm by comparing the numerical simulations to analytical solutions based on zero viscosity obtained with the Cagniard-de Hoop method. Finally, we illustrate the suitability of our algorithm for more complex models of porous media involving viscous pore fluids and strongly heterogeneous distributions of the elastic and hydraulic material properties.

Growth regulators, culture media and antibiotics in the in vitro shoot regeneration from mature tissue of citrus cultivars

The objective of this study was to evaluate the effects of 6-benzylaminopurine (BAP) and α-naphthaleneacetic acid (NAA) combinations, basal media and beta-lactam antibiotics on in vitro organogenesis from mature stem segments of 'Pêra', 'Valência' and 'Bahia' sweet oranges and 'Cravo' rangpur lime. For induction of shoot regeneration, the segments of the four cultivars were placed on Murashige and Skoog (MS) medium containing the following BAP/NAA concentrations: 0.0/0.0; 0.25/0.0; 0.25/0.25; 0.5/0.0; 0.5/0.5; 1.0/0.0; 2.0/0.0; 2.0/0.25; 2.0/0.5; and 2.0/1.0 mg L-1. In order to test the influence of the culture media on shoot-bud induction, (MS), Murashige and Tucker (MT), and woody plant medium (WPM) formulations were evaluated, associated with the best combination of plant growth regulators obtained in the previous experiment. The influence of four beta-lactam antibiotics (timentin, cefotaxime sodium salt, meropenem trihydrate and augmentin) on shoot regeneration was determined. Better regeneration responses were achieved when internodal segments were cultured onto MS-based medium with 500 mg L-1 cefotaxime with the following BAP/NAA concentrations: 0.5 + 0.25 mg L-1 for 'Cravo', 1.0 + 0.25 mg L-1 for 'Valência' and 'Bahia', and 1.0 + 0.5 mg L-1 for 'Pêra'. Genotype, growth regulators, basal media and beta-lactam antibiotics affect the morphogenetic response in mature tissues of citrus.

The media accountability of independent regulatory agencies

Independent regulatory agencies (IRAs) are increasingly attracting academic and societal attention, as they represent the institutional cornerstone of the regulatory state and play a key role in policy-making. Besides the expected benefits in terms of credibility and efficiency, these regulators are said to bring about a 'democratic deficit', following their statutory separation from democratic institutions. Consequently, a 'multi-pronged system of control' is required. This article focuses on a specific component of this system, that is, the media. The goal is to determine whether media coverage of IRAs meets the necessary prerequisites to be considered a potential 'accountability forum' for regulators. The results of a comparison of two contrasted cases - the British and Swiss competition commissions - mostly support the expectations, because they show that media coverage of IRAs corresponds to that of the most relevant policy issues and follows the regulatory cycle. Furthermore, a systematic bias in media coverage can be excluded.

Textural controls on induced polarization and permeability in granular media

The spatial resolution visualized with hydrological models and the conceptualized images of subsurface hydrological processes often exceed resolution of the data collected with classical instrumentation at the field scale. In recent years it was possible to increasingly diminish the inherent gap to information from point like field data through the application of hydrogeophysical methods at field-scale. With regards to all common geophysical exploration techniques, electric and electromagnetic methods have arguably to greatest sensitivity to hydrologically relevant parameters. Of particular interest in this context are induced polarisation (IP) measurements, which essentially constrain the capacity of a probed subsurface region to store an electrical charge. In the absence of metallic conductors the IP- response is largely driven by current conduction along the grain surfaces. This offers the perspective to link such measurements to the characteristics of the solid-fluid-interface and thus, at least in unconsolidated sediments, should allow for first-order estimates of the permeability structure.¦While the IP-effect is well explored through laboratory experiments and in part verified through field data for clay-rich environments, the applicability of IP-based characterizations to clay-poor aquifers is not clear. For example, polarization mechanisms like membrane polarization are not applicable in the rather wide pore-systems of clay free sands, and the direct transposition of Schwarz' theory relating polarization of spheres to the relaxation mechanism of polarized cells to complex natural sediments yields ambiguous results.¦In order to improve our understanding of the structural origins of IP-signals in such environments as well as their correlation with pertinent hydrological parameters, various laboratory measurements have been conducted. We consider saturated quartz samples with a grain size spectrum varying from fine sand to fine gravel, that is grain diameters between 0,09 and 5,6 mm, as well as corresponding pertinent mixtures which can be regarded as proxies for widespread alluvial deposits. The pore space characteristics are altered by changing (i) the grain size spectra, (ii) the degree of compaction, and (iii) the level of sorting. We then examined how these changes affect the SIP response, the hydraulic conductivity, and the specific surface area of the considered samples, while keeping any electrochemical variability during the measurements as small as possible. The results do not follow simple assumptions on relationships to single parameters such as grain size. It was found that the complexity of natural occurring media is not yet sufficiently represented when modelling IP. At the same time simple correlation to permeability was found to be strong and consistent. Hence, adaptations with the aim of better representing the geo-structure of natural porous media were applied to the simplified model space used in Schwarz' IP-effect-theory. The resulting semi- empiric relationship was found to more accurately predict the IP-effect and its relation to the parameters grain size and permeability. If combined with recent findings about the effect of pore fluid electrochemistry together with advanced complex resistivity tomography, these results will allow us to picture diverse aspects of the subsurface with relative certainty. Within the framework of single measurement campaigns, hydrologiste can than collect data with information about the geo-structure and geo-chemistry of the subsurface. However, additional research efforts will be necessary to further improve the understanding of the physical origins of IP-effect and minimize the potential for false interpretations.¦-¦Dans l'étude des processus et caractéristiques hydrologiques des subsurfaces, la résolution spatiale donnée par les modèles hydrologiques dépasse souvent la résolution des données du terrain récoltées avec des méthodes classiques d'hydrologie. Récemment il est possible de réduire de plus en plus cet divergence spatiale entre modèles numériques et données du terrain par l'utilisation de méthodes géophysiques, notamment celles géoélectriques. Parmi les méthodes électriques, la polarisation provoquée (PP) permet de représenter la capacité des roches poreuses et des sols à stocker une charge électrique. En l'absence des métaux dans le sous-sol, cet effet est largement influencé par des caractéristiques de surface des matériaux. En conséquence les mesures PP offrent une information des interfaces entre solides et fluides dans les matériaux poreux que nous pouvons lier à la perméabilité également dirigée par ces mêmes paramètres. L'effet de la polarisation provoquée à été étudié dans différentes études de laboratoire, ainsi que sur le terrain. A cause d'une faible capacité de polarisation des matériaux sableux, comparé aux argiles, leur caractérisation par l'effet-PP reste difficile a interpréter d'une manière cohérente pour les environnements hétérogènes.¦Pour améliorer les connaissances sur l'importance de la structure du sous-sol sableux envers l'effet PP et des paramètres hydrologiques, nous avons fait des mesures de laboratoire variées. En détail, nous avons considéré des échantillons sableux de quartz avec des distributions de taille de grain entre sables fins et graviers fins, en diamètre cela fait entre 0,09 et 5,6 mm. Les caractéristiques de l'espace poreux sont changées en modifiant (i) la distribution de taille des grains, (ii) le degré de compaction, et (iii) le niveau d'hétérogénéité dans la distribution de taille de grains. En suite nous étudions comment ces changements influencent l'effet-PP, la perméabilité et la surface spécifique des échantillons. Les paramètres électrochimiques sont gardés à un minimum pendant les mesures. Les résultats ne montrent pas de relation simple entre les paramètres pétro-physiques comme par exemples la taille des grains. La complexité des media naturels n'est pas encore suffisamment représenté par les modèles des processus PP. Néanmoins, la simple corrélation entre effet PP et perméabilité est fort et consistant. En conséquence la théorie de Schwarz sur l'effet-PP a été adapté de manière semi-empirique pour mieux pouvoir estimer la relation entre les résultats de l'effet-PP et les paramètres taille de graines et perméabilité. Nos résultats concernant l'influence de la texture des matériaux et celles de l'effet de l'électrochimie des fluides dans les pores, permettront de visualiser des divers aspects du sous-sol. Avec des telles mesures géo-électriques, les hydrologues peuvent collectionner des données contenant des informations sur la structure et la chimie des fluides des sous-sols. Néanmoins, plus de recherches sur les origines physiques de l'effet-PP sont nécessaires afin de minimiser le risque potentiel d'une mauvaise interprétation des données.

Dynamics of multiple lin gene expression in Sphingomonas paucimobilis B90A in response to different hexachlorocyclohexane isomers.

Sphingomonas paucimobilis B90A is able to degrade the alpha-, beta-, gamma-, and delta-isomers of hexachlorocyclohexane (HCH). It contains the genes linA, linB, linC, linD, linE, and linR, which have been implicated in HCH degradation. In this study, dynamic expression of the lin genes was measured in chemostat-grown S. paucimobilis B90A by RNA dot blot hybridization and real-time reverse transcriptase PCR upon exposure to a pulse of different HCH isomers. Irrespective of the addition of HCH, linA, linB, and linC were all expressed constitutively. In contrast, linD and linE were induced with alpha-HCH (2 mg/liter) and gamma-HCH (7 mg/liter). A sharp increase in mRNA levels for linD and linE was observed from 10 to 45 min after the addition of alpha- or gamma-HCH. Induction of linD and linE was not detectable upon the addition of 0.7 mg of gamma-HCH per liter, although the compound was degraded by the cells. The addition of beta-HCH (5 mg/liter) or delta-HCH (20 mg/liter) did not lead to linE and linD induction, despite the fact that 50% of the compounds were degraded. This suggests that degradation of beta- and delta-HCH proceeds by a different pathway than that of alpha- and gamma-HCH.

Social Media in health. What are the safety concerns for healthcare consumers?

Recent literature has discussed the unintended consequences of clinical information technologies (IT) on patient safety, yet there has been little discussion about the safety concerns in the area of consumer health IT. This paper presents a range of safety concerns for consumers in social media, with a case study on YouTube. We conducted a scan of abstracts on 'quality criteria' related to YouTube. Five areas regarding the safety of YouTube for consumers were identifi ed: (a) harmful health material targeted at consumers (such as inappropriate marketing of tobaccoor direct-to-consumer drug advertising); (b) public display of unhealthy behaviour (such as people displaying self-injury behaviours or hurting others); (c) tainted public health messages (i.e. the rise of negative voices againstpublic health messages); (d) psychological impact from accessing inappropriate, offensive or biased social media content; and (e) using social media to distort policy and research funding agendas. The examples presented should contribute to a better understanding about how to promote a safe consumption and production of social media for consumers, and an evidence-based approach to designing social media interventions for health. The potential harm associated with the use of unsafe social media content on the Internet is a major concern. More empirical and theoretical studies are needed to examine how social media infl uences consumer health decisions, behaviours and outcomes, and devise ways to deter the dissemination of harmful infl uences in social media.

Trichophyton rubrum secreted and membrane-associated carboxypeptidases

Dermatophytes are the most common agents of superficial mycoses, and exclusively infect stratum corneum, nails or hair. Therefore, secreted proteolytic activity is considered a virulence trait of these fungi. In a medium containing protein as a sole nitrogen and carbon source Trichophyton rubrum secretes a metallocarboxypeptidase (TruMcpA) of the M14 family according to the MEROPS proteolytic enzyme database. TruMcpA is homologous to human pancreatic carboxypeptidase A, and is synthesized as a precursor in a preproprotein form. The propeptide is removed to generate the mature active enzyme alternatively by either one of two subtilisins which are concomitantly secreted by the fungus. In addition, T. rubrum was shown to possess two genes (TruSCPA and TruSCPB) encoding serine carboxypeptidases of the S10 family which are homologues of the previously characterized Aspergillus and Penicillium secreted acid carboxypeptidases. However, in contrast to the Aspergillus and Penicillium homologues, TruScpA and TruScpB enzymes are not secreted into the environment, but are membrane-associated with a glycosylphosphatidylinositol (GPI) anchor. During infection, T. rubrum secreted and GPI-anchored carboxypeptidases may contribute to fungal virulence by cooperating with previously characterized endoproteases and aminopeptidases in the degradation of compact keratinized tissues into assimilable amino acids and short peptides.