Pattern scaling using ClimGen: monthly-resolution future climate scenarios including changes in the variability of precipitation

Development, testing and example applications of the pattern-scaling approach for generating future climate change projections are reported here, with a focus on a particular software application called “ClimGen”. A number of innovations have been implemented, including using exponential and logistic functions of global-mean temperature to represent changes in local precipitation and cloud cover, and interpolation from climate model grids to a finer grid while taking into account land-sea contrasts in the climate change patterns. Of particular significance is a new approach for incorporating changes in the inter-annual variability of monthly precipitation simulated by climate models. This is achieved by diagnosing simulated changes in the shape of the gamma distribution of monthly precipitation totals, applying the pattern-scaling approach to estimate changes in the shape parameter under a future scenario, and then perturbing sequences of observed precipitation anomalies so that their distribution changes according to the projected change in the shape parameter. The approach cannot represent changes to the structure of climate timeseries (e.g. changed autocorrelation or teleconnection patterns) were they to occur, but is shown here to be more successful at representing changes in low precipitation extremes than previous pattern-scaling methods

CRISPR/Cas9 and genetic screens in malaria parasites : small genomes, big impact

The ∼30 Mb genomes of the Plasmodium parasites that cause malaria each encode ∼5000 genes, but the functions of the majority remain unknown. This is due to a paucity of functional annotation from sequence homology, which is compounded by low genetic tractability compared with many model organisms. In recent years technical breakthroughs have made forward and reverse genome-scale screens in Plasmodium possible. Furthermore, the adaptation of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-Associated protein 9 (CRISPR/Cas9) technology has dramatically improved gene editing efficiency at the single gene level. Here, we review the arrival of genetic screens in malaria parasites to analyse parasite gene function at a genome-scale and their impact on understanding parasite biology. CRISPR/Cas9 screens, which have revolutionised human and model organism research, have not yet been implemented in malaria parasites due to the need for more complex CRISPR/Cas9 gene targeting vector libraries. We therefore introduce the reader to CRISPR-based screens in the related apicomplexan Toxoplasma gondii and discuss how these approaches could be adapted to develop CRISPR/Cas9 based genome-scale genetic screens in malaria parasites. Moreover, since more than half of Plasmodium genes are required for normal asexual blood-stage reproduction, and cannot be targeted using knockout methods, we discuss how CRISPR/Cas9 could be used to scale up conditional gene knockdown approaches to systematically assign function to essential genes.Instituto de BiotecnologíaFil: Ishizaki, Takahiro. Umeå University. Department of Molecular Biology; SueciaFil: Ishizaki, Takahiro. The Laboratory for Molecular Infection Medicine Sweden (MIMS); SueciaFil: Hernandez, Sophia. Umeå University. Department of Molecular Biology; SueciaFil: Hernandez, Sophia. The Laboratory for Molecular Infection Medicine Sweden (MIMS); SueciaFil: Paoletta, Martina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Paoletta, Martina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Paoletta, Martina. Umeå University. Department of Molecular Biology; SueciaFil: Paoletta, Martina. The Laboratory for Molecular Infection Medicine Sweden (MIMS); SueciaFil: Sanderson, Theo. Francis Crick Institute; Reino UnidoFil: Bushell, Ellen S. C. Umeå University. Department of Molecular Biology; SueciaFil: Bushell, Ellen S. C. The Laboratory for Molecular Infection Medicine Sweden (MIMS); Sueci

Quantum entanglement in photosynthetic light harvesting complexes

Light harvesting components of photosynthetic organisms are complex, coupled, many-body quantum systems, in which electronic coherence has recently been shown to survive for relatively long time scales despite the decohering effects of their environments. Within this context, we analyze entanglement in multi-chromophoric light harvesting complexes, and establish methods for quantification of entanglement by presenting necessary and sufficient conditions for entanglement and by deriving a measure of global entanglement. These methods are then applied to the Fenna-Matthews-Olson (FMO) protein to extract the initial state and temperature dependencies of entanglement. We show that while FMO in natural conditions largely contains bipartite entanglement between dimerized chromophores, a small amount of long-range and multipartite entanglement exists even at physiological temperatures. This constitutes the first rigorous quantification of entanglement in a biological system. Finally, we discuss the practical utilization of entanglement in densely packed molecular aggregates such as light harvesting complexes.Comment: 14 pages, 7 figures. Improved presentation, published versio

Hierarchical Equations of Motion Approach to Quantum Thermodynamics

We present a theoretical framework to investigate quantum thermodynamic processes under non-Markovian system-bath interactions on the basis of the hierarchical equations of motion (HEOM) approach, which is convenient to carry out numerically "exact" calculations. This formalism is valuable because it can be used to treat not only strong system-bath coupling but also system-bath correlation or entanglement, which will be essential to characterize the heat transport between the system and quantum heat baths. Using this formalism, we demonstrated an importance of the thermodynamic effect from the tri-partite correlations (TPC) for a two-level heat transfer model and a three-level autonomous heat engine model under the conditions that the conventional quantum master equation approaches are failed. Our numerical calculations show that TPC contributions, which distinguish the heat current from the energy current, have to be take into account to satisfy the thermodynamic laws.Comment: 9 pages, 4 figures. As a chapter of: F. Binder, L. A. Correa, C. Gogolin, J. Anders, and G. Adesso (eds.), "Thermodynamics in the quantum regime - Recent Progress and Outlook", (Springer International Publishing

Multiscale photosynthetic exciton transfer

Photosynthetic light harvesting provides a natural blueprint for bioengineered and biomimetic solar energy and light detection technologies. Recent evidence suggests some individual light harvesting protein complexes (LHCs) and LHC subunits efficiently transfer excitons towards chemical reaction centers (RCs) via an interplay between excitonic quantum coherence, resonant protein vibrations, and thermal decoherence. The role of coherence in vivo is unclear however, where excitons are transferred through multi-LHC/RC aggregates over distances typically large compared with intra-LHC scales. Here we assess the possibility of long-range coherent transfer in a simple chromophore network with disordered site and transfer coupling energies. Through renormalization we find that, surprisingly, decoherence is diminished at larger scales, and long-range coherence is facilitated by chromophoric clustering. Conversely, static disorder in the site energies grows with length scale, forcing localization. Our results suggest sustained coherent exciton transfer may be possible over distances large compared with nearest-neighbour (n-n) chromophore separations, at physiological temperatures, in a clustered network with small static disorder. This may support findings suggesting long-range coherence in algal chloroplasts, and provides a framework for engineering large chromophore or quantum dot high-temperature exciton transfer networks.Comment: 9 pages, 6 figures. A significantly updated version is now published online by Nature Physics (2012

Understanding User Behavior on Online Music Distribution Sites: A Discourse Approach

We analyze user behavior on two music distribution websites, SoundCloud.com and Last.fm, using a computer-mediated discourse analysis approach. The broad goal is to infer patterns of use that can inform the development of system/site designs to facilitate communication among online users. The specific goal is to analyze the actions users perform through comments posted to the sites. Based on a manually-coded sample of 49,324 comments, we address two research questions: What are the most common speech acts used in comments on the music distribution sites, and how, if at all, do design differences – between the two sites and between the two commenting modes available on SoundCloud – affect speech act use? From these comparisons, we identify site purpose (SoundCloud as a music sharing site, Last.fm as a music streaming site) and commenting mode (regular vs. timed comments) as important factors that contribute to the characteristics of user comments, and suggest implications of these findings for the design of music distribution sites.ye

Non-Markovian stochastic description of quantum transport in photosynthetic systems

We analyze several aspects of the transport dynamics in the LH1-RC core of purple bacteria, which consists basically in a ring of antenna molecules that transport the energy into a target molecule, the reaction center, placed in the center of the ring. We show that the periodicity of the system plays an important role to explain the relevance of the initial state in the transport efficiency. This picture is modified, and the transport enhanced for any initial state, when considering that molecules have different energies, and when including their interaction with the environment. We study this last situation by using stochastic Schr{\"o}dinger equations, both for Markovian and non-Markovian type of interactions.Comment: 21 pages, 5 figure

Impact of treatment policies on patient outcomes and resource utilization in acute cholecystitis in Japanese hospitals

BACKGROUND: Although currently available evidence predominantly recommends early laparoscopic cholecystectomy (LC) for the treatment of acute cholecystitis, this strategy has not been widely adopted in Japan. Herein, we describe a hospital-based study of patients with acute cholecystitis in 9 Japanese teaching hospitals in order to evaluate the impact of different institutional strategies in treating acute cholecystitis on overall patient outcomes and medical resource utilization. METHODS: From an administrative database and chart review, we identified 228 patients diagnosed with acute cholecystitis who underwent cholecystectomy between April 2001 and June 2003. In order to examine the relationship between hospitals' propensity to perform LC and patient outcomes and/or medical resource utilization, we divided the hospitals into three groups according to the observed to expected ratio of performing LC (LC propensity), and compared the postoperative complication rate, length of hospitalization (LOS), and medical charges. RESULTS: No hospital adopted the policy of early surgery, and the mean overall LOS among the subjects was 30.9 days. The use of laparoscopic surgery varied widely across the hospitals; the adjusted rates of LC to total cholecystectomies ranged from 9.5% to 77%. Although intra-operative complication rate was significantly higher among patients whom LC was initially attempted when compared to those whom OC was initially attempted (9.7% vs. 0%), there was no significant association between LC propensity and postoperative complication rates. Although the postoperative time to oral intake and postoperative LOS was significantly shorter in hospitals with high use of LC, the overall LOS did not differ among hospital groups with different LC propensities. Medical charges were not associated with LC propensity. CONCLUSION: Under the prevailing policy of delayed surgery, in terms of the postoperative complication rate and medical resource utilization, our study did not show the superiority of LC in treating acute cholecystitis patients. The timing of surgery and discharge was mainly determined by the institutional policy in Japan, rather than by the clinical course of the patient; however, considering the substantially less postoperative pain and shorter recovery time of LC compared to OC, LC should be actively applied for the treatment of acute cholecystitis. If the policy of early surgery were universally applied, the advantage of LC over OC may be more clearly demonstrated