A diagram of public spaces within urban landscape as a strategy for sustainable urban planning in Chinese cities

Destruction of historical urban fabric in many Chinese cities and towns, without the possibility of its recovery as an urban asset, leads us to consider alternative strategies and criteria for formulating new urban projects, using creative urban planning instruments and strategies to provide a sense of place and identity to the urban landscape. The challenge is to set up an urban structure that constitutes a spatial reference system, a structure consisting of a set of urban landmarks that construct a system of related public spaces, endowed with collective significance and identity. Such a network could include a wide variety of urban typologies and natural elements. An important result of this strategy would be the recovery of the social and cultural values attached to the natural landscape in Chinese civilization. Hangzhou city will be analyzed as a case study

Trophic dynamics in the northern Humboldt Current system: insights from stable isotopes and stomach content analyses

The northern Humboldt Current system (NHCS) off Peru is one of the most productive world marine regions. It represents less than 0.1% of the world ocean surface but presently sustains about 10% of the world fish catch, with the Peruvian anchovy or anchoveta Engraulis ringens as emblematic fish resource. Compared with other eastern boundary upwelling systems, the higher fish productivity of the NHCS cannot be explained by a corresponding higher primary productivity. On another hand, the NHCS is the region where El Niño, and climate variability in general, is most notable. Also, surface oxygenated waters overlie an intense and extremely shallow Oxygen Minimum Zone (OMZ). In this context, the main objective of this study is to better understand the trophic flows in the NHCS using both stomach content and stable isotope analyses. The study focuses on a variety of organisms from low trophic levels such as zooplankton to top predators (seabirds and fur seals). The approach combines both long-term and specific studies on emblematic species such as anchoveta, and sardine Sardinops sagax and a more inclusive analysis considering the 'global' food web in the recent years (2008 – 2012) using stable isotope analysis. Revisiting anchovy and sardine we show that whereas phytoplankton largely dominated anchoveta and sardine diets in terms of numerical abundance, the carbon content of prey items indicated that zooplankton was by far the most important dietary component. Indeed for anchovy euphausiids contributed 67.5% of dietary carbon, followed by copepods (26.3%). Selecting the largest prey, the euphausiids, provide an energetic advantage for anchoveta in its ecosystem where oxygen depletion imposes strong metabolic constrain to pelagic fish. Sardine feed on smaller zooplankton than do anchoveta, with sardine diet consisting of smaller copepods and fewer euphausiids than anchoveta diet. Hence, trophic competition between sardine and anchovy in the northern Humboldt Current system is minimized by their partitioning of the zooplankton food resource based on prey size, as has been reported in other systems. These results suggest an ecological role for pelagic fish that challenges previous understanding of their position in the foodweb (zooplanktophagous instead of phytophagous), the functioning and the trophic models of the NHCS. Finally to obtain a more comprehensive vision of the relative trophic position of NHCS main components we used stable isotope analyses. For that purpose we analyzed the δ13C and δ15N stable isotope values of thirteen taxonomic categories collected off Peru from 2008 - 2011, i.e., zooplankton, fish, squids and air-breathing top predators. The δ15N isotope signature was strongly impacted by the species, the body length and the latitude. Along the Peruvian coast, the OMZ get more intense and shallow south of ~7.5ºS impacting the baseline nitrogen stable isotopes. Employing a linear mixed-effects modelling approach taking into account the latitudinal and body length effects, we provide a new vision of the relative trophic position of key ecosystem components. Also we confirm stomach content-based results on anchoveta Engraulis ringens and highlight the potential remarkable importance of an often neglected ecosystem component, the squat lobster Pleuroncodes monodon. Indeed, our results support the hypothesis according to which this species forage to some extent on fish eggs and larvae and can thus predate on the first life stages of exploited species. However, the δ13C values of these two species suggest that anchoveta and squat lobster do not exactly share the same habitat. This would potentially reduce some direct competition and/or predation.

Direct simulation of interface dynamics: linking capillary pressure, interfacial area and surface energy

We perform direct numerical simulations of drainage by solving Navier- Stokes equations in the pore space and employing the Volume Of Fluid (VOF) method to track the evolution of the fluid-fluid interface. After demonstrating that the method is able to deal with large viscosity contrasts and to model the transition from stable flow to viscous fingering, we focus on the definition of macroscopic capillary pressure. When the fluids are at rest, the difference between inlet and outlet pressures and the difference between the intrinsic phase average pressure coincide with the capillary pressure. However, when the fluids are in motion these quantities are dominated by viscous forces. In this case, only a definition based on the variation of the interfacial energy provides an accurate measure of the macroscopic capillary pressure and allows separating the viscous from the capillary pressure components.

Evolutionary dynamics of coding and non-coding transcriptomes.

Gene expression changes may underlie much of phenotypic evolution. The development of high-throughput RNA sequencing protocols has opened the door to unprecedented large-scale and cross-species transcriptome comparisons by allowing accurate and sensitive assessments of transcript sequences and expression levels. Here, we review the initial wave of the new generation of comparative transcriptomic studies in mammals and vertebrate outgroup species in the context of earlier work. Together with various large-scale genomic and epigenomic data, these studies have unveiled commonalities and differences in the dynamics of gene expression evolution for various types of coding and non-coding genes across mammalian lineages, organs, developmental stages, chromosomes and sexes. They have also provided intriguing new clues to the regulatory basis and phenotypic implications of evolutionary gene expression changes.

Old ferricrete landscape dismantling in Central Africa rain forest zone: formation of the present downslope iron accumulations.

Present downslope iron accumulations were investigated in the rainforest zone in southern Cameroon. Six clay and Fe-hydroxide dominated patterns have been identified and occur on the lower part of hill slopes. They can be subdivided in three different sequences, related to gentle, moderate or steep slopes. They are discontinuous with respect to the dismantling zone of the old ferricrete cap formed at Cretaceous period. They show a gradual development from a soft Fe-crust (carapace) to a vesicular facies that will, with time, cover the whole landscape again.

Shaping the interaction landscape of bioactive molecules.

MOTIVATION: Most bioactive molecules perform their action by interacting with proteins or other macromolecules. However, for a significant fraction of them, the primary target remains unknown. In addition, the majority of bioactive molecules have more than one target, many of which are poorly characterized. Computational predictions of bioactive molecule targets based on similarity with known ligands are powerful to narrow down the number of potential targets and to rationalize side effects of known molecules. RESULTS: Using a reference set of 224 412 molecules active on 1700 human proteins, we show that accurate target prediction can be achieved by combining different measures of chemical similarity based on both chemical structure and molecular shape. Our results indicate that the combined approach is especially efficient when no ligand with the same scaffold or from the same chemical series has yet been discovered. We also observe that different combinations of similarity measures are optimal for different molecular properties, such as the number of heavy atoms. This further highlights the importance of considering different classes of similarity measures between new molecules and known ligands to accurately predict their targets. CONTACT: olivier.michielin@unil.ch or vincent.zoete@unil.ch SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Brownian dynamics simulation of DNA condensation.

DNA condensation observed in vitro with the addition of polyvalent counterions is due to intermolecular attractive forces. We introduce a quantitative model of these forces in a Brownian dynamics simulation in addition to a standard mean-field Poisson-Boltzmann repulsion. The comparison of a theoretical value of the effective diameter calculated from the second virial coefficient in cylindrical geometry with some experimental results allows a quantitative evaluation of the one-parameter attractive potential. We show afterward that with a sufficient concentration of divalent salt (typically approximately 20 mM MgCl(2)), supercoiled DNA adopts a collapsed form where opposing segments of interwound regions present zones of lateral contact. However, under the same conditions the same plasmid without torsional stress does not collapse. The condensed molecules present coexisting open and collapsed plectonemic regions. Furthermore, simulations show that circular DNA in 50% methanol solutions with 20 mM MgCl(2) aggregates without the requirement of torsional energy. This confirms known experimental results. Finally, a simulated DNA molecule confined in a box of variable size also presents some local collapsed zones in 20 mM MgCl(2) above a critical concentration of the DNA. Conformational entropy reduction obtained either by supercoiling or by confinement seems thus to play a crucial role in all forms of condensation of DNA.

Stratigraphical discontinuities, tropical landscape evolution and soil distribution relationships in a case study in SE-Brazil

On a regional summit surface in the county of Piracicaba (SP) within the Peripheric Depression of São Paulo, formed of discontinued flattened tops, there is an abrupt transition between a Typic Hapludox and a Kandiudalfic Eutrudox, together with two stoneline layers. Using stratigraphical, mineralogical, and cartographic studies, this transition and the soil distribution of this surface were studied, correlating them with the different parent materials and the morphoclimatic model of landscape evolution in Southeastern Brazil. The Typic Hapludox was formed on a sandy Cenozoic deposit (Q) that overlies a pellitic deposit of the Iratí formation (Pi), representing a regional erosive discordance. Westwards to the Piracicaba River, this sequence is interrupted by a diabase sill overlain by a red clayey material which gave origin to the Kandiudalfic Eutrudox. Two post-Permian depositional events were identified by the two stonelines and stratigraphical discontinuities. The first event generated the deposition of a sandy sediment in the form of levelled alveoluses on regional barriers, most of these formed by dikes and diabase sills, probably during a drier phase. The second depositional event, leading to the deposition of the red clay was probably the dissection of the previously formed pediplane during a humid climate, followed by another pedimentation process during a later, drier period.

Comunicar la ciudad desde el paisaje: hacia una teoría del landscape branding

La necesidad de descodificar los significados inherentes al paisaje, la interactuación sociedadpaisaje (comunicación intra e interpersonal) y, más recientemente, los usos de paisaje a modo de aparador territorial mediático en el ámbito, por ejemplo, de la comunicación publicitaria, del citymarketing o del place branding (comunicación masiva), sirven para plantear el estudio de lo que, de algún modo, representa la persuasión del paisaje, la cual incluye claros tintes emocionales y simbólicos y, por tanto, también comunicacionales. El paisaje en su condición de imagen y/o rostro del territorio acumula la esencia del mensaje implícito en el espacio, posicionándose, de este modo, como la gran metáfora comunicativa de la ciudad. En este sentido, el trabajo de comunicación específico con el intangible paisajístico, unido a la reciente explosión de las denominadas geografías emocionales, plantea una teoría del mensaje territorial basada en la unión de las variables geografía, paisaje, emoción y comunicación. Históricamente, de los estudios de paisaje se han ocupado los geógrafos, arquitectos, historiadores, sociólogos o ambientólogos, entre muchos otros, sin embargo, el paisaje se ha mantenido poco explorado desde la perspectiva de la comunicación. En este sentido, es notoria la proliferación de análisis que ponen el acento en el papel que desarrolla el territorio como mediador de procesos de comunicación o en el estudio de procesos de retroalimentación entre la sociedad y sus espacios (cognición y/o percepción). El actual mercadeo identitario con los lugares se concreta en la creciente producción de marcas territoriales, las cuales acumulan, en los últimos tiempos, un importante protagonismo.