Evaluating pathway enumeration algorithms in metabolic engineering case studies

The design of cell factories for the production of compounds involves the search for suitable heterologous pathways. Different strategies have been proposed to infer such pathways, but most are optimization approaches with specific objective functions, not suited to enumerate multiple pathways. In this work, we analyze two pathway enumeration algorithms based on graph representations: the Solution Structure Generation and the Find Path algorithms. Both are capable of enumerating exhaustively multiple pathways using network topology. We study their capabilities and limitations when designing novel heterologous pathways, by applying these methods on two case studies of synthetic metabolic engineering related to the production of butanol and vanillin

Giant nonlinearity and entanglement of single photons in photonic bandgap structures

Giantly enhanced cross-phase modulation with suppressed spectral broadening is predicted between optically-induced dark-state polaritons whose propagation is strongly affected by photonic bandgaps of spatially periodic media with multilevel dopants. This mechanism is shown to be capable of fully entangling two single-photon pulses with high fidelity.Comment: 7 pages, 1 figur

Urban rainwater harvesting systems: Research, implementation and future perspectives.

Published onlineJournal ArticleReviewThis is the author accepted manuscript. The final version is available from IWA Publishing via the DOI in this record.While the practice of rainwater harvesting (RWH) can be traced back millennia, the degree of its modern implementation varies greatly across the world, often with systems that do not maximize potential benefits. With a global focus, the pertinent practical, theoretical and social aspects of RWH are reviewed in order to ascertain the state of the art. Avenues for future research are also identified. A major finding is that the degree of RWH systems implementation and the technology selection are strongly influenced by economic constraints and local regulations. Moreover, despite design protocols having been set up in many countries, recommendations are still often organized only with the objective of conserving water without considering other potential benefits associated with the multiple-purpose nature of RWH. It is suggested that future work on RWH addresses three priority challenges. Firstly, more empirical data on system operation is needed to allow improved modelling by taking into account multiple objectives of RWH systems. Secondly, maintenance aspects and how they may impact the quality of collected rainwater should be explored in the future as a way to increase confidence on rainwater use. Finally, research should be devoted to the understanding of how institutional and socio-political support can be best targeted to improve system efficacy and community acceptance

LiFT: A Scalable Framework for Measuring Fairness in ML Applications

Many internet applications are powered by machine learned models, which are usually trained on labeled datasets obtained through either implicit / explicit user feedback signals or human judgments. Since societal biases may be present in the generation of such datasets, it is possible for the trained models to be biased, thereby resulting in potential discrimination and harms for disadvantaged groups. Motivated by the need for understanding and addressing algorithmic bias in web-scale ML systems and the limitations of existing fairness toolkits, we present the LinkedIn Fairness Toolkit (LiFT), a framework for scalable computation of fairness metrics as part of large ML systems. We highlight the key requirements in deployed settings, and present the design of our fairness measurement system. We discuss the challenges encountered in incorporating fairness tools in practice and the lessons learned during deployment at LinkedIn. Finally, we provide open problems based on practical experience.Comment: Accepted for publication in CIKM 202

Specific Recognition of p53 Tetramers by Peptides Derived from p53 Interacting Proteins

Oligomerization plays a major role in regulating the activity of many proteins, and in modulating their interactions. p53 is a homotetrameric transcription factor that has a pivotal role in tumor suppression. Its tetramerization domain is contained within its C-terminal domain, which is a site for numerous protein-protein interactions. Those can either depend on or regulate p53 oligomerization. Here we screened an array of peptides derived from proteins known to bind the tetrameric p53 C-terminal domain (p53CTD) and identified ten binding peptides. We quantitatively characterized their binding to p53CTD using fluorescence anisotropy. The peptides bound tetrameric p53CTD with micromolar affinities. Despite the high charge of the binding peptides, electrostatics contributed only mildly to the interactions. NMR studies indicated that the peptides bound p53CTD at defined sites. The most significant chemical shift deviations were observed for the peptides WS100B(81–92), which bound directly to the p53 tetramerization domain, and PKCα(281–295), which stabilized p53CTD in circular dichroism thermal denaturation studies. Using analytical ultracentrifugation, we found that several of the peptides bound preferentially to p53 tetramers. Our results indicate that the protein-protein interactions of p53 are dependent on the oligomerization state of p53. We conclude that peptides may be used to regulate the oligomerization of p53

Elimination, reversal, and directional bias of optical diffraction

We experimentally demonstrate the manipulation of optical diffraction, utilizing the atomic thermal motion in a hot vapor medium of electromagnetically-induced transparency (EIT). By properly tuning the EIT parameters, the refraction induced by the atomic motion may completely counterbalance the paraxial free-space diffraction and by that eliminates the effect of diffraction for arbitrary images. By further manipulation, the diffraction can be doubled, biased asymmetrically to induced deflection, or even reversed. The latter allows an experimental implementation of an analogy to a negative-index lens

Impact of system factors on the water saving efficiency of household grey water recycling

Copyright © 2010 Taylor & Francis. This is an Author's Accepted Manuscript of an article published in Desalination and Water Treatment Volume 24, Issue 1-3 (2010), available online at: http://www.tandfonline.com/10.5004/dwt.2010.1542A general concern when considering the implementation of domestic grey water recycling is to understand the impacts of system factors on water saving efficiency. Key factors include household occupancy, storage volumes, treatment capacity and operating mode. Earlier investigations of the impacts of these key factors were based on a one-tank system only. This paper presents the results of an investigation into the effect of these factors on the performance of a more realistic ‘two tank’ system with treatment using an object based household water cycle model. A Monte-Carlo simulation technique was adopted to generate domestic water appliance usage data which allows long-term prediction of the system's performance to be made. Model results reveal the constraints of treatment capacity, storage tank sizes and operating mode on percentage of potable water saved. A treatment capacity threshold has been discovered at which water saving efficiency is maximised for a given pair of grey and treated grey water tank. Results from the analysis suggest that the previous one-tank model significantly underestimates the tank volumes required for a given target water saving efficiency

Financial feasibility of end-user designed rainwater harvesting and greywater reuse systems for high water use households

© 2017, The Author(s). Water availability pressures, competing end-uses and sewers at capacity are all drivers for change in urban water management. Rainwater harvesting (RWH) and greywater reuse (GWR) systems constitute alternatives to reduce drinking water usage and in the case of RWH, reduce roof runoff entering sewers. Despite the increasing popularity of installations in commercial buildings, RWH and GWR technologies at a household scale have proved less popular, across a range of global contexts. For systems designed from the top-down, this is often due to the lack of a favourable cost-benefit (where subsidies are unavailable), though few studies have focused on performing full capital and operational financial assessments, particularly in high water consumption households. Using a bottom-up design approach, based on a questionnaire survey with 35 households in a residential complex in Bucaramanga, Colombia, this article considers the initial financial feasibility of three RWH and GWR system configurations proposed for high water using households (equivalent to >203L per capita per day). A full capital and operational financial assessment was performed at a more detailed level for the most viable design using historic rainfall data. For the selected configuration (‘Alt 2’), the estimated potable water saving was 44% (equivalent to 131m3/year) with a rate of return on investment of 6.5% and an estimated payback period of 23years. As an initial end-user-driven design exercise, these results are promising and constitute a starting point for facilitating such approaches to urban water management at the household scale