Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames.

Mammalian gene expression displays widespread circadian oscillations. Rhythmic transcription underlies the core clock mechanism, but it cannot explain numerous observations made at the level of protein rhythmicity. We have used ribosome profiling in mouse liver to measure the translation of mRNAs into protein around the clock and at high temporal and nucleotide resolution. We discovered, transcriptome-wide, extensive rhythms in ribosome occupancy and identified a core set of approximately 150 mRNAs subject to particularly robust daily changes in translation efficiency. Cycling proteins produced from nonoscillating transcripts revealed thus-far-unknown rhythmic regulation associated with specific pathways (notably in iron metabolism, through the rhythmic translation of transcripts containing iron responsive elements), and indicated feedback to the rhythmic transcriptome through novel rhythmic transcription factors. Moreover, estimates of relative levels of core clock protein biosynthesis that we deduced from the data explained known features of the circadian clock better than did mRNA expression alone. Finally, we identified uORF translation as a novel regulatory mechanism within the clock circuitry. Consistent with the occurrence of translated uORFs in several core clock transcripts, loss-of-function of Denr, a known regulator of reinitiation after uORF usage and of ribosome recycling, led to circadian period shortening in cells. In summary, our data offer a framework for understanding the dynamics of translational regulation, circadian gene expression, and metabolic control in a solid mammalian organ.

Aerosol particle size distributions at a traffic exposed site and an urban background location in Oporto, Portugal

Aerosol size distributions from 6 to 700 nm were measured simultaneously at an urban background site and a roadside station in Oporto. The particle number concentration was higher at the traffic exposed site, where up to 90% of the size spectrum was dominated by the nucleation mode. Larger aerosol mode diameters were observed in the urban background site possibly due to the coagulation processes or uptake of gases during transport. Factor analysis has shown that road traffic and the neighbour stationary sources localised upwind affect the urban area thought intra-regional pollutant transport.

GIS assessing traditional and modern agricultural land use/land cover change. A case study 1959-2005: Rekijoki, Somero, SW-Finland

Finland’s rural landscape has gone through remarkable changes from the 1950’s, due to agricultural developments. Changed farming practices have influenced especially traditional landscape management, and modifications in the arable land structure and grasslands transitions are notable. The review of the previous studies reveal the importance of the rural landscape composition and structure to species and landscape diversity, whereas including the relevance in presence of the open ditches, size of the field and meadow patches, topology of the natural and agricultural landscape. This land-change study includes applying remote sensed data from two time series and empirical geospatial analysis in Geographic Information Systems (GIS). The aims of this retrospective research is to detect agricultural landscape use and land cover change (LULCC) dynamics and discuss the consequences of agricultural intensification to landscape structure covering from the aspects of landscape ecology. Measurements of LULC are derived directly from pre-processed aerial images by a variety of analytical procedures, including statistical methods and image interpretation. The methodological challenges are confronted in the process of landscape classification and combining change detection approaches with landscape indices. Particular importance is paid on detecting agricultural landscape features at a small scale, demanding comprehensive understanding of such agroecosystems. Topological properties of the classified arable land and valley are determined in order to provide insight and emphasize the aspect the field edges in the agricultural landscape as important habitat. Change detection dynamics are presented with change matrix and additional calculations of gain, loss, swap, net change, change rate and tendencies are made. Transition’s possibility is computed following Markov’s probability model and presented with matrix, as well. Thesis’s spatial aspect is revealed with illustrative maps providing knowledge of location of the classified landscape categories and location of the dynamics of the changes occurred. It was assured that in Rekijoki valley’s landscape, remarkable changes in landscape has occurred. Landscape diversity has been strongly influenced by modern agricultural landscape change, as NP of open ditches has decreased and the MPS of the arable plot has decreased. Overall change in the diversity of the landscape is determined with the decrease of SHDI. Valley landscape considered as traditional land use area has experienced major transitional changes, as meadows class has lost almost one third of the area due to afforestation. Also, remarkable transitions have occurred from forest to meadow and arable land to built area. Boundaries measurement between modern and traditional landscape has indicated noticeable proportional increase in arable land-forest edge type and decrease in arable land-meadow edge type. Probability calculations predict higher future changes for traditional landscape, but also for arable land turning into built area.

Securing Tenure for Sustainable Livelihoods: A Case of Women Land Ownership in Anglophone Cameroon

The majority of women in Third World countries depend on land for their livelihood. Security of tenure is important for them to ensure sustainable development, especially in rural areas. In most parts of Africa, land ownership is affected by traditional values, inheritance rights, and government influence. These forces have provided varying types of tenure which are detrimental to the women in rural and urban areas. Land acquisition and its development has been an emotive issue due to traditional pressures and the law as regards the process of land certification. The government and traditional administrations are highly involved in the way women own land and subsequently develop it in Anglophone Cameroon. State authority over land acquisition is important, but the process for obtaining land title is herculean especially for the rural woman. This study illustrates that land acquisition and development by women constitute a problem because of traditional pressures and the law guiding the process of land certification. There is need to exhume the barriers of government’s legal instrument (The Land Consultative Board) that regulates the ownership of land and to revisit some traditional practices as regards land ownership that impact negatively on women in a changing and globalizing world. A compromise approach is advocated for land acquisition that can transcend traditional barriers as well as render the process of land registration more realistic especially for women.

Urban Detection From Hyperspectral Images Using Dimension-Reduction Model and Fusion of Multiple Segmentations Based on Stuctural and Textural Features

Ce mémoire de maîtrise présente une nouvelle approche non supervisée pour détecter et segmenter les régions urbaines dans les images hyperspectrales. La méthode proposée n ́ecessite trois étapes. Tout d’abord, afin de réduire le coût calculatoire de notre algorithme, une image couleur du contenu spectral est estimée. A cette fin, une étape de réduction de dimensionalité non-linéaire, basée sur deux critères complémentaires mais contradictoires de bonne visualisation; à savoir la précision et le contraste, est réalisée pour l’affichage couleur de chaque image hyperspectrale. Ensuite, pour discriminer les régions urbaines des régions non urbaines, la seconde étape consiste à extraire quelques caractéristiques discriminantes (et complémentaires) sur cette image hyperspectrale couleur. A cette fin, nous avons extrait une série de paramètres discriminants pour décrire les caractéristiques d’une zone urbaine, principalement composée d’objets manufacturés de formes simples g ́eométriques et régulières. Nous avons utilisé des caractéristiques texturales basées sur les niveaux de gris, la magnitude du gradient ou des paramètres issus de la matrice de co-occurrence combinés avec des caractéristiques structurelles basées sur l’orientation locale du gradient de l’image et la détection locale de segments de droites. Afin de réduire encore la complexité de calcul de notre approche et éviter le problème de la ”malédiction de la dimensionnalité” quand on décide de regrouper des données de dimensions élevées, nous avons décidé de classifier individuellement, dans la dernière étape, chaque caractéristique texturale ou structurelle avec une simple procédure de K-moyennes et ensuite de combiner ces segmentations grossières, obtenues à faible coût, avec un modèle efficace de fusion de cartes de segmentations. Les expérimentations données dans ce rapport montrent que cette stratégie est efficace visuellement et se compare favorablement aux autres méthodes de détection et segmentation de zones urbaines à partir d’images hyperspectrales.

Coordonner les transports et l'urbanisme dans un contexte urbain concret : le TOD comme instrument d'action publique, le cas de Sainte-Therese, QC

Le concept de transit-oriented development (TOD) est habituellement abordé en tant qu'ensemble fixe de caractéristiques physico-spatiales. Cette approche ne s'avere pas suffisante pour comprendre comment le TOD peut être pertinent pour coordonner les transports et l'urbanisme dans un contexte urbain concret. Afin de combler cette lacune, nous proposons d'étudier le TOD en tant qu'instrument d'action publique, adopté, produit et utilisé par les acteurs sur le territoire en fonction des enjeux, des ressources et des contraintes qui y sont présents. Ce travail exploratoire est fondé sur une étude de cas de la mise en place du TOD a Sainte-Thérese. Pour comprendre comment se sont arrimés les intérêts des acteurs impliqués et ce qui en a résulté, la collecte de données se fait a l'aide de sources écrites, mais aussi d’entretiens semi-directifs avec les acteurs clé. Les résultats de l'étude confirment la pertinence de l'approche adoptée pour aborder le TOD. Le TOD comme instrument d'action publique peut être qualifié d'opérateur de congruence, car il permet de faire converger les intérêts différents, et même potentiellement contradictoires, qui sont en jeu sur le territoire. Cependant, il n'y a pas de formule passe-partout: la production du TOD se fait en grande partie de façon incrémentale, en fonction des conditions sur le territoire. La mise en place du TOD n'exige pas nécessairement l'invention d'un nouveau cadre d'action et peut se faire en grande partie a l'aide des outils existants. Toutefois, pour pouvoir se servir pleinement de ces outils, le leadership des acteurs clé s'avere crucial.

Studies on rainfall variability and the influence of orography and land use on the climate of Peninsular India

The present study helped to understand the trend in rainfall patterns at smaller spatial scales and the large regional differences in the variability of rainfall. The effect of land use and orography on the diurnal variability is also understood. But a better understanding on the long term variation in rainfall is possible by using a longer dataset,which may provide insight into the rainfall variation over country during the past century. The basic mechanism behind the interannual rainfall variability would be possible with numerical studies using coupled Ocean-Atmosphere models. The regional difference in the active-break conditions points to the significance of regional studies than considering India as a single unit. The underlying dynamics of diurnal variability need to be studied by making use of a high resolution model as the present study could not simulate the local onshore circulation. Also the land use modification in this study, selected a region, which is surrounded by crop land. This implies the high possibility for the conversion of the remaining region to agricultural land. Therefore the study is useful than considering idealized conditions, but the adverse effect of irrigated crop is more than non-irrigated crop. Therefore, such studies would help to understand the climate changes occurred in the recent period. The large accumulation of rainfall between 300-600 m height of western Ghats has been found but the reason behind this need to be studied, which is possible by utilizing datasets that would better represent the orography and landuse over the region in high resolution model. Similarly a detailed analysis is needed to clearly identify the causative relations of the predictors identified with the predictant and the physical reasons behind them. New approaches that include nonlinear relationships and dynamical variables from model simulations can be included in the existing statistical models to improve the skill of the models. Also the statistical models for the forecasts of monsoon have to be continually updated.

Modeling the interplay between land use, bioenergy production and climate change

Land use has become a force of global importance, considering that 34% of the Earth’s ice-free surface was covered by croplands or pastures in 2000. The expected increase in global human population together with eminent climate change and associated search for energy sources other than fossil fuels can, through land-use and land-cover changes (LUCC), increase the pressure on nature’s resources, further degrade ecosystem services, and disrupt other planetary systems of key importance to humanity. This thesis presents four modeling studies on the interplay between LUCC, increased production of biofuels and climate change in four selected world regions. In the first study case two new crop types (sugarcane and jatropha) are parameterized in the LPJ for managed Lands dynamic global vegetation model for calculation of their potential productivity. Country-wide spatial variation in the yields of sugarcane and jatropha incurs into substantially different land requirements to meet the biofuel production targets for 2015 in Brazil and India, depending on the location of plantations. Particularly the average land requirements for jatropha in India are considerably higher than previously estimated. These findings indicate that crop zoning is important to avoid excessive LUCC. In the second study case the LandSHIFT model of land-use and land-cover changes is combined with life cycle assessments to investigate the occurrence and extent of biofuel-driven indirect land-use changes (ILUC) in Brazil by 2020. The results show that Brazilian biofuels can indeed cause considerable ILUC, especially by pushing the rangeland frontier into the Amazonian forests. The carbon debt caused by such ILUC would result in no carbon savings (from using plant-based ethanol and biodiesel instead of fossil fuels) before 44 years for sugarcane ethanol and 246 years for soybean biodiesel. The intensification of livestock grazing could avoid such ILUC. We argue that such an intensification of livestock should be supported by the Brazilian biofuel sector, based on the sector’s own interest in minimizing carbon emissions. In the third study there is the development of a new method for crop allocation in LandSHIFT, as influenced by the occurrence and capacity of specific infrastructure units. The method is exemplarily applied in a first assessment of the potential availability of land for biogas production in Germany. The results indicate that Germany has enough land to fulfill virtually all (90 to 98%) its current biogas plant capacity with only cultivated feedstocks. Biogas plants located in South and Southwestern (North and Northeastern) Germany might face more (less) difficulties to fulfill their capacities with cultivated feedstocks, considering that feedstock transport distance to plants is a crucial issue for biogas production. In the fourth study an adapted version of LandSHIFT is used to assess the impacts of contrasting scenarios of climate change and conservation targets on land use in the Brazilian Amazon. Model results show that severe climate change in some regions by 2050 can shift the deforestation frontier to areas that would experience low levels of human intervention under mild climate change (such as the western Amazon forests or parts of the Cerrado savannas). Halting deforestation of the Amazon and of the Brazilian Cerrado would require either a reduction in the production of meat or an intensification of livestock grazing in the region. Such findings point out the need for an integrated/multicisciplinary plan for adaptation to climate change in the Amazon. The overall conclusions of this thesis are that (i) biofuels must be analyzed and planned carefully in order to effectively reduce carbon emissions; (ii) climate change can have considerable impacts on the location and extent of LUCC; and (iii) intensification of grazing livestock represents a promising venue for minimizing the impacts of future land-use and land-cover changes in Brazil.

Understanding Recreational Services of Urban Riverfront Space for Planning Purposes

In the process of urbanization, natural and semi-natural landscapes are increasingly cherished as open space and recreational resource. Urban rivers are part of this kind of resource and thus play an important role in managing urban resilience and health. Employing the example of Tianjin, this doctoral dissertation research aims at learning to understand how to plan and design for the interface zones between urban water courses and for the land areas adjacent to such water courses. This research also aims at learning how to link waterfront space with other urban space in order to make a recreational space system for the benefit of people. Five questions of this dissertation are: 1) what is the role of rivers in spatial and open space planning? 2) What are the human needs regarding outdoor open space? 3) How do river and water front spatial structures affect people's recreational activities? 4) How to define the recreational service of urban river and waterfront open space? 5) How might answering these question change planning and design of urban open space? Quantitative and qualitative empirical approaches were combined in this study for which literature review and theoretical explorations provide the basis. Empirical investigations were conducted in the city of Tianjin. The quantitative approach includes conducting 267 quantitative interviews, and the qualitative approach includes carrying out field observations and mappings. GIS served to support analysis and visualization of empirical information that was generated through this study. By responding to the five research questions, findings and lessons include the following: 1) In the course of time rivers have gained importance in all levels and scales of spatial planning and decision making. Regarding the development of ecological networks, mainly at national scale, rivers are considered significant linear elements. Regarding regional and comprehensive development, river basins and watersheds are often considered as the structural link for strategic ecological, economic, social and recreational planning. For purposes of urban planning, particularly regarding recreational services in cities, the distribution of urban open spaces often follows the structure of river systems. 2) For the purpose of classifying human recreational needs that relate to outdoor open space Maslow's hierarchy of human needs serves as theoretical basis. The classes include geographical, safety, physiological, social and aesthetic need. These classes serve as references while analyzing river and waterfront open space and other kinds of open space. 3) Regarding the question how river and waterfront spatial structures might affect people's recreational activities, eight different landscape units were identified and compared in the case study area. Considering the thermal conditions of Tianjin, one of these landscape units was identified as affording the optimal spatial arrangement which mostly meets recreational needs. The size and the shape of open space, and the plants present in an open space have been observed as being most relevant regarding recreational activities. 4) Regarding the recreational service of urban river and waterfront open space the results of this research suggest that the recreational service is felt less intensively as the distances between water 183 front and open space user’s places of residence are increasing. As a method for estimating this ‘Service Distance Effect’ the following formula may be used: Y = a*ebx. In this equation Y means the ‘Service Distance’ between homes and open space, and X means the percentage of the people who live within this service distance. Coefficient "a" represents the distance of the residential area nearest to the water front. The coefficient "b" is a comprehensive capability index that refers to the size of the available and suitable recreational area. 5) Answers found to the questions above have implications for the planning and design of urban open space. The results from the quantitative study of recreational services of waterfront open space were applied to the assessment of river-based open space systems. It is recommended that such assessments might be done employing the network analysis function available with any GIS. In addition, several practical planning and designing suggestions are made that would help remedy any insufficient base for satisfying recreational needs. The understanding of recreational need is considered helpful for the proposing planning and designing ideas and for the changing of urban landscapes. In the course of time Tianjin's urban water system has shrunk considerably. At the same time rivers and water courses have shaped Tianjin's urban structure in noticeable ways. In the process of urbanization water has become increasingly important to the citizens and their everyday recreations. Much needs to be changed in order to improve recreational opportunities and to better provide for a livable city, most importantly when considering the increasing number of old people. Suggestions made that are based on results of this study, might be implemented in Tianjin. They are 1) to promote the quality of the waterfront open space and to make all linear waterfront area accessible recreational spaces. Then, 2), it is advisable to advocate the concept of green streets and to combine green streets with river open space in order to form an everyday recreational network. And 3) any sound urban everyday recreational service made cannot rely on only urban rivers; the whole urban structure needs to be improved, including adding small open space and optimize the form of urban communities, finally producing a multi-functional urban recreational network.

Extracting Urban Food Potential: design-based methods for digital and bodily cartography

Sweden’s recent report on Urban Sustainable Development calls out a missing link between the urban design process and citizens. This paper investigates if engaging citizens as design agents by providing a platform for alternate participation can bridge this gap, through the transfer of spatial agency and new modes of critical cartography. To assess whether this is the case, the approaches are applied to Stockholm’s urban agriculture movement in a staged intervention. The aim of the intervention was to engage citizens in locating existing and potential places for growing food and in gathering information from these sites to inform design in urban agriculture. The design-based methodologies incorporated digital and bodily interfaces for this cartography to take place. The Urban CoMapper, a smartphone digital app, captured real-time perspectives through crowd-sourced mapping. In the bodily cartography, participant’s used their bodies to trace the site and reveal their sensorial perceptions. The data gathered from these approaches gave way to a mode of artistic research for exploring urban agriculture, along with inviting artists to be engaged in the dialogues. In sum, results showed that a combination of digital and bodily approaches was necessary for a critical cartography if we want to engage citizens holistically into the urban design process as spatial agents informing urban policy. Such methodologies formed a reflective interrogation and encouraged a new intimacy with nature, in this instance, one that can transform our urban conduct by questioning our eating habits: where we get our food from and how we eat it seasonally.

Finding Spaces for Urban Food Production – Matching Spatial and Stakeholder Analysis with Urban Agriculture Approaches in the Urban Renewal Area of Dortmund-Hörde, Germany

Using the case of an economically declined neighbourhood in the post-industrial German Ruhr Area (sometimes characterized as Germany’s “Rust Belt”), we analyse, describe and conclude how urban agriculture can be used as a catalyst to stimulate and support urban renewal and regeneration, especially from a socio-cultural perspective. Using the methodological framework of participatory action research, and linking bottom-up and top-down planning approaches, a project path was developed to include the population affected and foster individual responsibility for their district, as well as to strengthen inhabitants and stakeholder groups in a permanent collective stewardship for the individual forms of urban agriculture developed and implemented. On a more abstract level, the research carried out can be characterized as a form of action research with an intended transgression of the boundaries between research, planning, design, and implementation. We conclude that by synchronously combining those four domains with intense feedback loops, synergies for the academic knowledge on the potential performance of urban agriculture in terms of sustainable development, as well as the benefits for the case-study area and the interests of individual urban gardeners can be achieved.

The Bogota – sabana region : the political economy behind the struggle to implement a sustainable urban development model

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Transformación de la ocupación del suelo en el marco de relaciones de clientelismo político. Estudio de caso: barrio Pablo Escobar, 1982-1995

El interés de este estudio de caso es evidenciar la relación que existe entre el clientelismo y las transformaciones de uso del suelo en el barrio Pablo Escobar en Medellín, entre 1982 y 1995. Se analiza como la marginación de la población del barrio Moravia conduce a la creación de capital social y el fortalecimiento de las redes sociales existentes dentro del mismo. Se muestra además cómo estas redes son aprovechadas por Pablo Escobar en su carrera política para aumentar su capital político. Por último, se muestra cómo su programa de Medellín sin Tugurios cambia el comportamiento y el uso de suelo de la población de los tugurios de Moravia, ahora reubicada en el barrio Pablo Escobar.

Simulating SOC changes in 11 land use change chronosequences from the Brazilian Amazon with RothC and Century models

Land use and land cover changes in the Brazilian Amazon have major implications for regional and global carbon (C) cycling. Cattle pasture represents the largest single use (about 70%) of this once-forested land in most of the region. The main objective of this study was to evaluate the accuracy of the RothC and Century models at estimating soil organic C (SOC) changes under forest-to-pasture conditions in the Brazilian Amazon. We used data from 11 site-specific 'forest to pasture' chronosequences with the Century Ecosystem Model (Century 4.0) and the Rothamsted C Model (RothC 26.3). The models predicted that forest clearance and conversion to well managed pasture would cause an initial decline in soil C stocks (0-20 cm depth), followed in the majority of cases by a slow rise to levels exceeding those under native forest. One exception to this pattern was a chronosequence in Suia-Missu, which is under degraded pasture. In three other chronosequences the recovery of soil C under pasture appeared to be only to about the same level as under the previous forest. Statistical tests were applied to determine levels of agreement between simulated SOC stocks and observed stocks for all the sites within the 11 chronosequences. The models also provided reasonable estimates (coefficient of correlation = 0.8) of the microbial biomass C in the 0-10 cm soil layer for three chronosequences, when compared with available measured data. The Century model adequately predicted the magnitude and the overall trend in delta C-13 for the six chronosequences where measured 813 C data were available. This study gave independent tests of model performance, as no adjustments were made to the models to generate outputs. Our results suggest that modelling techniques can be successfully used for monitoring soil C stocks and changes, allowing both the identification of current patterns in the soil and the projection of future conditions. Results were used and discussed not only to evaluate soil C dynamics but also to indicate soil C sequestration opportunities for the Brazilian Amazon region. Moreover, modelling studies in these 'forest to pasture' systems have important applications, for example, the calculation of CO, emissions from land use change in national greenhouse gas inventories. (0 2007 Elsevier B.V. All rights reserved.

Land use for England and Wales: evaluation of management options to support 'good ecological status' in surface freshwaters

This paper analyses historic records of agricultural land use and management for England and Wales from 1931 and 1991 and uses export coefficient modelling to hindcast the impact of these practices on the rates of diffuse nitrogen (N) and phosphorus (P) export to water bodies for each of the major geo-climatic regions of England and Wales. Key trends indicate the importance of animal agriculture as a contributor to the total diffuse agricultural nutrient loading on waters, and the need to bring these sources under control if conditions suitable for sustaining 'Good Ecological Status' under the Water Framework Directive are to be generated. The analysis highlights the importance of measuring changes in nutrient loading in relation to the catchment-specific baseline state for different water bodies. The approach is also used to forecast the likely impact of broad regional scale scenarios on nutrient export to waters and highlights the need to take sensitive land out of production, introduce ceilings on fertilizer use and stocking densities, and controls on agricultural practice in higher risk areas where intensive agriculture is combined with a low intrinsic nutrient retention capacity, although the uncertainties associated with the modelling applied at this scale should be taken into account in the interpretation of model output. The paper advocates the need for a two-tiered approach to nutrient management, combining broad regional policies with targeted management in high risk areas at the catchment and farm scale.