Effect of 5′UTR introns on gene expression in Arabidopsis thaliana

Background The majority of introns in gene transcripts are found within the coding sequences (CDSs). A small but significant fraction of introns are also found to reside within the untranslated regions (5′UTRs and 3′UTRs) of expressed sequences. Alignment of the whole genome and expressed sequence tags (ESTs) of the model plant Arabidopsis thaliana has identified introns residing in both coding and non-coding regions of the genome. Results A bioinformatic analysis revealed some interesting observations: (1) the density of introns in 5′UTRs is similar to that in CDSs but much higher than that in 3′UTRs; (2) the 5′UTR introns are preferentially located close to the initiating ATG codon; (3) introns in the 5′UTRs are, on average, longer than introns in the CDSs and 3′UTRs; and (4) 5′UTR introns have a different nucleotide composition to that of CDs and 3′UTR introns. Furthermore, we show that the 5′UTR intron of the A. thaliana EFIα-A3 gene affects the gene expression and the size of the 5′UTR intron influences the level of gene expression. Conclusion Introns within the 5′UTR show specific features that distinguish them from introns that reside within the coding sequence and the 3′UTR. In the EFIα-A3 gene, the presence of a long intron in the 5′UTR is sufficient to enhance gene expression in plants in a size dependent manner.

Effect of Coulomb blockade, gold resistance, and thermal expansion on the electrical resistance of ultrathin gold films

Controlling the electrical resistance of granular thin films is of great importance for many applications, yet a full understanding of electron transport in such films remains a major challenge. We have studied experimentally and by model calculations the temperature dependence of the electrical resistance of ultrathin gold films at temperatures between 2 K and 300 K. Using sputter deposition, the film morphology was varied from a discontinuous film of weakly coupled meandering islands to a continuous film of strongly coupled coalesced islands. In the weak-coupling regime, we compare the regular island array model, the cotunneling model, and the conduction percolation model with our experimental data. We show that the tunnel barriers and the Coulomb blockade energies are important at low temperatures and that the thermal expansion of the substrate and the island resistance affect the resistance at high temperatures. At low temperatures our experimental data show evidence for a transition from electron cotunneling to sequential tunneling but the data can also be interpreted in terms of conduction percolation. The resistivity and temperature coefficient of resistance of the meandering gold islands are found to resemble those of gold nanowires. We derive a simple expression for the temperature at which the resistance changes from non-metal-like behavior into metal-like behavior. In the case of strong island coupling, the total resistance is solely determined by the Ohmic island resistance.

Si quantum dots embedded in an amorphous SiC matrix : nanophase control by non-equilibrium plasma hydrogenation

Nanophase nc-Si/a-SiC films that contain Si quantum dots (QDs) embedded in an amorphous SiC matrix were deposited on single-crystal silicon substrates using inductively coupled plasma-assisted chemical vapor deposition from the reactive silane and methane precursor gases diluted with hydrogen at a substrate temperature of 200 °C. The effect of the hydrogen dilution ratio X (X is defined as the flow rate ratio of hydrogen-to-silane plus methane gases), ranging from 0 to 10.0, on the morphological, structural, and compositional properties of the deposited films, is extensively and systematically studied by scanning electron microscopy, high-resolution transmission electron microscopy, X-ray diffraction, Raman spectroscopy, Fourier-transform infrared absorption spectroscopy, and X-ray photoelectron spectroscopy. Effective nanophase segregation at a low hydrogen dilution ratio of 4.0 leads to the formation of highly uniform Si QDs embedded in the amorphous SiC matrix. It is also shown that with the increase of X, the crystallinity degree and the crystallite size increase while the carbon content and the growth rate decrease. The obtained experimental results are explained in terms of the effect of hydrogen dilution on the nucleation and growth processes of the Si QDs in the high-density plasmas. These results are highly relevant to the development of next-generation photovoltaic solar cells, light-emitting diodes, thin-film transistors, and other applications.

Thermodynamical and plasma-driven kinetic growth of high-aspect-ratio nanostructures : effect of hydrogen termination

The results of studies on the growth of high-aspect nanostructures in low-temperature non-equilibrium plasmas of reactive gas mixtures with or without hydrogen are presented. The results suggest that the hydrogen in the reactive plasma strongly affects the length of the nanostructures. This phenomenon is explained in terms of selective hydrogen passivation of the lateral and top surfaces of the surface-supported nanostructures. The theoretical model describes the effect of the atomic hydrogen passivation on the nanostructure shape and predicts the critical hydrogen coverage of the lateral surfaces necessary to achieve the nanostructure growth with the pre-determined shape. Our results demonstrate that the use of a strongly non-equilibrium plasma is very effective in significantly improving the shape control of quasi-one-dimensional single-crystalline nanostructures.

Rapid, low-temperature synthesis of nc-Si in high-density, non-equilibrium plasmas : enabling nanocrystallinity at very low hydrogen dilution

Nanocrystalline silicon thin films were deposited on single-crystal silicon and glass substrates simultaneously by inductively coupled plasma-assisted chemical vapor deposition from the reactive silane reactant gas diluted with hydrogen at a substrate temperature of 200 °C. The effect of hydrogen dilution ratio X (X is defined as the flow rate ratio of hydrogen to silane gas), ranging from 1 to 20, on the structural and optical properties of the deposited films, is extensively investigated by Raman spectroscopy, X-ray diffraction, Fourier transform infrared absorption spectroscopy, UV/VIS spectroscopy, and scanning electron microscopy. Our experimental results reveal that, with the increase of the hydrogen dilution ratio X, the deposition rate Rd and hydrogen content CH are reduced while the crystalline fraction Fc, mean grain size δ and optical bandgap ETauc are increased. In comparison with other plasma enhanced chemical vapor deposition methods of nanocrystalline silicon films where a very high hydrogen dilution ratio X is routinely required (e.g. X > 16), we have achieved nanocrystalline silicon films at a very low hydrogen dilution ratio of 1, featuring a high deposition rate of 1.57 nm/s, a high crystalline fraction of 67.1%, a very low hydrogen content of 4.4 at.%, an optical bandgap of 1.89 eV, and an almost vertically aligned columnar structure with a mean grain size of approximately 19 nm. We have also shown that a sufficient amount of atomic hydrogen on the growth surface essential for the formation of nanocrystalline silicon is obtained through highly-effective dissociation of silane and hydrogen molecules in the high-density inductively coupled plasmas. © 2009 The Royal Society of Chemistry.

Effect of soil properties on the response of pile to underground explosion

This paper develops and presents a fully coupled non-linear finite element procedure to treat the response of piles to ground shocks induced by underground explosions. The Arbitrary Lagrange Euler coupling formulation with proper state material parameters and equations are used in the study. Pile responses in four different soil types, viz, saturated soil, partially saturated soil and loose and dense dry soils are investigated and the results compared. Numerical results are validated by comparing with those from a standard design manual. Blast wave propagation in soils, horizontal pile deformations and damages in the pile are presented. The pile damage presented through plastic strain diagrams will enable the vulnerability assessment of the piles under the blast scenarios considered. The numerical results indicate that the blast performance of the piles embedded in saturated soil and loose dry soil are more severe than those in piles embedded in partially saturated soil and dense dry soil. Present findings should serve as a benchmark reference for future analysis and design.

Assessment of the temperature effect on childhood diarrhea using satellite imagery

A quasi-Poisson generalized linear model combined with a distributed lag non-linear model was used to quantify the main effect of temperature on emergency department visits (EDVs) for childhood diarrhea in Brisbane from 2001 to 2010. Residual of the model was checked to examine whether there was an added effect due to heat waves. The change over time in temperature-diarrhea relation was also assessed. Both low and high temperatures had significant impact on childhood diarrhea. Heat waves had an added effect on childhood diarrhea, and this effect increased with intensity and duration of heat waves. There was a decreasing trend in the main effect of heat on childhood diarrhea in Brisbane across the study period. Brisbane children appeared to have gradually adapted to mild heat, but they are still very sensitive to persistent extreme heat. Development of future heat alert systems should take the change in temperature-diarrhea relation over time into account.

Atmospheric-pressure plasma jets : effect of gas flow, active species, and snake-like bullet propagation

Cold atmospheric-pressure plasma jets have recently attracted enormous interest owing to numerous applications in plasma biology, health care, medicine, and nanotechnology. A dedicated study of the interaction between the upstream and downstream plasma plumes revealed that the active species (electrons, ions, excited OH, metastable Ar, and nitrogen-related species) generated by the upstream plasma plume enhance the propagation of the downstream plasma plume. At gas flows exceeding 2 l/min, the downstream plasma plume is longer than the upstream plasma plume. Detailed plasma diagnostics and discharge species analysis suggest that this effect is due to the electrons and ions that are generated by the upstream plasma and flow into the downstream plume. This in turn leads to the relatively higher electron density in the downstream plasma. Moreover, high-speed photography reveals a highly unusual behavior of the plasma bullets, which propagate in snake-like motions, very differently from the previous reports. This behavior is related to the hydrodynamic instability of the gas flow, which results in non-uniform distributions of long-lifetime active species in the discharge tube and of surface charges on the inner surface of the tube.

The effect of cryotherapy on the vascular regeneration following closed soft tissue trauma

INTRODUCTION Icing (cryotherapy) is being widely used for the treatment of closed soft tissue trauma (CSTT), such as those resulting from sport injuries. It is believed that cryotherapy induces vasoconstriction and through this mechanism reduces inflammation [1]. However, the impact of this technique on the healing of impaired vasculature and muscle injuries following trauma remains controversial. Recent evidence suggests that the muscle regeneration is delayed after cryotherapy [2]. Consequently, we aimed to investigate the effect of cryotherapy on the vascular morphology following CSTT using an experimental model in rats by contrast-enhanced micro-CT imaging. METHODS Fifty four rats were divided into three main groups: control (no injury, n=6), sham (CSTT but no icing treatment, n=24) and icing (CSTT, treated with one session of ice block massaged directly on the injured muscle for 20 minutes, n=24). The CSTT was induced to the left thigh (Biceps Femoris) of anaesthetised rats (Male, Wistar) to create a standardized and reproducible vascular and muscle injury using an impact device [3]. Following trauma, animals were euthanized after 1, 3, 7, and 28 days healing time (n=6 for each time point). For a three-dimensional vascular morphological assessment, the blood vessels of euthanised rats were flushed with heparinised saline and then perfused with a radio-opaque contrast agent (Microfil, MV 122, Flowtech, USA) using an infusion pump. Both hind-limbs were dissected, and then the injured and non-injured limbs were imaged using a micro-CT scanner (µCT 40, Scanco Medical, Switzerland) and total volume of the perfused blood vessels (TVV) was calculated. More detailed morphological parameters such as vessel volume (VV), diameter (VD), spacing (VSp), number (VN) and connectivity (VConn) were quantified through high resolution (6 µm), micro-CT-scanned biopsy samples (diameter: 8mm) taken directly from the region of the injured muscles. The biopsies were then analysed histologically to confirm the results derived from contrast-enhanced micro-CT imaging. RESULTS AND DISCUSSION The TVV was significantly higher in the injured legs compared to the non-injured legs at day 1 and 7 in the sham group and at day 28 in both sham and icing groups. The biopsies from the injured legs of the icing group showed a significant reduction in VV, VN, VD, VConn and an increase in VSp compared to those in the sham and control groups at days 1, 3 and 7, post injury. While the injured legs of the sham group exhibited a decrease in VN and VConn 28 days post trauma, indicating a return to the original values prior to trauma, these parameters had increased in the icing group (Figure 1). Also, at day 1 post injury, VV and VD of the injured legs were significantly higher in the sham group compared to the icing group, which may be attributed to the effect of vasoconstriction induced by icing. Further histomorphological evaluation of day 1 post injury, indicated that although cryotherapy significantly reduced the injury size and influx of inflammatory cells, including macrophages and neutrophils, a delay in vascular and muscle fiber regeneration was found at later time points confirming other reports from the literature [2]. CONCLUSIONS We have demonstrated using micro-CT imaging that the vascular morphology changes after CSTT, and that its recovery is affected by therapeutic modalities such as icing. This may be useful for the development of future clinical monitoring, diagnosis and treatment of CSTT. While icing reduces the swelling after trauma, our results suggest that it may delay the recovery of the vasculature in the injured tissue.

The effect of ß-alanine on buffering capacity and exercise performance during and following high-intensity exercise in healthy males

Introduction Intense exercise induced acidosis occurs from the accumulation of hydrogen ions as by-products of anaerobic metabolism. Oral ingestion of ß-alanine, a limiting precursor of the intracellular physiochemical buffer carnosine in skeletal muscle, may counteract any detrimental effect of acidosis and benefit performance. The aim of this study was to investigate the effect of ß-alanine as an ergogenic aid during high intensity exercise performance in healthy males. Methods Five males ingested either ß-alanine (BAl) (4.8 g.d-1 for 4wk, then 6.4 g.d-1 for 2wk) or placebo (Pl) (CaCO3) in a crossover design with 6 wk washout between. Following supplementation, participants performed two different intense exercise protocols over consecutive days. On the first day a repeated sprint ability (RSA) test of 5 x 6s, with 24s rest periods, was performed. On the second day a cycling capacity test measuring the time to exhaustion (TTE) was performed at 110% of their max workload achieved in a pre supplementation max test (CCT110%). Non-invasive quantification of carnosine, prior to, and following each supplementation, with magnetic resonance spectrometry was performed in the soleus and gastrocnemius. Time to fatigue (CCT110%), peak and mean power (RSA), blood pH, and plasma lactate were measured. Results Muscle carnosine concentration was not different prior to ß-alanine supplementation and increased 18% in the soleus and 26% in the gastrocnemius, respectively with 6 wk supplementation. There was no difference in the measured performance variables during the RSA test (peak and average power output). TTE during the CCT110% was significantly enhanced following the ingestion of BAl (155s ± 19.03) compared to Pl (134s ± 26.16). No changes were observed in blood pH during either exercise protocol and during the recovery from exercise. Plasma lactate in the BAl condition was significantly higher than Pl only from the 15th minute following exercise during the CCT110%. FIG. 1: Changes in carnosine concentration in the gastrocnemius prior and post 6 week chronic supplementation of placebo and β-alanine. Values expressed as mean.* p<0.05 from Pl at 6 weeks, # p<0.05 from pre supplementation. Conclusion/Discussion Greater muscle carnosine content following 6wk supplementation of ß-alanine enhanced the potential for intracellular buffering capacity. However, this only translated into enhanced performance during the CCT110% high intensity cycling exercise protocol, with no change observed during the RSA test. No differences in post exercise and recovery plasma lactates and blood pH, indicates that 6wks ß-alanine supplementation has no effect on anaerobic metabolism during multiple bout high intensity exercise. Changes in plasma lactate during recovery supports that ß-alanine supplementation may affect anaerobic metabolism however during single bout high intensity.

The effect of ß-alanine on buffering capacity and exercise performance during and following high-intensity exercise in healthy males

Intense exercise induced acidosis occurs after accumulation of hydrogen ions as by-products of anaerobic metabolism. Oral ingestion of ß-alanine, a limiting precursor of the intracellular physiochemical buffer carnosine in skeletal muscle, may counteract detrimental effects of acidosis and benefit performance. This study aimed to investigate the effect of ß-alanine as an ergogenic aid during high intensity exercise performance. Five healthy males ingested either ß-alanine or placebo (Pl) (CaCO3) in a crossover design with 6 wk washout between. Participants performed two different intense exercise protocols over consecutive days. On the first day a repeated sprint ability (RSA) test was performed. On the second day a cycling capacity test measuring the time to exhaustion (TTE) was performed at 110% of maximum workload achieved in a pre supplementation max test (CCT110%). Non-invasive quantification of carnosine, prior to, and following each supplementation, with in vivo magnetic resonance spectrometry was performed in the soleus and gastrocnemius muscle. Time to fatigue (CCT110%), peak and mean power (RSA), blood pH, and plasma lactate were measured. Muscle carnosine concentration was not different prior to ß-alanine supplementation and increased 18% in the soleus and 26% in the gastrocnemius, respectively after supplementation. There was no difference in the measured performance variables during the RSA test (peak and average power output). TTE during the CCT110% was significantly enhanced following the ingestion of BAl (155s ± 19.03) compared to Pl (134s ± 26.16). No changes were observed in blood pH during either exercise protocol and during the recovery from exercise. Plasma lactate after BAI was significantly higher than Pl only from the 15th minute following exercise during the CCT110%. Greater muscle carnosine content following 6wk supplementation of ß-alanine enhanced the potential for intracellular buffering capacity. This translated into enhanced performance during the CCT110% high intensity cycling exercise protocol but not during the RSA test. The lack of change in plasma lactate or blood pH indicates that 6wks ß-alanine supplementation has no effect on anaerobic metabolism during multiple-bout high-intensity exercise. Changes measured in plasma lactate during recovery support the hypothesis that ß-alanine supplementation may affect anaerobic metabolism particularly during single bout high intensity.

Solution-processed dual-gate polymer field-effect transistors for display applications

We describe the advantages of dual-gate thin-film transistors (TFTs) for display applications. We show that in TFTs with active semiconductor layers composed of diketopyrrolopyrrole-naphthalene copolymer, the on-current is increased, the off-current is reduced, and the sub-threshold swing is improved compared to single-gate devices. Charge transport measurements in steady-state and under non-quasi-static conditions reveal the reasons for this improved performance. We show that in dual-gate devices, a much smaller fraction of charge carriers move in slow trap states. We also compare the activation energies for charge transport in the top-gate and bottom-gate configurations.

The effect of trade openness on deforestation: empirical analysis for 142 countries

This study explores the effect of trade openness on deforestation. Previous studies do not find a clear effect of trade openness on deforestation. We use updated data on the annual rate of deforestation for 142 countries from 1990 to 2003, treat trade and income as endogenous, and take into consideration an adjustment process by applying a dynamic model. We find that an increase in trade openness increases deforestation for non-OECD countries while slowing down deforestation for OECD countries. There is a possibility that both capital-labor and environmental-regulation effects have a negative impact on deforestation in developing countries, whereas the opposite holds in developed countries. © 2012 Springer Japan.

The use of penumbrae to define and analyse non-standard fields

Aim A new method of penumbral analysis is implemented which allows an unambiguous determination of field size and penumbra size and quality for small fields and other non-standard fields. Both source occlusion and lateral electronic disequilibrium will affect the size and shape of cross-axis profile penumbrae; each is examined in detail. Method A new method of penumbral analysis is implemented where the square of the derivative of the cross-axis profile is plotted. The resultant graph displays two peaks in the place of the two penumbrae. This allows a strong visualisation of the quality of a field penumbra, as well as a mathematically consistent method of determining field size (distance between the two peak’s maxima), and penumbra (full-widthtenth-maximum of peak). Cross-axis profiles were simulated in a water phantom at a depth of 5 cm using Monte Carlo modelling, for field sizes between 5 and 30 mm. The field size and penumbra size of each field was calculated using the method above, as well as traditional definitions set out in IEC976. The effect of source occlusion and lateral electronic disequilibrium on the penumbrae was isolated by repeating the simulations removing electron transport and using an electron spot size of 0 mm, respectively. Results All field sizes calculated using the traditional and proposed methods agreed within 0.2 mm. The penumbra size measured using the proposed method was systematically 1.8 mm larger than the traditional method at all field sizes. The size of the source had a larger effect on the size of the penumbra than did lateral electronic disequilibrium, particularly at very small field sizes. Conclusion Traditional methods of calculating field size and penumbra are proved to be mathematically adequate for small fields. However, the field size definition proposed in this study would be more robust amongst other nonstandard fields, such as flattening filter free. Source occlusion plays a bigger role than lateral electronic disequilibrium in small field penumbra size.

Effect of the increase in "alcopops" tax on alcohol-related harms in young people : a controlled interrupted time series

Objective: To measure alcohol-related harms to the health of young people presenting to emergency departments (EDs) of Gold Coast public hospitals before and after the increase in the federal government "alcopops" tax in 2008. Design, setting and participants: Interrupted time series analysis over 5 years (28 April 2005 to 27 April 2010) of 15-29-year-olds presenting to EDs with alcohol-related harms compared with presentations of selected control groups. Main outcome measures: Proportion of 15-29-year-olds presenting to EDs with alcohol-related harms compared with (i) 30-49-year-olds with alcohol-related harms, (ii)15-29-year-olds with asthma or appendicitis, and (iii) 15-29-yearolds with any non-alcohol and non-injury related ED presentation. Results: Over a third of 15-29-year-olds presented to ED with alcohol-related conditions, as opposed to around a quarter for all other age groups. There was no significant decrease in alcohol-related ED presentations of 15-29-year-olds compared with any of the control groups after the increase in the tax. We found similar results for males and females, narrow and broad definitions of alcoholrelated harms, under-19s, and visitors to and residents of the Gold Coast. Conclusions: The increase in the tax on al copops was not associated with any reduction in alcohol-related harms in this population in a unique tourist and holiday region. A more comprehensive approach to reducing alcohol harms in young people is needed.