Designing mixed species tree plantations for the tropics : balancing ecological attributes of species with landholder preferences in the Philippines

A mixed species reforestation program known as the Rainforestation Farming system was undertaken in the Philippines to develop forms of farm forestry more suitable for smallholders than the simple monocultural plantations commonly used then. In this study, we describe the subsequent changes in stand structure and floristic composition of these plantations in order to learn from the experience and develop improved prescriptions for reforestation systems likely to be attractive to smallholders. We investigated stands aged from 6 to 11 years old on three successive occasions over a 6 year period. We found the number of species originally present in the plots as trees >5 cm dbh decreased from an initial total of 76 species to 65 species at the end of study period. But, at the same time, some new species reached the size class threshold and were recruited into the canopy layer. There was a substantial decline in tree density from an estimated stocking of about 5000 trees per ha at the time of planting to 1380 trees per ha at the time of the first measurement; the density declined by a further 4.9% per year. Changes in composition and stand structure were indicated by a marked shift in the Importance Value Index of species. Over six years, shade-intolerant species became less important and the native shade-tolerant species (often Dipterocarps) increased in importance. Based on how the Rainforestation Farming plantations developed in these early years, we suggest that mixed-species plantations elsewhere in the humid tropics should be around 1000 trees per ha or less, that the proportion of fast growing (and hence early maturing) trees should be about 30–40% of this initial density and that any fruit tree component should only be planted on the plantation margin where more light and space are available for crowns to develop.

Assessing the role of spatial correlations during collective cell spreading

Spreading cell fronts are essential features of development, repair and disease processes. Many mathematical models used to describe the motion of cell fronts, such as Fisher’s equation, invoke a mean–field assumption which implies that there is no spatial structure, such as cell clustering, present. Here, we examine the presence of spatial structure using a combination of in vitro circular barrier assays, discrete random walk simulations and pair correlation functions. In particular, we analyse discrete simulation data using pair correlation functions to show that spatial structure can form in a spreading population of cells either through sufficiently strong cell–to–cell adhesion or sufficiently rapid cell proliferation. We analyse images from a circular barrier assay describing the spreading of a population of MM127 melanoma cells using the same pair correlation functions. Our results indicate that the spreading melanoma cell populations remain very close to spatially uniform, suggesting that the strength of cell–to–cell adhesion and the rate of cell proliferation are both sufficiently small so as not to induce any spatial patterning in the spreading populations.

Increasing the length of single-wall carbon nanotubes in a magnetically enhanced arc discharge

It is demonstrated that a magnetic field has a profound effect on the length of a single-wall carbon nanotube (SWCNT) synthesized in the arc discharge. The average length of SWCNT increases by a factor of 2 in discharge with magnetic field as compared with the discharge without magnetic field, and the yield of long nanotubes with lengths above 5 μm also increases. A model of SWCNT growth on metal catalyst in arc plasma was developed. Monte-Carlo simulations confirm that the increase of the plasma density in the magnetic field leads to an increase in the nanotube growth rate and thus leads to longer nanotubes.

Pulsed dc- and sine-wave-excited cold atmospheric plasma plumes: A comparative analysis

Cold atmospheric-pressure plasma plumes are generated in the ambient air by a single-electrode plasma jet device powered by pulsed dc and ac sine-wave excitation sources. Comprehensive comparisons of the plasma characteristics, including electrical properties, optical emission spectra, gas temperatures, plasma dynamics, and bacterial inactivation ability of the two plasmas are carried out. It is shown that the dc pulse excited plasma features a much larger discharge current and stronger optical emission than the sine-wave excited plasma. The gas temperature in the former discharge remains very close to the room temperature across the entire plume length; the sine-wave driven discharge also shows a uniform temperature profile, which is 20-30 degrees higher than the room temperature. The dc pulse excited plasma also shows a better performance in the inactivation of gram-positive staphylococcus aureus bacteria. These results suggest that the pulsed dc electric field is more effective for the generation of nonequilibrium atmospheric pressure plasma plumes for advanced plasma health care applications.

Length control of He atmospheric plasma jet plumes: Effects of discharge parameters and ambient air

The effects of various discharge parameters and ambient gas on the length of He atmospheric plasma jet plumes expanding into the open air are studied. It is found that the voltage and width of the discharge-sustaining pulses exert significantly stronger effects on the plume length than the pulse frequency, gas flow rate, and nozzle diameter. This result is explained through detailed analysis of the I-V characteristics of the primary and secondary discharges which reveals the major role of the integrated total charges of the primary discharge in the plasma dynamics. The length of the jet plume can be significantly increased by guiding the propagating plume into a glass tube attached to the nozzle. This increase is attributed to elimination of the diffusion of surrounding air into the plasma plume, an absence which facilitates the propagation of the ionization front. These results are important for establishing a good level of understanding of the expansion dynamics and for enabling a high degree of control of atmospheric pressure plasmas in biomedical, materials synthesis and processing, environmental and other existing and emerging industrial applications. © 2009 American Institute of Physics.

Effect of doping with Co and/or Cu on electronic structure and optical properties of ZnO

This paper reports on ab initio numerical simulations of the effect of Co and Cu dopings on the electronic structure and optical properties of ZnO, pursued to develop diluted magnetic semiconductors vitally needed for spintronic applications. The simulations are based upon the Perdew-Burke-Enzerh generalized gradient approximation on the density functional theory. It is revealed that the electrons with energies close to the Fermi level effectively transfer only between Cu and Co ions which substitute Zn atoms, and are located in the neighbor sites connected by an O ion. The simulation results are consistent with the experimental observations that addition of Cu helps achieve stable ferromagnetism of Co-doped ZnO. It is shown that simultaneous insertion of Co and Cu atoms leads to smaller energy band gap, redshift of the optical absorption edge, as well as significant changes in the reflectivity, dielectric function, refractive index, and electron energy loss function of ZnO as compared to the doping with either Co or Cu atoms. These highly unusual optical properties are explained in terms of the computed electronic structure and are promising for the development of the next-generation room-temperature ferromagnetic semiconductors for future spintronic devices on the existing semiconductor micromanufacturing platform.

Surface fluxes of Si and C adatoms at initial growth stages of SiC quantum dots

Self-assembly of highly stoichiometric SiC quantum dots still remains a major challenge for the gas/plasma-based nanodot synthesis. By means of a multiscale hybrid numerical simulation of the initial stage (0.1-2.5 s into the process) of deposition of SiCSi (100) quantum dot nuclei, it is shown that equal Si and kst atom deposition fluxes result in strong nonstoichiometric nanodot composition due to very different surface fluxes of Si and C adatoms to the quantum dots. At this stage, the surface fluxes of Si and C adatoms to SiC nanodots can be effectively controlled by manipulating the SiC atom influx ratio and the Si (100) surface temperature. It is demonstrated that at a surface temperature of 800 K the surface fluxes can be equalized after only 0.05 s into the process; however, it takes more then 1 s at a surface temperature of 600 K. Based on the results of this study, effective strategies to maintain a stoichiometric ([Si] [C] =1:1) elemental ratio during the initial stages of deposition of SiCSi (100) quantum dot nuclei in a neutral/ionized gas-based process are proposed.

Spatially averaged model of complex-plasma discharge with self-consistent electron energy distribution

A global, or averaged, model for complex low-pressure argon discharge plasmas containing dust grains is presented. The model consists of particle and power balance equations taking into account power loss on the dust grains and the discharge wall. The electron energy distribution is determined by a Boltzmann equation. The effects of the dust and the external conditions, such as the input power and neutral gas pressure, on the electron energy distribution, the electron temperature, the electron and ion number densities, and the dust charge are investigated. It is found that the dust subsystem can strongly affect the stationary state of the discharge by dynamically modifying the electron energy distribution, the electron temperature, the creation and loss of the plasma particles, as well as the power deposition. In particular, the power loss to the dust grains can take up a significant portion of the input power, often even exceeding the loss to the wall.

Parameters and equilibrium profiles for large-area surface-wave sustained plasmas

The equilibrium profiles of the plasma parameters of large-area if discharges in a finite-length metal-shielded dielectric cylinder are computed using a two-dimensional fluid code. The rf power is coupled to the plasma through edge-localized surface waves traveling in the azimuthal direction along the plasma edge. It is shown that self-consistent accounting for axial plasma diffusion and radial nonuniformity of the electron temperature can explain the frequently reported deviations of experimentally measured radial density profiles from that of the conventional linear diffusion models. The simulation results are in a good agreement with existing experimental data obtained from surface-wave sustained large-diameter plasmas. © 2002 The American Physical Society.

Effect of an internal rotating current on low-frequency inductively coupled plasmas

The effects of an inductively rotating current were observed on low-frequency inductively coupled plasmas. The spatial distribution of electromagnetic fields was investigated in a cylindrical metallic chamber filled with dense plasma. The distribution of the magnetic field in plasma chamber was observed for rarefied and dense plasmas. The plasma was assumed as uniform in the electromagnetic fields. The results showed the plasma density increased with power and the electron density increased with pressure.

Two-dimensional simulation of nanoparticle deposition from high-density plasmas on microstructured surfaces

Selective and controlled deposition of plasma-grown nanoparticles is one of the pressing problems of plasma-aided nanofabrication. The results of advanced numerical simulations of motion of charge-variable nanoparticles in the plasma presheath and sheath areas and in localized microscopic electric fields created by surface microstructures are reported. Conditions for site-selective deposition of such nanoparticles onto individual microstructures and open surface areas within a periodic micropattern are formulated. The effects of plasma parameters, surface potential, and micropattern features on nanoparticle deposition are investigated and explained using particle charging and plasma force arguments. The results are generic and applicable to a broad range of nanoparticle-generating plasmas and practical problems ranging from management of nanoparticle contamination in microelectronics to site-selective nanoparticle deposition into specified device locations, and synthesis of advanced microporous materials and nanoparticle superlattices. © 2007 American Institute of Physics.

Electron tomography reveals the steps in filovirus budding

The filoviruses, Marburg and Ebola, are non-segmented negative-strand RNA viruses causing severe hemorrhagic fever with high mortality rates in humans and nonhuman primates. The sequence of events that leads to release of filovirus particles from cells is poorly understood. Two contrasting mechanisms have been proposed, one proceeding via a "submarine-like" budding with the helical nucleocapsid emerging parallel to the plasma membrane, and the other via perpendicular "rocketlike" protrusion. Here we have infected cells with Marburg virus under BSL-4 containment conditions, and reconstructed the sequence of steps in the budding process in three dimensions using electron tomography of plastic-embedded cells. We find that highly infectious filamentous particles are released at early stages in infection. Budding proceeds via lateral association of intracellular nucleocapsid along its whole length with the plasma membrane, followed by rapid envelopment initiated at one end of the nucleocapsid, leading to a protruding intermediate. Scission results in local membrane instability at the rear of the virus. After prolonged infection, increased vesiculation of the plasma membrane correlates with changes in shape and infectivity of released viruses. Our observations demonstrate a cellular determinant of virus shape. They reconcile the contrasting models of filovirus budding and allow us to describe the sequence of events taking place during budding and release of Marburg virus. We propose that this represents a general sequence of events also followed by other filamentous and rod-shaped viruses.

Suppression of mRNAs encoding tegument tetraspanins from schistosoma mansoni results in impaired tegument turnover

Schistosomes express a family of integral membrane proteins, called tetraspanins (TSPs), in the outer surface membranes of the tegument. Two of these tetraspanins, Sm-TSP-1 and Sm-TSP-2, confer protection as vaccines in mice, and individuals who are naturally resistant to S. mansoni infection mount a strong IgG response to Sm-TSP-2. To determine their functions in the tegument of S. mansoni we used RNA interference to silence expression of Sm-tsp-1 and Sm-tsp-2 mRNAs. Soaking of parasites in Sm-tsp dsRNAs resulted in 61% (p = 0.009) and 74% (p = 0.009) reductions in Sm-tsp-1 and Sm-tsp-2 transcription levels, respectively, in adult worms, and 67%–75% (p = 0.011) and 69%–89% (p = 0.004) reductions in Sm-tsp-1 and Sm-tsp-2 transcription levels, respectively, in schistosomula compared to worms treated with irrelevant control (luciferase) dsRNA. Ultrastructural morphology of adult worms treated in vitro with Sm-tsp-2 dsRNA displayed a distinctly vacuolated and thinner tegument compared with controls. Schistosomula exposed in vitro to Sm-tsp-2 dsRNA had a significantly thinner and more vacuolated tegument, and morphology consistent with a failure of tegumentary invaginations to close. Injection of mice with schistosomula that had been electroporated with Sm-tsp-1 and Sm-tsp-2 dsRNAs resulted in 61% (p = 0.005) and 83% (p = 0.002) reductions in the numbers of parasites recovered from the mesenteries four weeks later when compared to dsRNA-treated controls. These results imply that tetraspanins play important structural roles impacting tegument development, maturation or stability.

UNICEF, Jakarta, Indonesia : Review of Satap Schools

A. Background and context 1. Education, particularly basic education (grades1-9), has been considered critical to promoting national economic growth and social well being1. Three factors that con-tribute to the above are: (i) Education increases human capital inherent in a labor force and thus increases productivity. It also increases capacity for working with others and builds community consensus to support national development. (ii) Education can in-crease the innovative capacity of a community to support social and economic growth—use of new technologies, products and services to promote growth and wellbeing. (iii) Education can facilitate knowledge transfer needed to understand the social and eco-nomic innovations and new processes, practices and values. Cognizant of the above benefits of education, the Millennium Development Goals (MDG) and the Education for All (EFA) declarations advocating universal basic education were formulated and ratified by UN member countries. 2. Achieving universal primary education (grade 6) may not be sufficient to maxim-ize the above noted socio-economic and cultural benefits. There is general consensus that basic literacy and numeracy up to grade 9 are essential foundational blocks for any good education system to support national development. Basic Education provides an educational achievement threshold that ensures the learning is retained. To achieve this, the donor partner led interventions and the UN declarations such as the MDG goals have sought universal access to basic education (grades 1-9). As many countries progress towards achieving the universal access targets, recent research evidence suggests that we need more than just access to basic education to impact on the na-tional development. Measuring basic education completion cycle, gross enrolment rate (GER) and participation rate etc., has to now include a focus on quality and relevance of the education2. 3. While the above research finding is generally accepted by the Government of In-donesia (GoI), unlike many other developing countries, Indonesia is geographically and linguistically complex and has the fourth largest education sector in the world. It has over 3000 islands, 17,000 ethnic groups and it takes as long as 7 hours to travel from east to west of the country and has multiple time differences. The education system has six years of primary education (grades 1-6), 3 years of junior secondary education (grades 7-9) and three years of senior secondary education (grades 10-12). Therefore, applying the findings of the above cited research in a country like Indonesia is a chal-lenge. Nevertheless, since the adoption of the National Education Law (2003)3 the GoI has made significant progress in improving access to and quality of basic education (grades 1-9). The 2011/12 national education statistics show the primary education (grades 1-6) completion rate was 99.3%, the net enrolment rate (NER) was 95.4% and the GER was 115.4%. This is a significant achievement considering the complexities faced within Indonesia. This increase in the primary education sub-sector, however, has not flowed onto the Junior Secondary School (JSS) education. The transition from pri-mary to JSS is still short of the GoI targets. In 2012, there were 146,826 primary schools feeding into 33,668 junior secondary schools. The transition rate from primary to secondary in 2011/12 was 78%. When considering district or sub-district level data the transition in poor districts could be less than the aggregated national rate. Poverty and lack of parents’ education, confounded by opportunity cost, are major obstacles to transitioning to JSS4. 4. Table 1 presents a summary of GoI initiatives to accelerate the transition to JSS. GoI, with assistance from the donor community, has built 2465 new regular JSS, mak-ing the total number of regular JSS 33,668. In addition, 57,825 new classrooms have been added to existing regular JSS. Also, in rural and remote areas 4136 Satu-Atap5 (SATAP) schools were built to increase access to JSS. These SATAP schools are the focus of this study as they provide education opportunities to the most marginalized, ru-ral, remote children who otherwise would not have access to JSS and consequently not complete basic education.

Transcriptional pathway signatures predict MEK addiction and response to selumetinib (AZD6244)

Selumetinib (AZD6244, ARRY-142886) is a selective, non-ATP-competitive inhibitor of mitogen-activated protein/extracellular signal-regulated kinase kinase (MEK)-1/2. The range of antitumor activity seen preclinically and in patients highlights the importance of identifying determinants of response to this drug. In large tumor cell panels of diverse lineage, we show that MEK inhibitor response does not have an absolute correlation with mutational or phospho-protein markers of BRAF/MEK, RAS, or phosphoinositide 3-kinase (PI3K) activity. We aimed to enhance predictivity by measuring pathway output through coregulated gene networks displaying differential mRNA expression exclusive to resistant cell subsets and correlated to mutational or dynamic pathway activity. We discovered an 18-gene signature enabling measurement of MEK functional output independent of tumor genotype. Where the MEK pathway is activated but the cells remain resistant to selumetinib, we identified a 13-gene signature that implicates the existence of compensatory signaling from RAS effectors other than PI3K. The ability of these signatures to stratify samples according to functional activation of MEK and/or selumetinib sensitivity was shown in multiple independent melanoma, colon, breast, and lung tumor cell lines and in xenograft models. Furthermore, we were able to measure these signatures in fixed archival melanoma tumor samples using a single RT-qPCR-based test and found intergene correlations and associations with genetic markers of pathway activity to be preserved. These signatures offer useful tools for the study of MEK biology and clinical application of MEK inhibitors, and the novel approaches taken may benefit other targeted therapies.