Assessing the performance of a nucleus estate and smallholder scheme for oil palm production in West Sumatra: a stochastic frontier analysis

In this paper, we study the performance of smallholders in a nucleus estate and smallholder (NES) scheme in oil palm production schemein West Sumatra by measuring their technical efficiency using a stochastic frontier production function. Our results indicate a mean technical efficiency of 66%, which is below what we would have expected given the uniformity of the climate, soils and plantation construction among the sample farmers. The use of progressive farmers as a means of disseminating extension advice does not appear to have been successful, and more rigorous farmer selection procedures need to be put in place for similar schemes and for general agricultural extension in future. No clear relationship was established between technical efficiency and the use of female labour, suggesting there is no need to target extension services specifically at female labourers in the household. Finally, education was found to have an unexpectedly negative impact on technical efficiency, indicating that farmers with primary education may be more important than those with secondary and tertiary education as targets of development schemes and extension programs entailing non-formal education. (C) 2003 Elsevier Ltd. All rights reserved.

Changes in body water distribution during treatment with inhaled steroid in pre-school children

Primary objective: The study aimed to examine the changes in water distribution in the soft tissue during systemic steroid activity. Research design: A three-way cross-over, randomized, placebo-controlled, double-blind trial was used, including 4 weeks of fluticasone propionate pMDI 200 mug b.i.d. delivered via Babyhaler(R), budesonide pressurized metered dose inhaler (pMDI) 200 mug b.i.d. delivered via Nebuchamber(R) and placebo. Spacers were primed before use. In total, 40 children aged 1-3 years, with mild intermittent asthma were included. Twenty-five of the children completed all three treatments. At the end of each treatment period body impedance and skin ultrasonography were measured. Methods and procedures: We measured changes in water content of the soft tissues by two methods. Skin ultrasonography was used to detect small changes in dermal water content, and bioelectrical impedance was used to assess body water content and distribution. Main outcomes and results: We found an increase in skin density of the shin from fluticasone as measured by ultrasonography (p = 0.01). There was a tendency for a consistent elevation of impedance parameters from active treatments compared to placebo although overall this effect was not statistically significant (0.1< p <0.2). However, sub-analyses indicated a significant effect on whole-body and leg impedance from budesonide treatment (p <0.05). Conclusion: Decreased growth during inhaled steroid treatment seems to partly reflect generalized changes in body water.

Direct fermentation of potato starch in wastewater to lactic acid by Rhizopus oryzae

The fungal species of Rhizopus oryzae 2062 has the capacity to carry out a single stage fermentation process for lactic acid production from potato starch wastewater. Starch hydrolysis, reducing sugar accumulation, biomass formation, and lactic acid production were affected with variations in pH, temperature, and starch source and concentration. A growth condition with starch concentration approximately 20 g/L at pH 6.0 and 30degreesC was favourable for starch fermentation, resulting in a lactic acid yield of 78.3%similar to85.5% associated with 1.5similar to2.0 g/L fungal biomass produced in 36 h of fermentation.

A new method for identification of protein (sub)families in a set of proteins based on hydropathy distribution in proteins

Structural similarity among proteins is reflected in the distribution of hydropathicity along the amino acids in the protein sequence. Similarities in the hydropathy distributions are obvious for homologous proteins within a protein family. They also were observed for proteins with related structures, even when sequence similarities were undetectable. Here we present a novel method that employs the hydropathy distribution in proteins for identification of (sub)families in a set of (homologous) proteins. We represent proteins as points in a generalized hydropathy space, represented by vectors of specifically defined features. The features are derived from hydropathy of the individual amino acids. Projection of this space onto principal axes reveals groups of proteins with related hydropathy distributions. The groups identified correspond well to families of structurally and functionally related proteins. We found that this method accurately identifies protein families in a set of proteins, or subfamilies in a set of homologous proteins. Our results show that protein families can be identified by the analysis of hydropathy distribution, without the need for sequence alignment. (C) 2005 Wiley-Liss, Inc.

Genome reduction in Leptospira borgpetersenii reflects limited transmission potential

Leptospirosis is one of the most common zoonotic diseases in the world, resulting in high morbidity and mortality in humans and affecting global livestock production. Most infections are caused by either Leptospira borgpetersenii or Leptospira interrogans, bacteria that vary in their distribution in nature and rely on different modes of transmission. We report the complete genomic sequences of two strains of L. borgpetersenii serovar Hardjo that have distinct phenotypes and virulence. These two strains have nearly identical genetic content, with subtle frameshift and point mutations being a common form of genetic variation. Starkly limited regions of synteny are shared between the large chromosomes of L. borgpetersenii and L. interrogans, probably the result of frequent recombination events between insertion sequences. The L. borgpetersenii genome is ≈700 kb smaller and has a lower coding density than L. interrogans, indicating it is decaying through a process of insertion sequence-mediated genome reduction. Loss of gene function is not random but is centered on impairment of environmental sensing and metabolite transport and utilization. These features distinguish L. borgpetersenii from L. interrogans, a species with minimal genetic decay and that survives extended passage in aquatic environments encountering a mammalian host. We conclude that L. borgpetersenii is evolving toward dependence on a strict host-to-host transmission cycle.

Improved production of industrially relevant recombinant proteins: application of multi-factorial design of experiments and scalable process modelling

The work described in this thesis focuses on the use of a design-of-experiments approach in a multi-well mini-bioreactor to enable the rapid establishments of high yielding production phase conditions in yeast, which is an increasingly popular host system in both academic and industrial laboratories. Using green fluorescent protein secreted from the yeast, Pichia pastoris, a scalable predictive model of protein yield per cell was derived from 13 sets of conditions each with three factors (temperature, pH and dissolved oxygen) at 3 levels and was directly transferable to a 7 L bioreactor. This was in clear contrast to the situation in shake flasks, where the process parameters cannot be tightly controlled. By further optimisating both the accumulation of cell density in batch and improving the fed-batch induction regime, additional yield improvement was found to be additive to the per cell yield of the model. A separate study also demonstrated that improving biomass improved product yield in a second yeast species, Saccharomyces cerevisiae. Investigations of cell wall hydrophobicity in high cell density P. pastoris cultures indicated that cell wall hydrophobin (protein) compositional changes with growth phase becoming more hydrophobic in log growth than in lag or stationary phases. This is possibly due to an increased occurrence of proteins associated with cell division. Finally, the modelling approach was validated in mammalian cells, showing its flexibility and robustness. In summary, the strategy presented in this thesis has the benefit of reducing process development time in recombinant protein production, directly from bench to bioreactor.

Laminar distribution of the pathological changes in sporadic frontotemporal lobar degeneration with transactive response (TAR) DNA-binding protein of 43kDa (TDP-43) proteinopathy:a quantitative study using polynomial curve fitting

Aims: Previous data suggest heterogeneity in laminar distribution of the pathology in the molecular disorder frontotemporal lobar degeneration (FTLD) with transactive response (TAR) DNA-binding protein of 43kDa (TDP-43) proteinopathy (FTLD-TDP). To study this heterogeneity, we quantified the changes in density across the cortical laminae of neuronal cytoplasmic inclusions, glial inclusions, neuronal intranuclear inclusions, dystrophic neurites, surviving neurones, abnormally enlarged neurones, and vacuoles in regions of the frontal and temporal lobe. Methods: Changes in density of histological features across cortical gyri were studied in 10 sporadic cases of FTLD-TDP using quantitative methods and polynomial curve fitting. Results: Our data suggest that laminar neuropathology in sporadic FTLD-TDP is highly variable. Most commonly, neuronal cytoplasmic inclusions, dystrophic neurites and vacuolation were abundant in the upper laminae and glial inclusions, neuronal intranuclear inclusions, abnormally enlarged neurones, and glial cell nuclei in the lower laminae. TDP-43-immunoreactive inclusions affected more of the cortical profile in longer duration cases; their distribution varied with disease subtype, but was unrelated to Braak tangle score. Different TDP-43-immunoreactive inclusions were not spatially correlated. Conclusions: Laminar distribution of pathological features in 10 sporadic cases of FTLD-TDP is heterogeneous and may be accounted for, in part, by disease subtype and disease duration. In addition, the feedforward and feedback cortico-cortical connections may be compromised in FTLD-TDP. © 2012 The Authors. Neuropathology and Applied Neurobiology © 2012 British Neuropathological Society.

Setting up a bioreactor for recombinant protein production in yeast

Scale-up from shake flasks to bioreactors allows for the more reproducible, high-yielding production of recombinant proteins in yeast. The ability to control growth conditions through real-time monitoring facilitates further optimization of the process. The setup of a 3-L stirred-tank bioreactor for such an application is described. © 2012 Springer Science+business Media, LLC.

Resource enclavity and corporate social responsibility in Sub-Saharan Africa:the case of oil production in Ghana

Why has Corporate Social Responsibility (CSR) yielded such disappointing outcomes in oil-rich sub-Saharan Africa? Over the past decades, a sizable body of literature has emerged which draws attention to the shortcomings of oil-related development and complementary CSR exercises in the region. Most critiques on the topic, however, assess specific interventions and/or policies but fail to evaluate the complex decision-making processes, dictated heavily by setting, which produce such actions altogether. This thesis attributes CSR outcomes in oil-rich sub-Saharan Africa to the unique context in which the decisions underpinning actions take place. In doing so, the analysis borrows ideas from a diverse body of literature spanning the international development, accounting, management and political science disciplines. To explore these ideas further, the thesis focuses on the case of Ghana. The most recent “addition” to sub-Saharan Africa’s oil club, Ghana provides a rare glimpse of how decisions underpinning CSR have been identified, evolved and reshaped from the outset. To provide a comprehensive picture of CSR in the sector and its impacts at the local level, interviews and focus groups were conducted with a range of stakeholder groups. As is the case throughout sub-Saharan Africa, in Ghana, oil production occurs in offshore “enclaves”, which are disconnected geographically from local communities. This thesis argues that these dynamics have important implications for CSR. Findings point to companies also being disconnected ideologically from local development needs, which, in part explains the questionable CSR that has become such a contentious issue in the debate on oil and development in sub-Saharan Africa in recent years. The enclave-type setting in which oil production occurs appears to have stifled creativity and innovation in the area of CSR. This, along with institutional weaknesses, regulatory deficiencies and the Government of Ghana’s failure to adequately respond to local-level concerns, has produced these outcomes.

Luminescent techniques for studying free radical production and cell viability in relation to cardiovascular disease and HRT

Epidemiological studies have suggested that hormone replacement therapy (HRT) offers protection from atherosclerosis, a precursor of cardiovascular disease (CVD), in postmenopausal women. There is good evidence that oxidation of low-density lipoprotein (LDL) by leucocyte-derived reactive oxygen species plays a key role in development of an atherosclerotic plaque. Therefore we have investigated whether the possible protection against CVD by HRT could be due to immunomodulation, specifically of free radical production. The study involves 2 approaches: I) analysing the production of free radicals by leucocytes from women on HRT, 2) investigating the effect of I7p-oestradiol and progesterone on cultured myeloid cells (HL60 and U937). Free radical production by leucocytes was determined using a recently developed bioluminescent assay. In the assay, Pholasin® emits light in the presence of free radicals produced by the NADPH oxidase system of leucocytes stimulated with PMA or fMLP. Cell viability was also investigated using a bioluminescent assay (Cell Titer-Glo®) in which cytosolic ATP levels were measured by the production of luminescence in the presence of Luciferin/Luciferase reagent. Studies of leucocytes from HRT patients showed considerable variation in free radical production, which appeared to be dependent on HRT regime. Studies on the cultured cells showed that there was no cell proliferation at low hormone concentrations, while high concentrations caused cytotoxicity. The effect of hormones on free radical production in this in vitro model system is currently being investigated. The results show that the effects of the hormones on cells of the immune system are very dose dependent, and that both beneficial and adverse effects may occur. In conclusion, luminescent techniques offer a valuable and sensitive approach to studying inflammatory and oxidative processes both in vivo and in vitro.

Large-scale production of secreted proteins in Pichia pastoris

The production of recombinant therapeutic proteins is an active area of research in drug development. These bio-therapeutic drugs target nearly 150 disease states and promise to bring better treatments to patients. However, if new bio-therapeutics are to be made more accessible and affordable, improvements in production performance and optimization of processes are necessary. A major challenge lies in controlling the effect of process conditions on production of intact functional proteins. To achieve this, improved tools are needed for bio-processing. For example, implementation of process modeling and high-throughput technologies can be used to achieve quality by design, leading to improvements in productivity. Commercially, the most sought after targets are secreted proteins due to the ease of handling in downstream procedures. This chapter outlines different approaches for production and optimization of secreted proteins in the host Pichia pastoris. © 2012 Springer Science+business Media, LLC.

Power in distribution channels - Supplier assortment strategy for balancing power

This paper focuses on the move from buyer dominance toward interdependence between buyers and suppliers in a distribution channel. The paper introduces a case study collected through in-depth interviews and participative observations. It examines the relationships between a timber supplier and its customers in the builders' merchants sector. We stress the relevance of considering actions intended to change the power balance, rather than focusing only on trust. The power balance in a dyadic relationship is dynamic, and power positions need to be constantly re-evaluated. An important power resource is information asymmetry, manifested in the supplier's information about: products, regional and local demand, and the usage of the products. For practitioners, we highlight the possibility of exerting a non-coercive power resource, such as information asymmetry, in order to increase the relative power. Furthermore, being open about the power position between a buyer and a seller can foster a more efficient collaboration.

Distribution and ecology of amphibians and reptiles in a fragmented landscape, northeastern Bolivia

Habitat loss and fragmentation have been implicated as driving forces behind recent waves of extinction. The regional landscape where this study occurred is a mosaic of forest and grassland, and therefore provides an ideal system with which to investigate the implications of habitat patchiness for the distribution and ecology of organisms. Here I describe patterns of amphibian and reptile distribution among and within habitats at the study site, investigate associations between habitat and community structure, describe nested subset patterns on forest islands, and quantify the relationship between body size and density across ecological scales and taxonomic groups. ^ Species richness did not vary across habitats, between forest island isolation classes or between island edges and cores. In contrast, species composition varied at all three ecological scales, reflecting differences in the distribution of both forest and open-habitat affiliated species. Species composition was associated with multivariate habitat profiles, with differences occurring along the isolation gradient of forest islands rather than the area gradient. The relationship between species composition and habitat was stronger for amphibians than for reptiles, a pattern that may be ascribed to physiological differences between the two groups. Analysis of nested subset pattern of community structure indicated that species composition of islands is nested as a function of isolation. Four species whose distribution on forest islands seems to be dispersal-limited drive the relationship between nestedness and isolation. Although there were several examples of shifts in body size across spatial scales and taxonomic groups, body size was not associated with density as predicted by theory, which may reflect differences between real and habitat islands, or differential responses of poikilothermic vertebrates to changes in density relative to homeotherms. ^ Taken together, the strongest result to emerge from this research is the importance of isolation, rather than area, on community structure in this system. Much evidence suggested that different ecological groups of species show distinct patterns of distribution both within and among habitat types. This suggests that species distributions at this site are not the result of 'neutral' processes at the community level, but rather reflect fundamental differences in the ecology of component species. ^

Physical factors influencing the distribution of a top predator in a subtropical oligotrophic estuary

We used longline fishing to determine the effects of distance from the ocean, season, and short-term variation in abiotic conditions on the abundance of juvenile bull sharks (Carcharhinus leucas) in an estuary of the Florida Everglades, U.S.A. Logistic regression revealed that young-of-the-year sharks were concentrated at a protected site 20 km upstream and were present in greater abundance when dissolved oxygen (DO) levels were high. For older juvenile sharks (age 1+), DO levels had the greatest influence on catch probabilities followed by distance from the ocean; they were most likely to be caught at sites with .3.5 mg L21 DO and on the main branch of the river 20 km upstream. Salinity had a relatively small effect on catch rates and there were no seasonal shifts in shark distribution. Our results highlight the importance of considering DO as a possible driver of top predator distributions in estuaries, even in the absence of hypoxia. In Everglades estuaries hydrological drivers that affect DO levels (e.g., groundwater discharge, modification of primary productivity through nutrient fluxes) will be important in determining shark distributions, and the effects of planned ecosystem restoration efforts on bull sharks will not simply be mediated by changing salinity regimes and the location of the oligohaline zone. More generally, variation in DO levels could structure the nature and spatiotemporal pattern of top predator effects in the coastal Everglades, and other tropical and subtropical estuaries, because of interspecific variation in reliance on DO within the top predator guild.

Evaluating the Distribution of Terrestrial Dissolved Organic Matter in a Complex Coastal Ecosystem Using Fluorescence Spectroscopy

The coastal zone of the Florida Keys features the only living coral reef in the continental United States and as such represents a unique regional environmental resource. Anthropogenic pressures combined with climate disturbances such as hurricanes can affect the biogeochemistry of the region and threaten the health of this unique ecosystem. As such, water quality monitoring has historically been implemented in the Florida Keys, and six spatially distinct zones have been identified. In these studies however, dissolved organic matter (DOM) has only been studied as a quantitative parameter, and DOM composition can be a valuable biogeochemical parameter in assessing environmental change in coastal regions. Here we report the first data of its kind on the application of optical properties of DOM, in particular excitation emission matrix fluorescence with parallel factor analysis (EEM-PARAFAC), throughout these six Florida Keys regions in an attempt to assess spatial differences in DOM sources. Our data suggests that while DOM in the Florida Keys can be influenced by distant terrestrial environments such as the Everglades, spatial differences in DOM distribution were also controlled in part by local surface runoff/fringe mangroves, contributions from seasgrass communities, as well as the reefs and waters from the Florida Current. Application of principal component analysis (PCA) of the relative abundance of EEM-PARAFAC components allowed for a clear distinction between the sources of DOM (allochthonous vs. autochthonous), between different autochthonous sources and/or the diagenetic status of DOM, and further clarified contribution of terrestrial DOM in zones where levels of DOM were low in abundance. The combination between EEM-PARAFAC and PCA proved to be ideally suited to discern DOM composition and source differences in coastal zones with complex hydrology and multiple DOM sources.