PyLDM - An open source package for lifetime density analysis of time-resolved spectroscopic data

Ultrafast spectroscopy offers temporal resolution for probing processes in the femto- and picosecond regimes. This has allowed for investigation of energy and charge transfer in numerous photoactive compounds and complexes. However, analysis of the resultant data can be complicated, particularly in more complex biological systems, such as photosystems. Historically, the dual approach of global analysis and target modelling has been used to elucidate kinetic descriptions of the system, and the identity of transient species respectively. With regards to the former, the technique of lifetime density analysis (LDA) offers an appealing alternative. While global analysis approximates the data to the sum of a small number of exponential decays, typically on the order of 2-4, LDA uses a semi-continuous distribution of 100 lifetimes. This allows for the elucidation of lifetime distributions, which may be expected from investigation of complex systems with many chromophores, as opposed to averages. Furthermore, the inherent assumption of linear combinations of decays in global analysis means the technique is unable to describe dynamic motion, a process which is resolvable with LDA. The technique was introduced to the field of photosynthesis over a decade ago by the Holzwarth group. The analysis has been demonstrated to be an important tool to evaluate complex dynamics such as photosynthetic energy transfer, and complements traditional global and target analysis techniques. Although theory has been well described, no open source code has so far been available to perform lifetime density analysis. Therefore, we introduce a python (2.7) based package, PyLDM, to address this need. We furthermore provide a direct comparison of the capabilities of LDA with those of the more familiar global analysis, as well as providing a number of statistical techniques for dealing with the regularization of noisy data

Territorial development and Community currencies

Brazilian community development banks (CDBs) have established various coordinated financial mechanisms aiming to restructure poor and peripheral local economies. Their development strategy includes an instrument to facilitate access to microfinance and a community currency, combined with the definition of vocational training programmes and support for business start- ups. Put together, these different activities constitute the endogenous and resilient territorial development strategy defined by CDBs. Little scientific literature has been devoted to the study of community currencies in this process. This article presents an overview of the symbolic meanings conveyed by the currency of Banco Palmas, the first and most prominent CDB. First, we present some historical and territorial characteristics of Banco Palmas. Second, we analyse the symbolic role of its currency: money as a bond/link (the building of the community on its territory); money as a medium for institutionalisation (of the community itself and to the exogenous actors, as to define a federative project); and finally money as a vector-catalyst (when the plasticity of money allows to explore its different formats and so, to adapt it to the new perspectives of community and territorial development)

Self-organizing & stochastic behaviors during the regeneration of hair stem cells

Stem cells cycle through active and quiescent states. Large populations of stem cells in an organ may cycle randomly or in a coordinated manner. Although stem cell cycling within single hair follicles has been studied, less is known about regenerative behavior in a hair follicle population. By combining predictive mathematical modeling with in vivo studies in mice and rabbits, we show that a follicle progresses through cycling stages by continuous integration of inputs from intrinsic follicular and extrinsic environmental signals based on universal patterning principles. Signaling from the WNT/bone morphogenetic protein activator/inhibitor pair is coopted to mediate interactions among follicles in the population. This regenerative strategy is robust and versatile because relative activator/inhibitor strengths can be modulated easily, adapting the organism to different physiological and evolutionary needs

Effects of Color Attributes on Trap Capture Rates of Chrysobothris femorata (Coleoptera: Buprestidae) and Related Species

Chrysobothris spp. (Coleoptera: Buprestidae) and other closely related buprestids are common pests of fruit, shade, and nut trees in the United States. Many Chrysobothris spp., including Chrysobothris femorata, are polyphagous herbivores. Their wide host range leads to the destruction of numerous tree species in nurseries and orchards. Although problems caused by Chrysobothris are well known, there are no reliable monitoring methods to estimate local populations before substantial damage occurs. Other buprestid populations have been effectively estimated using colored sticky traps to capture beetles. However, the attraction of Chrysobothris to specific color attributes has not been directly assessed. A multi-color trapping system was utilized to determine color attraction of Chrysobothris spp. Specific color attributes (lightness [L*], red to green [a*], blue to yellow [b*], chroma [C*], hue [h*], and peak reflectance [PR]) were then evaluated to determine beetle responses. In initial experiments with mostly primary colors, Chrysobothris were most attracted to traps with red coloration. Thus, additional experiments were performed using a range of trap colors with red reflectance values. Among these red reflectance colors, it was determined that the violet range of the electromagnetic spectrum had greater attractance to Chrysobothris. Additionally, Chrysobothris attraction correlated with hue and b*, suggesting a preference for traps with hues between red to blue. However, males and females of some Chrysobothris species showed differentiated responses. These findings provide information on visual stimulants that can be used in Chrysobothris trapping and management. Furthermore, this information can be used in conjunction with ecological theory to understand host-location methods of Chrysobothris

Reconstructing nonparametric productivity networks

Network models provide a general representation of inter-connected system dynamics. This ability to connect systems has led to a proliferation of network models for economic productivity analysis, primarily estimated non-parametrically using Data Envelopment Analysis (DEA). While network DEA models can be used to measure system performance, they lack a statistical framework for inference, due in part to the complex structure of network processes. We fill this gap by developing a general framework to infer the network structure in a Bayesian sense, in order to better understand the underlying relationships driving system performance. Our approach draws on recent advances in information science, machine learning and statistical inference from the physics of complex systems to estimate unobserved network linkages. To illustrate, we apply our framework to analyze the production of knowledge, via own and cross-disciplinary research, for a world-country panel of bibliometric data. We find significant interactions between related disciplinary research output, both in terms of quantity and quality. In the context of research productivity, our results on cross-disciplinary linkages could be used to better target research funding across disciplines and institutions. More generally, our framework for inferring the underlying network production technology could be applied to both public and private settings which entail spillovers, including intra-and inter-firm managerial decisions and public agency coordination. This framework also provides a systematic approach to model selection when the underlying network structure is unknown

Research Data Management 'Green Shoots' Pilot Programme, Final Reports

This document contains the final reports of six Research Data Management Green Shoots projects run at Imperial College in 2014

Map Supplements for The Metallic Woodboring Beetles (Coleoptera: Buprestidae) of Tennessee

Following compilation of distribution records and seasonal flight activity information for 106 metallic wood-boring beetle (Coleoptera: Buprestidae) species for Tennessee, maps were updated to provide county-level collection notations for 10,543 published records and specimen collections made from 1934 to 2013. County collection tallies across the ecoregions in Tennessee are also presented. Maps for individual species highlight gaps in key geographic areas where specimens have not been collected and can be valuable for future biosurveillance, monitoring and management efforts for these economically and ecologically important insects

Seasonal Flight Activity and Distribution of Metallic Woodboring Beetles (Coleoptera: Buprestidae) Collected in North Carolina and Tennessee

Distribution records and seasonal flight activity information for metallic woodboring beetle (Coleoptera: Buprestidae) species have not been compiled for North Carolina and Tennessee. Institutional, research, and private collections in North Carolina and Tennessee were reviewed to provide seasonal activity data of 5 subfamilies of buprestid beetle species. Label information was checked for 15,217 specimens of 135 species collected between 1901 and 2013 (North Carolina) and between 1934 and 2013 (Tennessee). These collections provided data on adult seasonal activity and county records for 121 species (4,467 specimens) and 105 species (10,750 specimens) from North Carolina and Tennessee, respectively. Two species, Agrilus carpini Knull and A. pensus Horn, are reported as New State Records for North Carolina. The data reveal key geographic areas in both states where few to no collections have been made, highlighting opportunities to validate species distributions and locations where future collecting efforts can be matched with the occurrence of larval and adult host plant resources. Seasonal activity records will inform future biosurveillance efforts for invasive and endemic pests and facilitate predictions of buprestid species that are likely to be active within the hunting flight season of Cerceris fumipennis (Say) (Hymenoptera: Crabronidae) wasps. Activity periods of the buprestids also can focus the management of selected economic pest species to times of the year when treatment efforts, particularly through use of contact insecticides, are likely to be most effective

Clinical Outcomes of Patients With Metastatic Urothelial Carcinoma After Progression to Immune Checkpoint Inhibitors: A Retrospective Analysis by the Meet-Uro Group (Meet-URO 1 Study)

Background: Immune checkpoint inhibitors (ICIs) are currently the standard of care for metastatic urothelial cancer (mUC) after the failure of previous platinum-based chemotherapy. The choice of further therapy after ICI progression is a new challenge, and scarce data support it. We aimed to examine the outcomes of mUC patients after progression to ICI, especially when receiving chemotherapy. Methods: Data were retrospectively collected from clinical records of mUC patients whose disease progressed to anti-programmed death 1 (PD-1)or programmed death ligand 1 (PD-L1) therapy at 14 Italian centers. Patients were grouped according to ICI therapy setting into SALVAGE (ie, ICI delivered ⩾ second-line therapy after platinum-based chemotherapy) and NAÏVE (ie, first-line therapy) groups. Progression-free survival (PFS) and overall survival (OS) rates were calculated using the Kaplan-Meier method and compared among subgroups. Cox regression assessed the effect of treatments after progression to ICI on OS. Objective response rate (ORR) was calculated as the sum of partial and complete radiologic responses. Results: The study population consisted of 201 mUC patients who progressed after ICI: 59 in the NAÏVE cohort and 142 in the SALVAGE cohort. Overall, 52 patients received chemotherapy after ICI progression (25.9%), 20 (9.9%) received ICI beyond progression, 115 (57.2%) received best supportive care only, and 14 (7.0%) received investigational drugs. Objective response rate to chemotherapy in the post-ICI setting was 23.1% (28.0% in the NAÏVE group and 18.5% in the SALVAGE group). Median PFS and OS to chemotherapy after ICI-PD was 5 months (95% confidence interval [CI]: 3-11) and 13 months (95% CI: 7-NA) for the NAÏVE group; 3 months (95% CI: 2-NA) and 9 months (95% CI: 6-NA) for the SALVAGE group, respectively. Overall survival from ICI initiation was 17 months for patients receiving chemotherapy (hazard ratio [HR] = 0.09, p < 0.001), versus 8 months for patients receiving ICI beyond progression (HR = 0.13, p < 0.001), and 2 months for patients who did not receive further active treatment (p < 0.001). Conclusions: Chemotherapy administered after ICI progression for mUC patients is advisable irrespective of the treatment line