Incorporating bio-physical sciences into a decision support tool for sustainable urban planning

Deciding upon optimum planning actions in terms of sustainable urban planning involves the consideration of multiple environmental and socio-economic criteria. The transformation of natural landscapes to urban areas affects energy and material fluxes. An important aspect of the urban environment is the urban metabolism, and changes in such metabolism need to be considered for sustainable planning decisions. A spatial Decision Support System (DSS) prototyped within the European FP7-funded project BRIDGE (sustainaBle uRban plannIng Decision support accountinG for urban mEtabolism), enables accounting for the urban metabolism of planning actions, by exploiting the current knowledge and technology of biophysical sciences. The main aim of the BRIDGE project was to bridge the knowledge and communication gap between urban planners and environmental scientists and to illustrate the advantages of considering detailed environmental information in urban planning processes. The developed DSS prototype integrates biophysical observations and simulation techniques with socio-economic aspects in fiveEuropean cities, selected as case studies for the pilot application of the tool. This paper describes the design and implementation of the BRIDGE DSS prototype, illustrates some examples of use, and highlights the need for further research and development in the field

Transport Spectroscopy of Symmetry-Broken Insulating States in Bilayer Graphene

The flat bands in bilayer graphene(BLG) are sensitive to electric fields E\bot directed between the layers, and magnify the electron-electron interaction effects, thus making BLG an attractive platform for new two-dimensional (2D) electron physics[1-5]. Theories[6-16] have suggested the possibility of a variety of interesting broken symmetry states, some characterized by spontaneous mass gaps, when the electron-density is at the carrier neutrality point (CNP). The theoretically proposed gaps[6,7,10] in bilayer graphene are analogous[17,18] to the masses generated by broken symmetries in particle physics and give rise to large momentum-space Berry curvatures[8,19] accompanied by spontaneous quantum Hall effects[7-9]. Though recent experiments[20-23] have provided convincing evidence of strong electronic correlations near the CNP in BLG, the presence of gaps is difficult to establish because of the lack of direct spectroscopic measurements. Here we present transport measurements in ultra-clean double-gated BLG, using source-drain bias as a spectroscopic tool to resolve a gap of ~2 meV at the CNP. The gap can be closed by an electric field E\bot \sim13 mV/nm but increases monotonically with a magnetic field B, with an apparent particle-hole asymmetry above the gap, thus providing the first mapping of the ground states in BLG.Comment: 4 figure

Os efeitos do cigarro e do consumo de café sobre a formação óssea e a integração óssea de implantes de hidroxiapatita

The present study aims to assess the effects of cigarette smoke inhalation and/or coffee consumption on bone formation and osseous integration of a dense hydroxyapatite (DHA) implant in rats. For this study, 20 male rats were divided into four groups (n = 5): CT (control) group, CE (coffee) group, CI (cigarette) group and CC (coffee + cigarette) group. During 16 weeks, animals in the CI group were exposed to cigarette smoke inhalation equivalent to 6 cigarettes per day; specimens in the CE group drank coffee as liquid diet; and rats in the CC group were submitted to both substances. In the 6th week a 5 mm slit in the parietal bone and a 4 mm slit in the tibia were performed on the left side: the former was left open while the latter received a DHA implant. As soon as surgeries were finished, the animals returned to their original protocols and after 10 weeks of exposure they were euthanised (ethically sacrificed) and the mentioned bones collected for histological processing. Data showed that exposure to cigarette smoke inhalation and coffee consumption did not interfere in weight gain and that solid and liquid diet consumption was satisfactory. Rats in the CC group showed a decrease in bone neoformation around the tibial DHA implant (31.8 ± 2.8) as well as in bone formation in the parietal slit (28.6 ± 2.2). On their own, cigarette smoke inhalation or coffee consumption also led to diminished bone neoformation around the implant and delayed the bone repair process in relation to the CT group. However, reduction in the bone repair process was accentuated with exposure to both cigarette smoke inhalation and coffee consumption in this study.O presente estudo teve como objetivo avaliar os efeitos do tabagismo e do consumo de café, isolada ou concomitantemente, sobre a formação óssea e a osseointegração de implantes hidroxiapatita densa. Foram utilizados 20 ratos machos, divididos em quatro grupos (n = 5): grupo CT (controle); grupo CA (café); grupo CI (cigarro), e grupo CC (cigarro + café). Durante 16 semanas, os animais do grupo CI foram expostos à fumaça de seis cigarros/dia; os animais do grupo CA consumiram café como dieta líquida, e os animais do grupo CC, ambas as substâncias. Após seis semanas de exposição, uma falha óssea de 5 mm foi produzida no osso parietal esquerdo e de 4 mm, na tíbia esquerda dos animais. A falha do parietal foi mantida aberta, enquanto na tíbia corpos cerâmicos de hidroxiapatita densa (HAD) foram implantados em cavidade produzida cirurgicamente. Após as cirurgias, os animais retornaram aos protocolos experimentais e, ao término de dez semanas, foram eutanasiados, sendo as tíbias e os parietais coletados para processamento histológico. A exposição à fumaça do cigarro e o consumo de café não interferiram no ganho de peso dos animais, e os consumos de dieta líquida e sólida foram satisfatórios entre os grupos. Os animais do grupo CC apresentaram menor volume de osso neoformado ao redor do implante de HAD na tíbia (31,8 ± 2,8) e menor osteogênese na falha produzida no osso parietal (28,6 ± 2,2). O café e o cigarro consumidos isoladamente provocam a diminuição do volume de osso ao redor do implante e o atraso no processo de reparação óssea. Observou-se que o consumo de café associado à exposição à fumaça do cigarro reduziu de forma acentuada o processo de reparação óssea, no presente estudo.Universidade José do Rosário VellanoUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de MedicinaUniversidade Federal de AlfenasUniversidade Estadual de CampinasUniversidade José do Rosário Vellano Faculdade de MedicinaUNIFESP, EPMSciEL

STM Spectroscopy of ultra-flat graphene on hexagonal boron nitride

Graphene has demonstrated great promise for future electronics technology as well as fundamental physics applications because of its linear energy-momentum dispersion relations which cross at the Dirac point. However, accessing the physics of the low density region at the Dirac point has been difficult because of the presence of disorder which leaves the graphene with local microscopic electron and hole puddles, resulting in a finite density of carriers even at the charge neutrality point. Efforts have been made to reduce the disorder by suspending graphene, leading to fabrication challenges and delicate devices which make local spectroscopic measurements difficult. Recently, it has been shown that placing graphene on hexagonal boron nitride (hBN) yields improved device performance. In this letter, we use scanning tunneling microscopy to show that graphene conforms to hBN, as evidenced by the presence of Moire patterns in the topographic images. However, contrary to recent predictions, this conformation does not lead to a sizable band gap due to the misalignment of the lattices. Moreover, local spectroscopy measurements demonstrate that the electron-hole charge fluctuations are reduced by two orders of magnitude as compared to those on silicon oxide. This leads to charge fluctuations which are as small as in suspended graphene, opening up Dirac point physics to more diverse experiments than are possible on freestanding devices.Comment: Nature Materials advance online publication 13/02/201

Predicting the targeting of tail-anchored proteins to subcellular compartments in mammalian cells

This is the author accepted manuscript. The final version is available from Company of Biologists via the DOI in this record.Tail-anchored (TA) proteins contain a single transmembrane domain (TMD) at the Cterminus, anchoring them to organelle membranes where they mediate a variety of critical cellular processes. Mutations in individual TA proteins cause a number of severe inherited disorders. However, the molecular mechanisms and signals facilitating proper TA protein targeting are not fully understood, in particular in mammals. Here, we identify additional TA proteins at peroxisomes or shared by multiple organelles in mammals and reveal that a combination of TMD hydrophobicity and tail charge determines targeting to distinct organelles. Specifically, an increase in tail charge can override a hydrophobic TMD signal and re-direct a protein from the ER to peroxisomes or mitochondria and vice versa. We demonstrate that subtle alterations in those physicochemical parameters can shift TA protein targeting between organelles, explaining why peroxisomes and mitochondria share many TA proteins. Our analyses enabled us to allocate characteristic physicochemical parameters to different organelle groups. This classification allows for the first time, successful prediction of the location of uncharacterized TA proteins.We thank colleagues who provided materials (see Tables S1-S4) and acknowledge support from A. C. Magalhães, M. Almeida, D. Tuerker, S. Kuehl and C. Davies. This work was supported by the Biotechnology and Biological Sciences Research Council (BB/K006231/1 to M.S.), a Wellcome Trust Institutional Strategic Support Award (WT097835MF, WT105618MA to M.S.), the Portuguese Foundation for Science and Technology and FEDER/COMPETE (PTDC/BIA-BCM/118605/2010 to M.S.; SFRH/BD/37647/2007 to N.B.; SFRH/BPD/77619/2011 and UID/BIM/04501/2013 to D.R.). M.W., E.A.G., and M.S. are supported by Marie Curie Initial Training Network (ITN) action PerFuMe (316723)

Quantum Topologically Massive Gravity in de Sitter Space

We consider three dimensional gravity with a positive cosmological constant and non- zero gravitational Chern-Simons term. This theory has inflating de Sitter solutions and local metric degrees of freedom. The Euclidean signature partition function of the theory is evaluated including both perturbative and non-perturbative corrections. The perturbative one-loop correction is computed using heat kernel techniques. The non- perturbative corrections come from gravitational instantons with non-trivial topology which can be enumerated explicitly. We compute the sum over an infinite class of ge- ometries and show that, unlike the case of pure Einstein gravity, the partition function is finite. This demonstrates that the inclusion of non-trivial local degrees of freedom can render the sum over geometries convergent.Comment: 25 pages, 1 figure; v2: minor correction

Face Video Competition

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-01793-3_73Person recognition using facial features, e.g., mug-shot images, has long been used in identity documents. However, due to the widespread use of web-cams and mobile devices embedded with a camera, it is now possible to realise facial video recognition, rather than resorting to just still images. In fact, facial video recognition offers many advantages over still image recognition; these include the potential of boosting the system accuracy and deterring spoof attacks. This paper presents the first known benchmarking effort of person identity verification using facial video data. The evaluation involves 18 systems submitted by seven academic institutes.The work of NPoh is supported by the advanced researcher fellowship PA0022121477of the Swiss NSF; NPoh, CHC and JK by the EU-funded Mobio project grant IST-214324; NPC and HF by the EPSRC grants EP/D056942 and EP/D054818; VS andNP by the Slovenian national research program P2-0250(C) Metrology and Biomet-ric System, the COST Action 2101 and FP7-217762 HIDE; and, AAS by the Dutch BRICKS/BSIK project.Poh, N.; Chan, C.; Kittler, J.; Marcel, S.; Mc Cool, C.; Rua, E.; Alba Castro, J.... (2009). Face Video Competition. En Advances in Biometrics: Third International Conference, ICB 2009, Alghero, Italy, June 2-5, 2009. Proceedings. 715-724. https://doi.org/10.1007/978-3-642-01793-3_73S715724Messer, K., Kittler, J., Sadeghi, M., Hamouz, M., Kostyn, A., Marcel, S., Bengio, S., Cardinaux, F., Sanderson, C., Poh, N., Rodriguez, Y., Kryszczuk, K., Czyz, J., Vandendorpe, L., Ng, J., Cheung, H., Tang, B.: Face authentication competition on the BANCA database. In: Zhang, D., Jain, A.K. (eds.) ICBA 2004. LNCS, vol. 3072, pp. 8–15. Springer, Heidelberg (2004)Messer, K., Kittler, J., Sadeghi, M., Hamouz, M., Kostin, A., Cardinaux, F., Marcel, S., Bengio, S., Sanderson, C., Poh, N., Rodriguez, Y., Czyz, J., Vandendorpe, L., McCool, C., Lowther, S., Sridharan, S., Chandran, V., Palacios, R.P., Vidal, E., Bai, L., Shen, L.-L., Wang, Y., Yueh-Hsuan, C., Liu, H.-C., Hung, Y.-P., Heinrichs, A., Muller, M., Tewes, A., vd Malsburg, C., Wurtz, R., Wang, Z., Xue, F., Ma, Y., Yang, Q., Fang, C., Ding, X., Lucey, S., Goss, R., Schneiderman, H.: Face authentication test on the BANCA database. In: Int’l. Conf. Pattern Recognition (ICPR), vol. 4, pp. 523–532 (2004)Phillips, P.J., Flynn, P.J., Scruggs, T., Bowyer, K.W., Chang, J., Hoffman, K., Marques, J., Min, J., Worek, W.: Overview of the Face Recognition Grand Challenge. In: IEEE Computer Society Conference on Computer Vision and Pattern Recognition, pp. 947–954 (2005)Bailly-Baillière, E., Bengio, S., Bimbot, F., Hamouz, M., Kittler, J., Marithoz, J., Matas, J., Messer, K., Popovici, V., Porée, F., Ruiz, B., Thiran, J.-P.: The BANCA Database and Evaluation Protocol. In: Kittler, J., Nixon, M.S. (eds.) AVBPA 2003. LNCS, vol. 2688. Springer, Heidelberg (2003)Turk, M., Pentland, A.: Eigenfaces for Recognition. Journal of Cognitive Neuroscience 3(1), 71–86 (1991)Martin, A., Doddington, G., Kamm, T., Ordowsk, M., Przybocki, M.: The DET Curve in Assessment of Detection Task Performance. In: Proc. Eurospeech 1997, Rhodes, pp. 1895–1898 (1997)Bengio, S., Marithoz, J.: The Expected Performance Curve: a New Assessment Measure for Person Authentication. In: The Speaker and Language Recognition Workshop (Odyssey), Toledo, pp. 279–284 (2004)Poh, N., Bengio, S.: Database, Protocol and Tools for Evaluating Score-Level Fusion Algorithms in Biometric Authentication. Pattern Recognition 39(2), 223–233 (2005)Martin, A., Przybocki, M., Campbell, J.P.: The NIST Speaker Recognition Evaluation Program, ch. 8. Springer, Heidelberg (2005

Disentangling astroglial physiology with a realistic cell model in silico

Electrically non-excitable astroglia take up neurotransmitters, buffer extracellular K+ and generate Ca2+ signals that release molecular regulators of neural circuitry. The underlying machinery remains enigmatic, mainly because the sponge-like astrocyte morphology has been difficult to access experimentally or explore theoretically. Here, we systematically incorporate multi-scale, tri-dimensional astroglial architecture into a realistic multi-compartmental cell model, which we constrain by empirical tests and integrate into the NEURON computational biophysical environment. This approach is implemented as a flexible astrocyte-model builder ASTRO. As a proof-of-concept, we explore an in silico astrocyte to evaluate basic cell physiology features inaccessible experimentally. Our simulations suggest that currents generated by glutamate transporters or K+ channels have negligible distant effects on membrane voltage and that individual astrocytes can successfully handle extracellular K+ hotspots. We show how intracellular Ca2+ buffers affect Ca2+ waves and why the classical Ca2+ sparks-and-puffs mechanism is theoretically compatible with common readouts of astroglial Ca2+ imaging

State of the California current 2012-13: No such thing as an “average” year

This report reviews the state of the California Current System (CCS) between winter 2012 and spring 2013, and includes observations from Washington State to Baja California. During 2012, large-scale climate modes indicated the CCS remained in a cool, productive phase present since 2007. The upwelling season was delayed north of 42°N, but regions to the south, especially 33° to 36°N, experienced average to above average upwelling that persisted throughout the summer. Contrary to the indication of high production suggested by the climate indices, chlorophyll observed from surveys and remote sensing was below average along much of the coast. As well, some members of the forage assemblages along the coast experienced low abundances in 2012 surveys. Specifically, the concentrations of all lifestages observed directly or from egg densities of Pacific sardine, Sardinops sagax, and northern anchovy, Engraulis mordax, were less than previous years’ survey estimates. However, 2013 surveys and observations indicate an increase in abundance of northern anchovy. During winter 2011/2012, the increased presence of northern copepod species off northern California was consistent with stronger southward transport. Krill and small-fraction zooplankton abundances, where examined, were generally above average. North of 42°N, salps returned to typical abundances in 2012 after greater observed concentrations in 2010 and 2011. In contrast, salp abundance off central and southern California increased after a period of southward transport during winter 2011/2012. Reproductive success of piscivorous Brandt’s cormorant, Phalacrocorax penicillatus, was reduced while planktivorous Cassin’s auklet, Ptychoramphus aleuticus was elevated. Differences between the productivity of these two seabirds may be related to the available forage assemblage observed in the surveys. California sea lion pups from San Miguel Island were undernourished resulting in a pup mortality event perhaps in response to changes in forage availability. Limited biological data were available for spring 2013, but strong winter upwelling coastwide indicated an early spring transition, with the strong upwelling persisting into early summer