Photo-bioconvection: towards light control of flows in active suspensions.

The persistent motility of individual constituents in microbial suspensions represents a prime example of the so-called active matter systems. Cells consume energy, exert forces and move, overall releasing the constraints of equilibrium statistical mechanics of passive elements and allowing for complex spatio-temporal patterns to emerge. Moreover, when subject to physico-chemical stimuli their collective behaviour often drives large-scale instabilities of a hydrodynamic nature, with implications for biomixing in natural environments and incipient industrial applications. In turn, our ability to exert external control of these driving stimuli could be used to govern the emerging patterns. Light, being easily manipulable and, at the same time, an important stimulus for a wide variety of microorganisms, is particularly well suited to this end. In this paper, we will discuss the current state, developments and some of the emerging advances in the fundamentals and applications of light-induced bioconvection with a focus on recent experimental realizations and modelling efforts. This article is part of the theme issue 'Stokes at 200 (part 2)'.

Effects of microwaves (950 MHZ mobile phone) on morphometric and apoptotic changes of rabbit epididymis.

The effect of mobile phone radiation on human reproduction system is still a matter of debate. In this study, 18 male rabbits were randomly divided into two experimental groups and one control group. Experimental groups received simulated microwaves with the frequency of 950 MHz and the output power of 3 and 6 watts for 2 weeks, 2 h a day. After a week of rest, the microscopic slides from the quada of the excised epididymis were prepared. Then, the diameter of epididymis, the height of epithelium and the number of apoptotic cells in epithelium in study groups were determined. The data were compared using spss software and one-way anova test. The epithelial height and diameter of the epididymis in 3 watt and 6 watt groups had a significant decrease compared to the control group (P < 0.001), while the testosterone level only in 6 watt group was significantly decreased compared to control group. The rate of apoptosis in the epithelial cells of the epididymis had a significant increase only in 6 watt group compared to the control group (P < 0.001). This study showed that the microwaves with the frequency of 950 MHz can have negative impacts on morphometric and apoptotic changes of rabbit epididymis.

Emergence of plasmid-mediated quinolone-resistant determinants in Klebsiella pneumoniae isolates from Tehran and Qazvin provinces, Iran.

BACKGROUND: Plasmid-mediated quinolone resistance is an increasing clinical concern, globally. The major objective of the present study was to identify the qnr-encoding genes among the quinolone non-susceptible K. pneumoniae isolates obtained from two provinces in Iran. METHODS: A total of 200 K. pneumoniae isolates were obtained from hospitals of Qazvin and Tehran, Iran. The identification of bacterial isolates was carried out by standard laboratory methods and API 20E strips. Susceptibility to quinolone compounds were examined by standard Kirby-Bauer disk diffusion method according to the CLSI guideline. PCR and sequencing were employed to detect qnrA, qnrB and qnrS-encoding genes. RESULTS: Of 200 K. pneumoniae isolates, 124 (62%) were nonsusceptible to quinolone compounds among those 66 (53.2%) and 58 (46.8%) isolates showed high and low-level quinolone resistance rates, respectively. Out of 124 quinolone non-susceptible isolates, qnr-encoding genes were present in 49 (39.5%) isolates with qnrB1 (30.6%) as the most dominant gene followed by qnrB4 (9.7%), and qnrS1 (1.6%) either alone or in combination. CONCLUSIONS: This study, for the first time, revealed the high appearance of qnrB1, qnrS1 and qnrB4 genes among the clinical isolates of K. pneumoniae in Iran. Therefore, the application of proper infection control measures and well-established antibiotic administration guideline should be strictly considered within our medical centers.

Near-unity coupling efficiency of a quantum emitter to a photonic crystal waveguide.

A quantum emitter efficiently coupled to a nanophotonic waveguide constitutes a promising system for the realization of single-photon transistors, quantum-logic gates based on giant single-photon nonlinearities, and high bit-rate deterministic single-photon sources. The key figure of merit for such devices is the ß factor, which is the probability for an emitted single photon to be channeled into a desired waveguide mode. We report on the experimental achievement of ß=98.43%±0.04% for a quantum dot coupled to a photonic crystal waveguide, corresponding to a single-emitter cooperativity of η=62.7±1.5. This constitutes a nearly ideal photon-matter interface where the quantum dot acts effectively as a 1D "artificial" atom, since it interacts almost exclusively with just a single propagating optical mode. The ß factor is found to be remarkably robust to variations in position and emission wavelength of the quantum dots. Our work demonstrates the extraordinary potential of photonic crystal waveguides for highly efficient single-photon generation and on-chip photon-photon interaction.

Adsorption of proteins at the solution/air interface influenced by added nonionic surfactants at very low concentrations for both components. 2. Effect of different surfactants and theoretical model.

The influence of the addition of the nonionic surfactants dodecyl dimethyl phosphine oxide (C12DMPO), tetradecyl dimethyl phosphine oxide (C14DMPO), decyl alcohol (C10OH), and C10EO5 at concentrations between 10(-5) and 10(-1) mmol/L to solutions of ß-casein (BCS) and ß-lactoglobulin (BLG) at a fixed concentration of 10(-5) mmol/L on the surface tension is studied. It is shown that a significant decrease of the water/air surface tension occurs for all the surfactants studied at very low concentrations (10(-5)-10(-3) mmol/L). All measurements were performed with the buoyant bubble profile method. The dynamics of the surface tension was simulated using the Fick and Ward-Tordai equations. The calculation results agree well with the experimental data, indicating that the equilibration times in the system studied do not exceed 30 000 s, while the time required to attain the equilibrium on a plane surface is by one order of magnitude higher. To achieve agreement between theory and experiment for the mixtures, a supposition was made about the influence of the concentration of nonionic surfactant on the adsorption activity of the protein. The adsorption isotherm equation of the protein was modified accordingly, and this corrected model agrees well with all experimental data.

Thermodynamics of adsorption of ionic surfactants at water/alkane interfaces.

On the basis of experimental data for the homologous series of alkyltrimethylammonium bromides (CnTAB) the equilibrium surface tension isotherms at three types of liquid-fluid interfaces are discussed: solution/air, solution/alkane vapor and solution/liquid alkane interfaces. It is shown that the adsorption characteristics can be described at all three interfaces by the same thermodynamic approach. In the presence of alkane molecules (in the liquid alkane phase or in the alkane vapor phase) the CnTAB adsorption layers can be best described by a co-adsorption of the alkane molecules.

A phylogenetic study of Dothiorella and Spencermartinsia species associated with woody plants in Iran, New Zealand, Portugal and Spain.

Dothiorella and Spencermartinsia are two botryosphaeriaceous genera with dark 2-celled conidia and found in parasitic, saprophytic or endophytic association with various woody host plants. Based on ITS and EF1-α sequence data and morphology, eight new species are described from Iran, New Zealand, Portugal and Spain. Of these, five species are placed in Dothiorella, namely D. iranica, D. parva, D. prunicola, D. sempervirentis and D. striata, and three species belong to Spencermartinsia named as S. citricola, S. mangiferae and S. plurivora. An identification key to the species of each genus is provided.

Delayed capillary breakup of falling viscous jets.

Thin jets of viscous fluid like honey falling from capillary nozzles can attain lengths exceeding 10 m before breaking up into droplets via the Rayleigh-Plateau (surface tension) instability. Using a combination of laboratory experiments and WKB analysis of the growth of shape perturbations on a jet being stretched by gravity, we determine how the jet's intact length l(b) depends on the flow rate Q, the viscosity η, and the surface tension coefficient γ. In the asymptotic limit of a high-viscosity jet, l(b)∼(gQ(2)η(4)/γ(4))(1/3), where g is the gravitational acceleration. The agreement between theory and experiment is good, except for very long jets.

Detection of West Nile virus genome and specific antibodies in Iranian encephalitis patients.

West Nile virus (WNV) is a mosquito-borne flavivirus which circulates in birds, horses and humans. An estimated 80% of WNV infections are asymptomatic. Fewer than 1% of infected persons develop neuroinvasive disease, which typically presents as encephalitis, meningitis, or acute flaccid paralysis. This study was conducted from January 2008 to June 2009 in Isfahan, Iran. Patients attending the emergency department with fever and loss of consciousness were consecutively included. Cerebrospinal fluids (CSF) were initially analysed through bacteriology and biochemistry examinations, resulting in those with evidence of meningitis being excluded. Patients' CSF and serum were diagnosed by serological and molecular assays. A total of 632 patients with fever and loss of consciousness were tested by CSF analyses. Samples of the remaining patients (39·4%) were referred for WNV investigation. Three (1·2%) of the patients were positive for both serum and CSF by RT-PCR, and six (2·4%) were positive only for IgG antibodies. History of insect bite, and blood transfusion and transplantation were risk factors for being positive by RT-PCR (P=0·048) and being IgG positive (P=0·024), respectively. The results of this study showed that the prevalence of West Nile fever is low in patients with encephalitis.

Wafer-scale epitaxial modulation of quantum dot density.

Precise control of the properties of semiconductor quantum dots (QDs) is vital for creating novel devices for quantum photonics and advanced opto-electronics. Suitable low QD-densities for single QD devices and experiments are challenging to control during epitaxy and are typically found only in limited regions of the wafer. Here, we demonstrate how conventional molecular beam epitaxy (MBE) can be used to modulate the density of optically active QDs in one- and two- dimensional patterns, while still retaining excellent quality. We find that material thickness gradients during layer-by-layer growth result in surface roughness modulations across the whole wafer. Growth on such templates strongly influences the QD nucleation probability. We obtain density modulations between 1 and 10 QDs/µm2 and periods ranging from several millimeters down to at least a few hundred microns. This method is universal and expected to be applicable to a wide variety of different semiconductor material systems. We apply the method to enable growth of ultra-low noise QDs across an entire 3-inch semiconductor wafer.

Preventive effect of ginger (Zingiber officinale) pretreatment on renal ischemia-reperfusion in rats.

BACKGROUND/AIMS: The present study examined the preventive effect of ginger against renal ischemia-reperfusion (I-R) injury. METHODS: 30 adult male rats were used. The animals were allocated to five groups of 6 rats: (1) normal (N), (2) normal + ginger (N+G), (3) right nephrectomy (Sham), (4) I-R, and (5) I-R + ginger (I-R+G). To induce renal ischemia, animals were unilaterally nephrectomized and subjected to 45 min of left renal pedicle occlusion with 24 h reperfusion. Ginger was administered orally 24 h and just before ischemia. At the end of the experiment, blood samples and urine were collected. The following renal functional parameters were studied: serum and urinary levels of creatinine and urea, fractional excretion of sodium, and creatinine clearance. Histopathological examination of the kidney was also performed. RESULTS: Rats with renal I-R showed a significant increase in creatinine and urea concentration in serum and also a significant decrease in creatinine clearance compared with the other groups. In addition, renal histopathology in the I-R group showed severe alterations such as tubular dilatation and tubular epithelial necrosis. However, these changes were significantly reduced in the I-R+G group. CONCLUSION: This study suggests that ginger is a useful agent for the prevention of renal ischemia reperfusion-induced injury.

Do non-rearfoot runners experience greater second metatarsal stresses than rearfoot runners?

Stress fracture of the second metatarsal is a common and problematic injury for runners. The choice of foot strike pattern is known to affect external kinetics and kinematics but its effect on internal loading of the metatarsals is not well understood. Models of various complexities can be used to investigate the effects of running characteristics on metatarsal stresses. This study aimed to compare second metatarsal stress between habitual rearfoot and non-rearfoot strikers during barefoot running, using a novel participant-specific finite element model, including accurate metatarsal and soft tissue geometry. Synchronised force and kinematic data were collected during barefoot overground running from 20 participants (12 rearfoot strikers). Stresses were calculated using a previously evaluated and published 3D finite element model. Non-rearfoot strikers demonstrated greater external loading and joint contact forces than rearfoot runners, but there were no differences in stresses between groups. Additionally, the study allowed for a qualitative assessment of bone geometries and stresses. No correlation was found between bone volume and stresses, however, there was found to be a large variation in metatarsal shapes, possibly accounting for the lack of difference in stresses. This emphasises the importance of bone geometry when estimating bone stress and supports the suggestion that external forces should not be assumed to be representative of internal loading.

First detection of mobilized colistin resistance mcr-1 gene in Escherichia coli isolated from livestock and sewage in Iran.

Currently, few studies have investigated the mechanisms of resistance to colistin in Iran. The aim of this study was to investigate mcr-harbouring Escherichia coli dissemination in livestock and sewage in Iran. A total of 115 samples from cows (n = 38), chickens (n = 47) and urban sewage samples (n = 30) were collected. The presence of genes including mcr1-6 and ampC ß-lactamase (bla MOX, bla CIT, bla DHA, bla ACC, bla EBC, bla FOX) for colistin-resistant isolates was investigated by multiplex PCR method. Genetic association of colistin-resistant strains was also evaluated by ERIC PCR. Sixty-five isolates were identified as E. coli. Meaningless were resistant to colistin. The highest (26.1%) and lowest (3.07%) resistance were shown to ampicillin and meropenem respectively. Among the three colistin-resistant isolates, 2 (66%) were multidrug resistant, with one of them being mcr-1 positive and the other one positive for DHA ampC ß-lactamase gene. No mcr2-6 genes were found. Minimum inhibitory concentration of mcr-producing isolate was 4 mg/L by microbroth dilution. This study reports, first the detection of mcr-1 in E. coli from farm animals in Iran, a finding that is indicative of a global distribution of this plasmidic element and threatning the use of colistin as a last resort antibiotic. No clonal relationship was observed between the colistin-resistant E. coli isolates by ERIC-PCR. Monitoring the presence of these strains in animal sources help as to controlling the spread of resistance genes from animal to human is vital.

Incorporating subject-specific geometry to compare metatarsal stress during running with different foot strike patterns.

Stress fracture of the second metatarsal is a common and problematic injury for runners. The choice of foot strike pattern is known to affect external kinetics and kinematics but its effect on internal loading of the metatarsals is not well understood. Subject-specific models of the second metatarsal can be used to investigate internal loading in a non-invasive manner. This study aimed to compare second metatarsal stress between habitual rearfoot and non-rearfoot strikers during barefoot running, using a novel subject-specific mathematical model, including accurate metatarsal geometry. Synchronised force and kinematic data were collected during barefoot overground running from 20 participants (12 rearfoot strikers). Stresses were calculated at the plantar and dorsal periphery of the midshaft of the metatarsal using a subject-specific beam theory model. Non-rearfoot strikers demonstrated greater external loading, bending moments and compressive forces than rearfoot strikers, but there were no differences in peak stresses between groups. Statistical parametric analysis revealed that non-rearfoot strikers had greater second metatarsal stresses during early stance but that there was no difference in peak stresses. This emphasises the importance of bone geometry when estimating bone stress and supports the suggestion that external forces should not be assumed to be representative of internal loading.

Three dimensional finite element modelling of metatarsal stresses during running.

Second metatarsal stress fractures are a problematic injury for runners and are formed when the rate of repair of bone is outpaced by the damage accumulated during loading. Measuring the peak stresses on the bone during running gives an indication of damage accumulation but direct measurement is invasive. Finite element modelling is a viable alternative method of accurately estimating bone stresses but tends to be too computationally expensive for use in applied research. This study presents a novel and simple finite element model which can estimate bone stresses on the second metatarsal during the stance phase of walking and running, accounting for joint reaction forces and soft tissue effects. The influence of the forces and kinematic inputs to the model and the presence of the soft tissues was quantified using a sensitivity analysis. The magnitudes of maximum stress from the model are similar to existing finite element models and bone staple strain gauge values collected during walking and running. The model was found to be most sensitive to the pitch angle of the metatarsal and the joint reaction forces and was less sensitive to the ground reaction forces under the metatarsal head, suggesting that direct measurement of external forces should not be assumed to represent internal stresses.

New view of the adsorption of surfactants at water/alkane interfaces - Competitive and cooperative effects of surfactant and alkane molecules.

The theoretical description of the adsorption of surfactants at interfaces between aqueous solutions and oil was based over a very long time on models derived for the solution/air interface. Thus, most of the experimentally observed peculiarities could not be specifically considered but were merely interpreted in terms of a penetration of oil molecules into the alkyl chain layer of the adsorbed surfactant molecules. These penetrating oil molecules enhance the surfactant adsorption as compared to the water/air interface. Later on, for the special situations at water/oil interfaces a competitive adsorption of surfactant and oil molecules was postulated, allowing a much better description of experimental data. This picture, however, was unable to explain why the interfacial tension of the water/oil interface decreases very quickly when extremely small amounts of surfactants are added to the water. This effect cannot be of competitive nature, but a cooperativity of surfactant and oil molecules forming a mixed adsorption layer is required instead. This cooperative effect means that already few surfactant molecules adsorbed at the interface can induce a significant ordering of oil molecules in the interfacial layer. This new interfacial structure, in turn, attracts further surfactant molecules to adsorb. Improving the theoretical description of experimental data was finally achieved by applying suitable adsorption models for the two adsorbing compounds, i.e. a Frumkin adsorption model for the oil molecules and a Langmuir, Frumkin, or reorientation model for the adsorbing surfactant molecules. Here, the progress in modelling surfactant adsorption at water/oil interfaces is discussed mainly for the homologous series of the cationic surfactants CnTAB, of the anionic surfactant SDS, and members of the homologous series of the non-ionic surfactants CnDMPO at water/alkane interfaces.

Studies of the rate of water evaporation through adsorption layers using drop shape analysis tensiometry.

With modified measuring procedure and measuring cell design in the drop profile tensiometer PAT, it became possible to study the rate of water evaporation through adsorbed or spread surface layers. This method was employed to measure the rate of water evaporation from drops covered by adsorbed layers of some proteins and surfactants, in particular n-dodecanol. It was shown that the formation of dense (double or condensed) adsorbed layers of protein and the formation of 2D-condensed n-dodecanol layer decrease the water evaporation rate by 20-25% as compared with pure water. At the same time, the adsorbed layers of ordinary surfactants (sodium dodecyl sulfate and nonionic ethoxylated surfactant C(14)EO(8)) do not affect the water evaporation rate remarkably.

Finite element modeling of contaminant transport in soils including the effect of chemical reactions.

The movement of chemicals through soils to the groundwater is a major cause of degradation of water resources. In many cases, serious human and stock health implications are associated with this form of pollution. Recent studies have shown that the current models and methods are not able to adequately describe the leaching of nutrients through soils, often underestimating the risk of groundwater contamination by surface-applied chemicals, and overestimating the concentration of resident solutes. Furthermore, the effect of chemical reactions on the fate and transport of contaminants is not included in many of the existing numerical models for contaminant transport. In this paper a numerical model is presented for simulation of the flow of water and air and contaminant transport through unsaturated soils with the main focus being on the effects of chemical reactions. The governing equations of miscible contaminant transport including advection, dispersion-diffusion and adsorption effects together with the effect of chemical reactions are presented. The mathematical framework and the numerical implementation of the model are described in detail. The model is validated by application to a number of test cases from the literature and is then applied to the simulation of a physical model test involving transport of contaminants in a block of soil with particular reference to the effects of chemical reactions. Comparison of the results of the numerical model with the experimental results shows that the model is capable of predicting the effects of chemical reactions with very high accuracy. The importance of consideration of the effects of chemical reactions is highlighted.

Comparison of serum PCR assay and histopathology for the diagnosis of invasive aspergillosis and mucormycosis in immunocompromised patients with sinus involvement.

BACKGROUND AND PURPOSE: Invasive fungal infections cause morbidity and mortality in patients with hematologic malignancies and immunosuppression. Although these infections are commonly caused by Candida and Aspergillus species, infections caused by Mucoralean fungi are also on a growing trend. The definitive diagnosis of mucormycosis includes visualization of non-septate hyphae on pathology or growth of Mucoralean fungi culture. Polymerase chain reaction (PCR) is used to diagnose mucormycosis from paraffin blocks; however, it yields discrepant results in diagnosis of mucormycosis from blood samples. In the current study, we sought to examine the efficiency of PCR test for the diagnosis of mucormycosis and aspergillosis. MATERIALS AND METHODS: Thirty-one patients with suspected fungal sinus infection were recruited from the Hematology-Oncology unit in Taleghani Hospital, Tehran, Iran. DNA was extracted and semi-nested PCR was performed. RESULTS: PCR was reported negative for all the 31 serum samples. Our assay had a sensitivity of 1.3 ng and 12 pg for Mucoralean and Aspergillus species, respectively. CONCLUSION: Using serum PCR, we detected Aspergillus and Mucoralean species in patients with suspected fungal sinus infection. While this test may have utility in diagnosis directly from biopsy site, it appears unreliable for use as a noninvasive blood test.

Development of a conceptual framework of holistic risk assessment - Landfill as a particular type of contaminated land.

Landfills can be regarded as a particular type of contaminated land that has a potential to directly and indirectly pollute all of the four main spheres of the environment which are the lithosphere, atmosphere, hydrosphere and eventually adversely impact the biosphere. Therefore, environmental risk assessment of a landfill has to be more integrated and holistic by virtue of its nature of being a multidimensional pollutant source. Despite this, although various risk assessment approaches have been adopted for landfill waste disposal sites, there are still wide-ranging knowledge gaps and limitations which need to be addressed. One important knowledge gap and limitation of current risk assessment approaches is the inability to fully identify, categorise and aggregate all individual risks from all combinations of hazards, pathways and targets/receptors (e.g. water, air, soil and biota) in connection to a certain landfill leachate and yet at any stage of the landfill cycle. So such an approach is required that could not only integrate all possible characteristics of varying scenarios but also contain the ability to establish an overall risk picture, irrespective of the lifecycle stage of the landfill (e.g. planning stage/pre-operation, in-operation or post-operation/closed). One such approach to address the wide-breadth of landfill impact risks is by developing a more holistic risk assessment methodology, whose conceptual framework is presented in this paper for landfill leachate in a whole-system format. This conceptual framework does not only draw together various constituting factors and sub-factors of risk assessment in a logical sequence and categorical order, but also indicates the "what, why, when and how" outputs of and inputs to these factors and sub-factors can be useful. The framework is designed to identify and quantify a range of risks associated with all stages of the landfill lifecycle, and yet in a more streamlined, logical, categorical and integrated format, offering a more standardised and unified whole-system approach.