Roles of binding elements, FOXL2 domains, and interactions with cJUN and SMADs in regulation of FSHβ.

We previously identified FOXL2 as a critical component in FSHβ gene transcription. Here, we show that mice deficient in FOXL2 have lower levels of gonadotropin gene expression and fewer LH- and FSH-containing cells, but the same level of other pituitary hormones compared to wild-type littermates, highlighting a role of FOXL2 in the pituitary gonadotrope. Further, we investigate the function of FOXL2 in the gonadotrope cell and determine which domains of the FOXL2 protein are necessary for induction of FSHβ transcription. There is a stronger induction of FSHβ reporter transcription by truncated FOXL2 proteins, but no induction with the mutant lacking the forkhead domain. Specifically, FOXL2 plays a role in activin induction of FSHβ, functioning in concert with activin-induced SMAD proteins. Activin acts through multiple promoter elements to induce FSHβ expression, some of which bind FOXL2. Each of these FOXL2-binding sites is either juxtaposed or overlapping with a SMAD-binding element. We determined that FOXL2 and SMAD4 proteins form a higher order complex on the most proximal FOXL2 site. Surprisingly, two other sites important for activin induction bind neither SMADs nor FOXL2, suggesting additional factors at work. Furthermore, we show that FOXL2 plays a role in synergistic induction of FSHβ by GnRH and activin through interactions with the cJUN component of the AP1 complex that is necessary for GnRH responsiveness. Collectively, our results demonstrate the necessity of FOXL2 for proper FSH production in mice and implicate FOXL2 in integration of transcription factors at the level of the FSHβ promoter

The role of water markets in climate change adaptation

Abstract Water markets were first introduced in Australia in the 1980s, and water entitlement and allocation trade have been increasingly adopted by both private individuals and government.Irrigators turned to water markets (particularly for allocation water) to manage water scarcity and Governments to acquire water for the environment (particularly water entitlements. It is expected that further adoption of water markets will be essential for coping with future climate change impacts. This report reviews the available literature related to the relationship between southern Murray-Darling Basin (sMDB) water markets and anticipated climate change effects; the economic, social and environmental impacts of water reallocation through markets; and future development requirements to enhance positive outcomes in these areas. The use of water markets by irrigators can involve both transformational (selling all water entitlements and relocating or switching to dryland) and incremental (e.g. buying water allocations/entitlements, using carry-over, changing water management techniques) adaptation to climate change. Barriers to both adaptations include: current and future climate uncertainty; poor (or non-existent) market signals; financial constraints; information barriers; mental processing limits; inherent attitudes toward or beliefs about climate change; institutional barriers and disincentives to adapt. A better understanding of trade behaviour, especially strategic trade issues that can lead to market failures, will improve the economic advantages of water trade. There remains community concerns about the impacts of transfers away from regional areas such as reduced community spending and reinvestment; population losses; loss of jobs; declining taxation base, loss of local services and businesses, regional production changes; and legacy issues for remaining farmers. However, it is hard to disentangle these impacts from those caused by ongoing structural change in agriculture. Rural communities that are most vulnerable to water scarcity under climate change and water trade adjustment include smaller irrigation-dependent towns. Communities less dependent on irrigation are better able to adapt. Further, where environmental managers use water markets to deal with water variability and to ensure ecological benefits, irrigators are concerned about its impact on their traditional use of markets to manage scarcity. Climate change and water scarcity management are intertwined, suggesting that policy, institutional and governance arrangements to deal with such issues should be similarly structured. Water users will adapt, either out of necessity or opportunity. The cost of that adaptation at individual, regional and national levels—particularly to future water supply variability—can be mitigated by the consideration of the existing advantages from future opportunities for water marketing in Australia

Water purchases to save the Murray-Darling Basin

Murray-Darling Basin communities have suffered recurring and prolonged droughts over the past decade. Now that the rains have returned, these communities see the Sustainable Diversion Limits (SDLs) planned by the Commonwealth as a new threat. Modelling with TERM-H2O assumes that since the SDL process is voluntary, Commonwealth purchases will proceed slowly over the next 12 years. This gives farmers time to utilize water saving technologies as they emerge. This is in contrast to the relatively rapid purchase of 920 GL up until September 2010 that has already occurred. These relatively rapid sales reflect hardship associated with drought. If the Commonwealth is to reach the 3500 GL target, it may need to pay over $4 billion more to farmers for water (2010 dollars). The Commonwealth’s budget constraint will limit the volume purchased. Implementing (SDLs) will raise the price of water and the asset value of water held by farmers. At the same time, the value of irrigated land will fall, partly offsetting the increase in the asset value of water. This means that some irrigators may gain more than others. Those who do best will be those whose water entitlements have a high value relative to the value of their land. Under a voluntary scheme that proceeds slowly and gives time for further water savings to occur, there will be modest job losses across the basin. These might fall to 500 jobs below forecast by the year 2026. The extent to which farmers who sell water to the Commonwealth leave the region will have a moderate influence on regional outcomes. TERM-H2O is the only model which has been calibrated by using the drought of 2006-07 to 2008-09 to estimate regional impacts. In the drought scenario, over 6,000 jobs were lost in the short term relative to forecast across the basin. Therefore, SDL impacts are much smaller than drought impacts.Environmental Economics and Policy,

Advanced solutions for quality-oriented multimedia broadcasting

Multimedia content is increasingly being delivered via different types of networks to viewers in a variety of locations and contexts using a variety of devices. The ubiquitous nature of multimedia services comes at a cost, however. The successful delivery of multimedia services will require overcoming numerous technological challenges many of which have a direct effect on the quality of the multimedia experience. For example, due to dynamically changing requirements and networking conditions, the delivery of multimedia content has traditionally adopted a best effort approach. However, this approach has often led to the end-user perceived quality of multimedia-based services being negatively affected. Yet the quality of multimedia content is a vital issue for the continued acceptance and proliferation of these services. Indeed, end-users are becoming increasingly quality-aware in their expectations of multimedia experience and demand an ever-widening spectrum of rich multimedia-based services. As a consequence, there is a continuous and extensive research effort, by both industry and academia, to find solutions for improving the quality of multimedia content delivered to the users; as well, international standards bodies, such as the International Telecommunication Union (ITU), are renewing their effort on the standardization of multimedia technologies. There are very different directions in which research has attempted to find solutions in order to improve the quality of the rich media content delivered over various network types. It is in this context that this special issue on broadcast multimedia quality of the IEEE Transactions on Broadcasting illustrates some of these avenues and presents some of the most significant research results obtained by various teams of researchers from many countries. This special issue provides an example, albeit inevitably limited, of the richness and breath of the current research on multimedia broadcasting services. The research i- - ssues addressed in this special issue include, among others, factors that influence user perceived quality, encoding-related quality assessment and control, transmission and coverage-based solutions and objective quality measurements

Bundle methods in nonsmooth DC optimization

Due to the complexity of many practical applications, we encounter optimization problems with nonsmooth functions, that is, functions which are not continuously differentiable everywhere. Classical gradient-based methods are not applicable to solve such problems, since they may fail in the nonsmooth setting. Therefore, it is imperative to develop numerical methods specifically designed for nonsmooth optimization. To date, bundle methods are considered to be the most efficient and reliable general purpose solvers for this type of problems. The idea in bundle methods is to approximate the subdifferential of the objective function by a bundle of subgradients. This information is then used to build a model for the objective. However, this model is typically convex and, due to this, it may be inaccurate and unable to adequately reflect the behaviour of the objective function in the nonconvex case. These circumstances motivate to design new bundle methods based on nonconvex models of the objective function. In this dissertation, the main focus is on nonsmooth DC optimization that constitutes an important and broad subclass of nonconvex optimization problems. A DC function can be presented as a difference of two convex functions. Thus, we can obtain a model that utilizes explicitly both the convexity and concavity of the objective by approximating separately the convex and concave parts. This way we end up with a nonconvex DC model describing the problem more accurately than the convex one. Based on the new DC model we introduce three different bundle methods. Two of them are designed for unconstrained DC optimization and the third one is capable of solving also multiobjective and constrained DC problems. The finite convergence is proved for each method. The numerical results demonstrate the efficiency of the methods and show the benefits obtained from the utilization of the DC decomposition. Even though the usage of the DC decomposition can improve the performance of the bundle methods, it is not always available or possible to construct. Thus, we present another bundle method for a general objective function implicitly collecting information about the DC structure. This method is developed for large-scale nonsmooth optimization and its convergence is proved for semismooth functions. The efficiency of the method is shown with numerical results. As an application of the developed methods, we consider the clusterwise linear regression (CLR) problems. By applying the support vector machines (SVM) approach a new model for these problems is proposed. The objective in the new formulation of the CLR problem is expressed as a DC function and a method based on one of the presented bundle methods is designed to solve it. Numerical results demonstrate robustness of the new approach to outliers.Monissa käytännön sovelluksissa tarkastelun kohteena oleva ongelma on monimutkainen ja joudutaan näin ollen mallintamaan epäsileillä funktioilla, jotka eivät välttämättä ole jatkuvasti differentioituvia kaikkialla. Klassisia gradienttiin perustuvia optimointimenetelmiä ei voida käyttää epäsileisiin tehtäviin, sillä epäsileillä funktioilla ei ole olemassa klassista gradienttia kaikkialla. Näin ollen epäsileään optimointiin on välttämätöntä kehittää omia numeerisia ratkaisumenetelmiä. Näistä kimppumenetelmiä pidetään tällä hetkellä kaikista tehokkaimpina ja luotettavimpina yleismenetelminä kyseisten tehtävien ratkaisemiseksi. Ideana kimppumenetelmissä on approksimoida kohdefunktion alidifferentiaalia kimpulla, joka on muodostettu keräämällä kohdefunktion aligradientteja edellisiltä iteraatiokierroksilta. Tätä tietoa hyödyntämällä voidaan muodostaa kohdefunktiolle malli, joka on alkuperäistä tehtävää helpompi ratkaista. Käytetty malli on tyypillisesti konveksi ja näin ollen se voi olla epätarkka ja kykenemätön esittämään alkuperäisen tehtävän rakennetta epäkonveksissa tapauksessa. Tästä syystä väitöskirjassa keskitytään kehittämään uusia kimppumenetelmiä, jotka mallinnusvaiheessa muodostavat kohdefunktiolle epäkonveksin mallin. Pääpaino väitöskirjassa on epäsileissä optimointitehtävissä, joissa funktiot voidaan esittää kahden konveksin funktion erotuksena (difference of two convex functions). Kyseisiä funktioita kutsutaan DC-funktioiksi ja ne muodostavat tärkeän ja laajan epäkonveksien funktioiden osajoukon. Tämä valinta mahdollistaa kohdefunktion konveksisuuden ja konkaavisuuden eksplisiittisen hyödyntämisen, sillä uusi malli kohdefunktiolle muodostetaan yhdistämällä erilliset konveksille ja konkaaville osalle rakennetut mallit. Tällä tavalla päädytään epäkonveksiin DC-malliin, joka pystyy kuvaamaan ratkaistavaa tehtävää tarkemmin kuin konveksi arvio. Väitöskirjassa esitetään kolme erilaista uuden DC-mallin pohjalta kehitettyä kimppumenetelmää sekä todistetaan menetelmien konvergenssit. Kaksi näistä menetelmistä on suunniteltu rajoitteettomaan DC-optimointiin ja kolmannella voidaan ratkaista myös monitavoitteisia ja rajoitteellisia DC-optimointitehtäviä. Numeeriset tulokset havainnollistavat menetelmien tehokkuutta sekä DC-hajotelman käytöstä saatuja etuja. Vaikka DC-hajotelman käyttö voi parantaa kimppumenetelmien suoritusta, sitä ei aina ole saatavilla tai mahdollista muodostaa. Tästä syystä väitöskirjassa esitetään myös neljäs kimppumenetelmä konvergenssitodistuksineen yleiselle kohdefunktiolle, jossa kerätään implisiittisesti tietoa kohdefunktion DC-rakenteesta. Menetelmä on kehitetty erityisesti suurille epäsileille optimointitehtäville ja sen tehokkuus osoitetaan numeerisella testauksella Sovelluksena väitöskirjassa tarkastellaan datalle klustereittain tehtävää lineaarista regressiota (clusterwise linear regression). Kyseiselle sovellukselle muodostetaan uusi malli hyödyntäen koneoppimisessa käytettyä SVM-lähestymistapaa (support vector machines approach) ja saatu kohdefunktio esitetään DC-funktiona. Näin ollen yhtä kehitetyistä kimppumenetelmistä sovelletaan tehtävän ratkaisemiseen. Numeeriset tulokset havainnollistavat uuden lähestymistavan robustisuutta ja tehokkuutta

Pilot in loop assessment of fault tolerant flight control schemes in a motion flight simulator

This research presents the pilot in the loop tests carried out in a Six-Degree of Freedom (6-DOF) motion flight simulator to evaluate failure detection, isolation and identification (FDII) schemes for an advanced F-15 aircraft. The objective behind this study is to leverage the capability of the flight simulator at West Virginia University (WVU) to carry out a performance assessment of neurally augmented control algorithms developed on a Matlab/Simulink RTM platform. The experimental setup features an interface setup of Gen-2 SimulinkRTM schemes with MOTUS Flight Simulator (MFS). The set up is a close substitute to a real flight and thus is helpful in evaluation of the schemes in a realistic manner. The graphics in X-plane is used to obtain visual cues and the motion platform is used to obtain motion cues in the simulator cockpit. The whole set-up enables the pilot to respond with a joystick in the advent of a failure as he would otherwise in a real flight. The pilot response in maintaining the mission profile is different for different neural network augmentations and thus an indication of performance comparison of these schemes. Secondly, FDII schemes are developed for a sensor and actuator failure using an adaptive threshold for cross-correlation coefficients of the angular rates of the aircraft. Failure detection, isolation and identification logic is formulated based on monitoring the cross-correlation parameters with their Floating Limiter (FL) bounds. The FDII scheme developed shows a good performance with desktop simulation because of no pilot activity but with a pilot in the loop significant cross-correlation of the rates occur and hence the scheme become more susceptible to wrongs FDII. In addition, the pilot might induce some coupling of the cross-correlation parameters between detection and identification time which may trigger false detections and may configure the controller differently based on incorrect detection. Thus it is necessary that FDII scheme accommodate real flight conditions. The performance of the FDII schemes is improved with a pilot in the loop by monitoring the cross-correlation parameters and fine tuning FDII algorithms for real situations. This study has set up an excellent example to effectively utilize the aural, visual and motion cues to create a higher level of simulation complexity in designing control algorithms

The Golden Gift of Groundwater in Australia’s MDB

The Murray-Darling Basin (MDB) has the second-most variable surface flows in the world. The unreliable nature of MDB surface water supply is expected to increase under climate change. To partially address this future problem, Australia’s government released 927 gigalitres (GL = 1 billion litres) of groundwater rights to agricultural users in the basin under the Murray-Darling Basin Plan (2012-2026). A key argument for that action was the perception that groundwater resources in the basin are sustainable, and more reliable, than surface water resources. Access to more reliable water often transforms agricultural cropping choices. This chapter uses an optimization model of the MDB to explore how basin agriculture may transform in response to reliable water access—particularly in the northern part of the MDB. We find that traditional opportunistic cropping systems (i.e., annuals) shift towards high-value systems (e.g., perennials) and change irrigation practices when access to groundwater resources is increased. We also examine the change in value for those new groundwater rights as climate change impacts take hold.David Adamson, Christopher Auricht and Adam Loc

Understanding adaptation and water market behaviour of irrigators and non-landholder stakeholders in the Murray-Darling Basin

The impacts of water scarcity and climate change, such as a drier future with increased frequency of extreme events, have resulted in increasing pressure on already over-allocated Murray-Darling Basin (MDB) water resources. Therefore, understanding how irrigators adapt to future uncertainty is important for both economic, social and environmental reasons in the MDB. This thesis examines the key drivers for different types of MDB irrigators’ planned future adaptation. One key mechanism that irrigators have used for adapting and mitigating water shortage includes participating in water markets. The evolution of water markets in the MDB, and the implementation of unbundling from the 2000s onwards, has seen both a) the emergence of new water products, and b) increasing involvement of environmental and non-landholder stakeholders. However, little is known about non-landholder behaviour and involvement in water markets. This thesis extends the current literature by exploring water ownership and trading strategies of all major MDB water market stakeholder groups, including environmental and non-landholder actors, and gives special focus to “derivative-type” temporary trading products. The first analytical chapter used a quantitative data set of 1,000 sMDB irrigators to investigate irrigators’ planned adaptation strategies and their drivers. Seemingly unrelated regressions, recursive biprobit, and multivariate probit modelling found that while all types of capital (e.g. farm, physical, etc.) are significant drivers of planned future adaptation, financial capital (e.g. debt, net farm income) is one of the most important. Other drivers vary in importance across types of adaptation and industry. The second analytical chapter explores MDB stakeholders’ water ownership and trading strategies, with special attention given to agri-corporate and non-landholder stakeholders, and new water products such as water futures and leases. Three different data sets are drawn upon: 1) the quantitative sMDB irrigator survey; 2) quantitative water forward and parking trade data provided by a private broker; and 3) qualitative in-depth interview data from 63 experts representing a variety of stakeholders. It was found that agri-corporates and non-landholders hold more diverse water portfolios, and engage more in derivative-type water product trading. Three areas of water policy reform are identified: data, rules and regulations, and new institutional development. The third analytical chapter explored valuation and accounting methods used to estimate the financial asset value of MDB water entitlements. Drawing mainly upon the qualitative interview dataset, a wide divergence in methods was found with comparative valuation the most common valuation method used. Most MDB stakeholders account for water entitlement value at historic cost, while financial investors use fair market accounting to represent current market values. Historical cost accounting undervalues entitlements compared to fair value accounting. The case study of the environmental strategic purchase of Kia Ora overland-flow entitlements in southern Queensland illustrates the impact of valuation discretion on water entitlement values, leading to value differences for the same entitlement, of up to 97%. As the need to adapt to climate change and future uncertainty increases, it is important to utilise all tools available to incentivise more irrigator adaptive behaviour. Water markets will remain an important adaptation tool, but along with their increased adoption there must be a similar evolution in the design of water markets for their efficient and equitable functionality for all stakeholders.Thesis (Ph.D.) -- University of Adelaide, Centre for Global Food & Resources, 202

Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes

An increasing number of evidences show that genes are not distributed randomly across eukaryotic chromosomes, but rather in functional neighborhoods. Nevertheless, the driving force that originated and maintains such neighborhoods is still a matter of controversy. We present the first detailed multispecies cartography of genome regions enriched in genes with related functions and study the evolutionary implications of such clustering. Our results indicate that the chromosomes of higher eukaryotic genomes contain up to 12% of genes arranged in functional neighborhoods, with a high level of gene co-expression, which are consistently distributed in phylogenies. Unexpectedly, neighborhoods with homologous functions are formed by different (non-orthologous) genes in different species. Actually, instead of being conserved, functional neighborhoods present a higher degree of synteny breaks than the genome average. This scenario is compatible with the existence of selective pressures optimizing the coordinated transcription of blocks of functionally related genes. If these neighborhoods were broken by chromosomal rearrangements, selection would favor further rearrangements reconstructing other neighborhoods of similar function. The picture arising from this study is a dynamic genomic landscape with a high level of functional organization