Visual Performance Fields: Frames of Reference

Performance in most visual discrimination tasks is better along the horizontal than the vertical meridian (Horizontal-Vertical Anisotropy, HVA), and along the lower than the upper vertical meridian (Vertical Meridian Asymmetry, VMA), with intermediate performance at intercardinal locations. As these inhomogeneities are prevalent throughout visual tasks, it is important to understand the perceptual consequences of dissociating spatial reference frames. In all studies of performance fields so far, allocentric environmental references and egocentric observer reference frames were aligned. Here we quantified the effects of manipulating head-centric and retinotopic coordinates on the shape of visual performance fields. When observers viewed briefly presented radial arrays of Gabors and discriminated the tilt of a target relative to homogeneously oriented distractors, performance fields shifted with head tilt (Experiment 1), and fixation (Experiment 2). These results show that performance fields shift in-line with egocentric referents, corresponding to the retinal location of the stimulus

Moduli backreaction and supersymmetry breaking in string-inspired inflation models

We emphasize the importance of effects from heavy fields on supergravity models of inflation. We study, in particular, the backreaction of stabilizer fields and geometric moduli in the presence of supersymmetry breaking. Many effects do not decouple even if those fields are much heavier than the inflaton field. We apply our results to successful models of Starobinsky-like inflation and natural inflation. In most scenarios producing a plateau potential it proves difficult to retain the flatness of the potential after backreactions are taken into account. Some of them are incompatible with non-perturbative moduli stabilization. In natural inflation there exist a number of models which are not constrained by backreactions at all. In those cases the correction terms from heavy fields have the same inflaton-dependence as the uncorrected potential, so that inflation may be possible even for very large gravitino masses.Comment: 29 pages, 1 figure, comments added, subsection 2.3 added, published versio

Genetic architecture of host proteins involved in SARS-CoV-2 infection

Understanding the genetic architecture of host proteins interacting with SARS-CoV-2 or mediating the maladaptive host response to COVID-19 can help to identify new or repurpose existing drugs targeting those proteins. We present a genetic discovery study of 179 such host proteins among 10,708 individuals using an aptamer-based technique. We identify 220 host DNA sequence variants acting in cis (MAF 0.01-49.9%) and explaining 0.3-70.9% of the variance of 97 of these proteins, including 45 with no previously known protein quantitative trait loci (pQTL) and 38 encoding current drug targets. Systematic characterization of pQTLs across the phenome identified protein-drug-disease links and evidence that putative viral interaction partners such as MARK3 affect immune response. Our results accelerate the evaluation and prioritization of new drug development programmes and repurposing of trials to prevent, treat or reduce adverse outcomes. Rapid sharing and detailed interrogation of results is facilitated through an interactive webserver (https://omicscience.org/apps/covidpgwas/).We further acknowledge support for genomics from the Medical Research Council (MC_PC_13046). Proteomic measurements were supported and governed by a collaboration agreement between the University of Cambridge and Somalogic. JCZ and VPWA are supported by a 4-year Wellcome Trust PhD Studentship and the Cambridge Trust, CL, EW, and NJW are funded by the Medical Research Council (MC_UU_12015/1). NJW and ADH are an NIHR Senior Investigator. GK is supported by grants from the National Institute on Aging (NIA): R01 AG057452, RF1 AG058942, RF1 AG059093, U01 AG061359, and U19 AG063744. MR acknowledges funding from the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001134), the UK Medical Research Council (FC001134), and the Wellcome Trust (FC001134). ERG is supported by the National Human Genome Research Institute of the National Institutes of Health under Award Numbers R35HG010718 and R01HG011138. JR is supported by the German Federal Ministry of Education and Research (BMBF) within the framework of the e:Med research and funding concept (grant no. 01ZX1912D). This work was supported by the UCL British Heart Foundation Research Accelerator Award (AA/18/6/34223), the National Institute for Health Research University College London Hospitals Biomedical Research Centre, and arises from one of the national "Covid-19 Cardiovascular Disease Flagship Projects" designated by the NIHR-BHF Cardiovascular Partnership

Exploring the potential of phone call data to characterize the relationship between social network and travel behavior

[EN] Social network contacts have significant influence on individual travel behavior. However, transport models rarely consider social interaction. One of the reasons is the difficulty to properly model social influence based on the limited data available. Non-conventional, passively collected data sources, such as Twitter, Facebook or mobile phones, provide large amounts of data containing both social interaction and spatiotemporal information. The analysis of such data opens an opportunity to better understand the influence of social networks on travel behavior. The main objective of this paper is to examine the relationship between travel behavior and social networks using mobile phone data. A huge dataset containing billions of registers has been used for this study. The paper analyzes the nature of co-location events and frequent locations shared by social network contacts, aiming not only to provide understanding on why users share certain locations, but also to quantify the degree in which the different types of locations are shared. Locations have been classified as frequent (home, work and other) and non-frequent. A novel approach to identify co-location events based on the intersection of users' mobility models has been proposed. Results show that other locations different from home and work are frequently associated to social interaction. Additionally, the importance of non-frequent locations in co-location events is shown. Finally, the potential application of the data analysis results to improve activity-based transport models and assess transport policies is discussed.The authors would like to thank the anonymous reviewers for their valuable comments and suggestions to improve the quality of the paper. The research leading to these results has received funding from the European Union Seventh Framework Programme FP7/2007-2013 under grant agreement no 318367 (EUNOIA project) and no 611307 (INSIGHT project). The work of ML has been funded under the PD/004/2013 project, from the Conselleria de Educacion, Cultura y Universidades of the Government of the Balearic Islands and from the European Social Fund through the Balearic Islands ESF operational program for 2013-2017.Picornell Tronch, M.; Ruiz Sánchez, T.; Lenormand, M.; Ramasco, JJ.; Dubernet, T.; Frías-Martínez, E. (2015). Exploring the potential of phone call data to characterize the relationship between social network and travel behavior. Transportation. 42(4):647-668. https://doi.org/10.1007/s11116-015-9594-1S647668424Ahas, R., Aasa, A., Silm, S., Tiru, M.: Daily rhythms of suburban commuters’ movements in the tallinn metropolitan area: case study with mobile positioning data. Transp. Res. Part C 18, 45–54 (2010)Arentze, T.,Timmermans, H. J.: social networks, social interactions and activity-travel behavior: a framework for micro-simulation. Paper presented at the 85th annual meeting of the Transportation Research Board, Washington, D. C., Jan 2006 (2006)Arentze, T., Timmermans, H.: Social networks, social interactions, and activity-travel behavior: a framework for microsimulation. Environ. Plan. 35, 1012–1027 (2008)Axhausen, K.W.: Social networks and travel: some hypotheses. In: Donaghy, K.P., Poppelreuter, S., Rudinger, G. (eds.) Social Aspects of Sustainable Transport: Transatlantic Perspectives, pp. 90–108. Ashgate, Aldershot (2005)Bagrow, J.P., Lin, Y.-R.: Mesoscopic structure and social aspects of human mobility. PLoS One 7(5), 1–11 (2012)Bar-Gera, H.: Evaluation of a cellular phone-based system for measurements of traffic speeds and travel times: a case study from israel. Transp. Res. Part C 15(2007), 380–391 (2007)Becker, R.A., Cáceres, R., Hanson, K., Loh, J.M., Urbanek, S., Varshavsky, A., Volinsky, C.: A tale of one city: using cellular network data for urban planning. Pervasive Comput. IEEE 10(4), 18–26 (2011)Brockmann, D., Hufnagel, L., Geisel, T.: The scaling laws of human travel. Nature 439, 462 (2006)Caceres, N., Wideberg, J.P., Benitez, F.G.: Deriving origin–destination data from a mobile phone network. IET Intell. Transp. Syst. 1(1), 5–26 (2007)Caceres, N., Wideberg, J.P., Benitez, F.G.: Review of traffic data estimations extracted from cellular networks. IET Intell. Transp. Syst. 2(3), 179–192 (2008)Caceres, N., Romero, L.M., Benitez, F.G., Castillo, J.M.D.: Traffic flow estimation models using cellular phone data. IEEE Trans. Intell. Transp. Syst. 13(3), 1430–1441 (2012)Calabrese, F., Pereira, F. C., Lorenzo, G. D., Liu, L., Ratti, C.: The geography of taste: analyzing cell-phone mobility and social events. In: Proceedings of IEEE International Conference on Pervasive Computing (2010)Calabrese, F., Smoreda, Z., Blondel, V.D., Ratti, C.: Interplay between telecommunications and face-to-face interactions: a study using mobile phone data. PLoS One 6(7), e20814 (2011a). doi: 10.1371/journal.pone.0020814Calabrese, F., Lorenzo, G.D., Liu, L., Ratti, C.: Estimating origin-destination flows using mobile phone location data. Pervasive Comput. IEEE 10(4), 36–44 (2011b)Carrasco, J.A., Miller, E.J.: Exploring the propensity to perform social activities: social networks approach. Transportation 33, 463–480 (2006)Carrasco, J.A., Hogan, B., Wellman, B., Miller, E.J.: Collecting social network data to study social activity-travel behaviour: an egocentric approach. Environ. Plan. B 35(6), 961–980 (2008a)Carrasco, J.A., Hogan B., Wellman B., Miller E. J.: Agency in social activity and ICT interactions: The role of social networks in time and space, Tijdschrift voor Economische en Sociale Geografie (J. Eco. Soc. Geogr.), 99(5), 562–583 (2008b)Carrasco, J.A., Miller, E.J., Wellman, B.: How far and with whom do people socialize? Empirical evidence about the distance between social network members. Transp. Res. Rec. 2076, 114–122 (2008b)Carrasco, J.A., Miller, E.J.: The social dimension in action: a multilevel, personal networks model of social activity frequency. Transp. Res. Part A 43(1), 90–104 (2009)Chen, C., Mei, Y.: Does distance still matter in facilitating social ties? The roles of mobility patterns and the built environment. Presented at 93rd TRB annual meeting (2014)Cho E., Myers S.A., Leskovek J.: Friendship and mobility: user movement in location-based social networks. In: KDD ‘11 Proceedings of the 17th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 1082–1090 (2011)Clifton, K.J.: The social context of travel behavior. In: Zmud, J., et al. (eds.) Transport Survey Methods: Best Practice for Decision Making, pp. 441–448. Emerald Press, London (2013)Do T., Gatica-Perez D.: Contextual conditional models for smartphone-based human mobility prediction. In: Proceedings ACM International Conference on Ubiquitous Computing, Pittsburgh, Sept (2012)Doyle, J., Hung, P., Kelly, D., Mcloone, S., Farrell, R.: Utilising mobile phone billing records for travel mode discovery. ISSC 2011, Trinity College Dublin, June (2011)Dubernet, T., Axhausen K. W.: Solution concepts for the simulation of household-level joint descision making in multi-agent travel simulation tools, paper presented at the 14th Swiss Transport Research Conference (STRC), Ascona (2014)Dugundji, E., Walker, J.: Discrete choice with social and spatial network interdependencies: an empirical example using mixed GEV models with field and “panel” effects. Transp. Res. Rec. 1921, 70–78 (2005)Eagle, N., Pentland, A., Lazer, D.: Inferring social network structure using mobile phone data. Proc. Natl. Acad. Sci. (PNAS) 106(36), 15274–15278 (2009)González, M.C., Hidalgo, C.A., Barabási, A.-L.: Understanding individual human mobility patterns. Nature 453(2008), 779–782 (2008)Gould, J.: Cell phone enabled travel surveys: the medium moves the message. In: Zmud, J., et al. (eds.) Transport Survey Methods: Best Practice for Decision Making, pp. 51–70. Emerald Press, Bingley (2013)Habib, K.N., Carrasco, J.A.: Investigating the role of social networks in start time and duration of activities: a trivariate simultaneous econometric model. Transportation Research Record: Journal of the Transportation Research Board 2230, 1–8 (2011)Hackney, Jeremy K., Kay W. Axhausen: An agent model of social network and travel behavior interdependence. Paper presented at the 11th international conference on Travel Behaviour Research, Kyoto, Aug (2006)Hackney, J., Marchal, F.: A model for coupling multi-agent social interactions and traffic simulation, in: TRB 2009 annual meeting (2009)Hackney, J., Marchal, F.: A coupled multi-agent microsimulation of social interactions and transportation behavior. Transp. Res. Part A 45, 296–309 (2011)Horni, A.: Destination choice modeling of discretionary activities in transport microsimulations, Ph.D. Thesis, ETH Zurich, Zurich (2013)Isaacman, S.,Becker, R., Caceres, R., Kobourov, S., Martonosi, M., Rowland, J., Varshavsky, A.: Identifying important places in people’s lives from cellular network data. In: Procedings International Conference on Pervasive Computing, San Francisco, June (2011)Lane, N.D., Miluzzo, E., Lu, H., Peebles, D., Choudhury, T., Campbell, A.T.: A survey of mobile phone sensing. Commun. Mag. IEEE 48(9), 140–150 (2010)Lazer, D., Pentland, A., Adamic, L., Aral, S., Barabasi, A.-L., Brewer, D., Christakis, N., Contractor, N., Fowler, J., Gutmann, M., Jebara, T., King, G., Macy, M., Roy, D., Van Alstyne, M.: Computational Social Science. Science 323, 721 (2009)Ma, H., Ronald, N., Arentze, T.A., Timmermans, H.J.P.: New credit mechanism for semicooperative agent-mediated joint activity-travel scheduling. Transp. Res. Rec. 2230, 104–110 (2011)Ma, H., Arentze, T. A., Timmermans, H. J. P.: Incorporating selfishness and altruism into dynamic joint activity-travel scheduling. Paper presented at the 13th international conference on Travel Behaviour Research (IATBR), Toronto, July (2012)Marchal, F., Nagel, K.: Allowed cooperative agents in a microsimulation to share information with each other about activity locations and about other agents, in order to optimize trip chains (2006)Molin, E.J.E., Arentze, T.A., Timmermans, H.J.P.: Social activities and travel demands : a model-based analysis of social-network data. Transp. Res. Rec. 2082, 168–175 (2007)Moore, J., Carrasco, J.A., Tudela, A.: Exploring the links between personal networks, time use, and the spatial distribution of social contacts. Transportation 40(4), 773–788 (2013)Onnela, J.-P., Saramaki, J., Hyvonen, J., Szabo, G., Lazer, D., et al.: Structure and tie strengths in mobile communication networks. Proc. Natl. Acad. Sci. U.S.A. 104, 7332–7336 (2007)Páez, A., Scott, D.M.: Social influence on travel behavior: a simulation example of the decision to telecommute. Environ. Plan. A 39(3), 647–665 (2007)Phithakkitnukoon, S., Calabrese, F., Smoreda, Z., Ratti, C.: Out of sight out of mind: how our mobile social network changes during migration. Proceedings of the IEEE International Conference on Social Computing, pp. 515–520. Cambridge University Press, Cambridge (2011)Phithakkitnukoon, S., Smoreda, Z., Olivier, P.: Socio-geography of human mobility: a study using longitudinal mobile phone data. PLoS One 7(6), e39253 (2012). doi: 10.1371/journal.pone.0039253Ronald, N.A., Arentze, T.A., Timmermans, H.J.P.: Modeling social interactions between individuals for joint activity scheduling. Transp. Res. Part B 46, 276–290 (2012a)Ronald, N.A., Dignum, V., Jonker, C., Arentze, T.A., Timmermans, H.J.P.: On the engineering of agent-based simulations of social activities with social networks. Inf. Softw. Technol. 54(6), 625–638 (2012b)Rose, G.: Mobile phones as traffic probes: practices, prospects and issues. Transp. Rev. 26(3), 275–291 (2006)Sharmeen, F., Arentze, T., Timmermans, H.: A multilevel path analysis of social network dynamics and the mutual interdependencies between face-to-face and ICT modes of social interaction in the context of life-cycle events. In: Roorda, M.J., Miller, E.J. (eds.) Travel Behaviour Research: Current Foundations, Future Prospects, pp. 411–432. Lulu Press, Toronto (2013)Sharmeen, F., Arentze, T.A., Timmermans, H.J.P.: Dynamics of face-to-face social interaction frequency: role of accessibility, urbanization, changes in geographical distance and path dependence. J. Transp. Geogr. 34, 211–220 (2014)Silm, S., Ahas, R.: The seasonal variability of population in estonian municipalities. Environ. Plan. A 42, 2527–2546 (2010)Silvis, J., Niemeier, D., D’Souza, R.: Social networks and travel behavior: report from an integrated travel diary. Paper presented at the 11th international conference on Travel Behaviour Research, Kyoto, Aug (2006)Sobolevsky, S., Szell, M., Campari, R., Couronné, T., Smoreda, Z., et al.: Delineating geographical regions with networks of human interactions in an extensive set of countries. PLoS One 8(12), e81707 (2013)Sohn, K., Kim, D.: Dynamic origin–destination flow estimation using cellular communication system. IEEE Trans. Veh. Technol. 57(5), 2703–2713 (2008)Song, C., Koren, T., Wang, P., Barabási, A.-L.: Modelling the scaling properties of human mobility. Nat. Phys. 6(2010), 818–823 (2010a)Song, C., Qu, Z., Blumm, N., Barabási, L.-L.: Limits of predictability in human mobility. Science 327(5968), 1018–1021 (2010b)Steenbruggen, J., Borzacchiello, M.T., Nijkamp, P., Scholten, H.: Mobile phone data from gsm networks for traffic parameter and urban spatial pattern assessment: A review of applications and opportunities. GeoJournal 78, 223–243 (2011). doi: 10.1007/s10708-011-9413-yVan den Berg, P., Arentze, T., Timmermans, H.J.P.: A path analysis of social networks, telecommunication and social activity–travel patterns. Transp. Res. Part C 26(2013), 256–268 (2013)Wang, H., Calabrese, F., Lorenzo, G. D., Ratti, C.: Transportation mode inference from anonymized and aggregated mobile phone call detail records. In: 13th international IEEE annual conference on intelligent transportation systems, 318–323 (2010)White, J. and Wells, I.: Extracting origin destination information from mobile phone data. Road transport information and Control, 19–21 Mar (2002)Yim, Y.: The state of cellular probes. California PATH Working Paper, UCB-ITS-PRR-2003-25 (2003)Ythier, J., Walker, J.L., Bierlaire, M.: The influence of social contacts and communication use on travel behavior: a smartphone-based study. In: Transportation Research Board annual meeting (2013

The Structure of n-Point One-Loop Open Superstring Amplitudes

In this article we present the worldsheet integrand for one-loop amplitudes in maximally supersymmetric superstring theory involving any number n of massless open string states. The polarization dependence is organized into the same BRST invariant kinematic combinations which also govern the leading string correction to tree level amplitudes. The dimensions of the bases for both the kinematics and the associated worldsheet integrals is found to be the unsigned Stirling number S_3^{n-1} of first kind. We explain why the same combinatorial structures govern on the one hand finite one-loop amplitudes of equal helicity states in pure Yang Mills theory and on the other hand the color tensors at quadratic alpha prime order of the color dressed tree amplitude.Comment: 75 pp, 8 figs, harvmac TeX, v2: published versio

Regulation of RasGRP1 Function in T Cell Development and Activation by Its Unique Tail Domain

The Ras-guanyl nucleotide exchange factor RasGRP1 plays a critical role in T cell receptor-mediated Erk activation. Previous studies have emphasized the importance of RasGRP1 in the positive selection of thymocytes, activation of T cells, and control of autoimmunity. RasGRP1 consists of a number of well-characterized domains, which it shares with its other family members; however, RasGRP1 also contains an ∼200 residue-long tail domain, the function of which is unknown. To elucidate the physiological role of this domain, we generated knock-in mice expressing RasGRP1 without the tail domain. Further analysis of these knock-in mice showed that thymocytes lacking the tail domain of RasGRP1 underwent aberrant thymic selection and, following TCR stimulation, were unable to activate Erk. Furthermore, the deletion of the tail domain led to enhanced CD4+ T cell expansion in aged mice, as well as the production of autoantibodies. Mechanistically, the tail-deleted form of RasGRP1 was not able to traffic to the cell membrane following stimulation, indicating a potential reason for its inability to activate Erk. While the DAG-binding C1 domain of RasGRP1 has long been recognized as an important factor mediating Erk activation, we have revealed the physiological relevance of the tail domain in RasGRP1 function and control of Erk signaling

Transport most likely to cause air pollution peak exposures in everyday life: Evidence from over 2000 days of personal monitoring

Background Air quality standards are typically based on long term averages – whereas a person may encounter exposure peaks throughout the day. Exposure peaks may contribute meaningfully to health impacts beyond their contribution to long term averages, and therefore should be considered alongside longer-term exposures. We aim to define and explain peak exposure to black carbon air pollution and look at the relationship between short peak exposures and longer term personal exposure. Methods A peak detection algorithm was applied to pooled data from two independent studies. High-resolution personal black carbon monitoring was performed in 175 healthy adult volunteers for a minimum of two 24-h periods per person. At the same time, we retrieved information on the time-activity pattern. Data covered Belgium, Spain, and the United Kingdom. In total, 2053 monitoring days were included. Results Exposure profiles revealed 2.8 ± 1.6 (avg ± SD) peaks per person per day. The average black carbon concentration during a peak was 4206 ng/m³. On 5.5% of the time participants were exposed to peak concentrations, but this contributed to 21.0% of their total exposure. The short time in transport (8%), was responsible for 32.7% of the peaks. 24.1% of the measurements in transport were categorized as peak exposure; while sleeping this was only 0.9%. When considering transport modes, participants were most likely to encounter peaks while cycling (34.0%). Most peaks were encountered at rush hour, from Monday through Friday, and in the cold season. Gender and age had no impact on the presence of peaks. Daily average black carbon exposure showed only a moderate correlation with peak frequency (r = 0.44). This correlation coefficient increased when considering longer term exposure to r > 0.60 from 10 days onward. Conclusions The occurrence of peaks varied substantially over time, across microenvironments and transport modes. Daily average exposure was moderately correlated with peak frequency. Real-time air pollution alerting systems may use the peak detection algorithm to support citizens in self-management of air pollution health effects

bioNMF: a versatile tool for non-negative matrix factorization in biology

BACKGROUND: In the Bioinformatics field, a great deal of interest has been given to Non-negative matrix factorization technique (NMF), due to its capability of providing new insights and relevant information about the complex latent relationships in experimental data sets. This method, and some of its variants, has been successfully applied to gene expression, sequence analysis, functional characterization of genes and text mining. Even if the interest on this technique by the bioinformatics community has been increased during the last few years, there are not many available simple standalone tools to specifically perform these types of data analysis in an integrated environment. RESULTS: In this work we propose a versatile and user-friendly tool that implements the NMF methodology in different analysis contexts to support some of the most important reported applications of this new methodology. This includes clustering and biclustering gene expression data, protein sequence analysis, text mining of biomedical literature and sample classification using gene expression. The tool, which is named bioNMF, also contains a user-friendly graphical interface to explore results in an interactive manner and facilitate in this way the exploratory data analysis process. CONCLUSION: bioNMF is a standalone versatile application which does not require any special installation or libraries. It can be used for most of the multiple applications proposed in the bioinformatics field or to support new research using this method. This tool is publicly available at

ALMA survey of Class II protoplanetary disks in Corona Australis: a young region with low disk masses

In recent years, the disk populations in a number of young star-forming regions have been surveyed with ALMA. Understanding the disk properties and their correlation with those of the central star is critical to understand planet formation. In particular, a decrease of the average measured disk dust mass with the age of the region has been observed. We conducted high-sensitivity continuum ALMA observations of 43 Class II young stellar objects in CrA at 1.3 mm (230 GHz). The typical spatial resolution is 0.3". The continuum fluxes are used to estimate the dust masses of the disks, and a survival analysis is performed to estimate the average dust mass. We also obtained new VLT/X-Shooter spectra for 12 of the objects in our sample. 24 disks are detected, and stringent limits have been put on the average dust mass of the non-detections. Accounting for the upper limits, the average disk mass in CrA is $6\pm3\,\rm M_\oplus$, significantly lower than that of disks in other young (1-3 Myr) star forming regions (e.g. Lupus) and appears consistent with the 5-10 Myr old Upper Sco. The position of the stars in our sample on the HR diagram, however, seems to confirm that that CrA has age similar to Lupus. Neither external photoevaporation nor a lower than usual stellar mass distribution can explain the low disk masses. On the other hand, a low-mass disk population could be explained if the disks are small, which could happen if the parent cloud has a low temperature or intrinsic angular momentum, or if the the angular momentum of the cloud is removed by some physical mechanism such as magnetic braking. In order to fully explain and understand the dust mass distribution of protoplanetary disks and their evolution, it may also be necessary to take into consideration the initial conditions of star and disk formation process, which may vary from region to region, and affect planet formation.Includes STF