Cache-oblivious dynamic dictionaries with update/query tradeoffs

Several existing cache-oblivious dynamic dictionaries achieve O(logB N) (or slightly better O(logB N over M )) memory transfers per operation, where N is the number of items stored, M is the memory size, and B is the block size, which matches the classic B-tree data structure. One recent structure achieves the same query bound and a sometimes-better amortized update bound of O (...) memory transfers. This paper presents a new data structure, the xDict, implementing predecessor queries in O(...)worstcase memory transfers and insertions and deletions in O (...) amortized memory transfers, for any constant " with 0 < epsilon < 1. For example, the xDict achieves subconstant amortized update cost when N = ..., whereas the B-tree’s ... is subconstant only when ... is subconstant only when N = .... The xDict attains the optimal tradeoff between insertions and queries, even in the broader external-memory model, for the range where inserts cost between (...) and O(1= lg3 N) memory transfers.Danish National Research Foundation (MADALGO (Center for Massive Data Algorithmics))National Science Foundation (U.S.) (NSF Grants CCF-0541209)National Science Foundation (U.S.) (NSF Grants CCF-0541209)Computing Innovation Fellow

Copper oxide nanoparticles induce oxidative stress, DNA strand breaks and laccase activity in aquatic fungi

This work was supported by the DAAD-FCT-2010-2011 project (Micro)analysis of nanoparticles on aquatic fungi and A. Pradhan received the FCT grant SFRH/BD/45614/2008

Responses of freshwater microbial decomposers to copper oxide nanoparticles

Intensive use of nano metals increases the chance of their release into natural watercourses and may pose at risk aquatic biota and their ecological functions. In streams, microbial decomposers, predominantly aquatic fungi, play a crucial role in organic matter turnover. We investigated the impact of nano CuO on stream-dwelling microbial decomposers of leaf litter by examining i) structure and functions of fungal and bacterial communities retrieved from a non-polluted stream, and ii) the physiological and cellular responses of fungal populations isolated from metal-polluted and non-polluted streams. Results were compared to those obtained after exposure to Cu2+. The exposure to nano CuO (≤500 ppm, 4 levels) and Cu2+ (≤30 ppm, 4 levels) significantly reduced leaf decomposition, bacterial and fungal biomass, fungal reproduction and diversity. Cluster analysis of DGGE based on DNA fingerprints showed that both forms of copper induced shifts in community structure. However, impacts were stronger for bacteria than fungi. At the cellular level, increased nano CuO concentrations (≤200 ppm, 5 levels) induced activity of laccase by single fungal populations. Fungal populations from non-polluted streams were more affected by nano CuO than those from polluted streams, as shown by stronger inhibition of biomass production, accumulation of reactive oxygen species (ROS), plasma membrane disruption and DNA strand breaks. Results showed that nano forms are less toxic than ionic forms, and further suggest that the toxicity of nano CuO to freshwater microbial decomposers may occur due to induction of oxidative stress.FEDER-POFC-COMPETE and FCT supported this study (PEst-C/BIA/UI4050/2011, PTDC/AAC- AMB/121650/2010 and FCT-DAAD: 2010-2011) and AP (SFRH/BD/45614/2008)

Effects of nano CuO on aquatic decomposers: from community to cellular responses

ntensive use of metal nanoparticles increases the chance of their release into freshwaters that may pose risk to biota and associated ecological processes. In streams, microbes play a key role in detritus foodwebs transferring carbon and energy from plant litter to invertebrate shredders. Here, we investigated the effects of nano CuO (<50 nm, nanopowder, Sigma) on aquatic detritus foodwebs by examining i) leaf-litter decomposition by bacterial and fungal communities, ii) cellular damage and physiological responses of fungal populations collected from non-polluted and metal-polluted streams, and iii) survival, growth and leaf consumption by an invertebrate shredder. Results were compared with those obtained with ionic copper. Stream-dwelling microbial communities were obtained by immersion of leaves in a non- polluted stream (Portugal). Microbial communities were exposed in microcosms to nano CuO (≤ 500 mg L-1) and Cu2+ (≤ 30 mg L-1). Leaf decomposition decreased with increasing concentrations of nano and ionic copper. Both copper forms reduced biomass of bacteria and fungi, and fungal reproduction. Cu2+ had stronger effects than nano CuO. Exposure to Cu2+ and nano CuO led to a decrease in fungal diversity and to shifts in species dominance. Increased concentrations of nano CuO (≤ 100 mg L–1) stimulated extracellular laccase activity by fungi. Populations from non-polluted streams were more affected by nano CuO than those from polluted streams, as shown by a stronger inhibition of biomass production, higher Cu adsorption, higher levels of reactive oxygen species and DNA strand breaks. Acute lethality tests suggested low toxicity of nano CuO to the shredder Allogamus ligonifer. However, sublethal concentrations of nano CuO (≤ 75 mg L–1) strongly reduced leaf consumption and invertebrate growth under aqueous and dietary exposure. Concentration of leached Cu2+ in the stream water increased with increasing nano CuO concentration. Exposure to 75 mg L–1 of nano CuO via water or food led to higher Cu adsorption and accumulation in larvae. Moreover, leached Cu2+ appeared to have a role in inducing toxicity of nano CuO.Acknowledgement: FEDER-POFC-COMPETE, DAAD and FCT supported this work (PEst-C/BIA/UI4050/2011, FCT-DAAD-2010-2011, NANOECOTOX-PTDC/AAC-AMB/121650/2010) and A. Pradhan (SFRH/BD/45614/2008)

Ultra-fast detector for wide range spectral measurements

KALYPSO is a novel detector operating at line rates above 10 Mfps. The detector board holds a silicon or InGaAs linear array sensor with spectral sensitivity ranging from 400 nm to 2600 nm. The sensor is connected to a cutting-edge, custom designed, ASIC readout chip which is responsible for the remarkable frame rate. The FPGA readout architecture enables continuous data acquisition and processing in real time. This detector is currently employed in many synchrotron facilities for beam diagnostics and for the characterization of self-built Ytterbium-doped fiber laser emitting around 1050 nm with a bandwidth of 40 nm

The Tacrolimus Metabolism Rate Influences Renal Function after Kidney Transplantation

The effective calcineurin inhibitor (CNI) tacrolimus (Tac) is an integral part of the standard immunosuppressive regimen after renal transplantation (RTx). However, as a potent CNI it has nephrotoxic potential leading to impaired renal function in some cases. Therefore, it is of high clinical impact to identify factors which can predict who is endangered to develop CNI toxicity. We hypothesized that the Tac metabolism rate expressed as the blood concentration normalized by the dose (C/D ratio) is such a simple predictor. Therefore, we analyzed the impact of the C/D ratio on kidney function after RTx. Renal function was analyzed 1, 2, 3, 6, 12 and 24 months after RTx in 248 patients with an immunosuppressive regimen including basiliximab, tacrolimus, mycophenolate mofetil and prednisolone. According to keep the approach simple, patients were split into three C/D groups: fast, intermediate and slow metabolizers. Notably, compared with slow metabolizers fast metabolizers of Tac showed significantly lower estimated glomerular filtration rate (eGFR) values at all the time points analyzed. Moreover, fast metabolizers underwent more indication renal biopsies (p = 0.006) which revealed a higher incidence of CNI nephrotoxicity (p = 0.015) and BK nephropathy (p = 0.024) in this group. We herein identified the C/D ratio as an easy calculable risk factor for the development of CNI nephrotoxicity and BK nephropathy after RTx. We propose that the simple C/D ratio should be taken into account early in patient’s risk management strategies.</p

3D segmentation of plant root systems using spatial pyramid pooling and locally adaptive field-of-view inference

BackgroundThe non-invasive 3D-imaging and successive 3D-segmentation of plant root systems has gained interest within fundamental plant research and selectively breeding resilient crops. Currently the state of the art consists of computed tomography (CT) scans and reconstruction followed by an adequate 3D-segmentation process.ChallengeGenerating an exact 3D-segmentation of the roots becomes challenging due to inhomogeneous soil composition, as well as high scale variance in the root structures themselves.Approach(1) We address the challenge by combining deep convolutional neural networks (DCNNs) with a weakly supervised learning paradigm. Furthermore, (2) we apply a spatial pyramid pooling (SPP) layer to cope with the scale variance of roots. (3) We generate a fine-tuned training data set with a specialized sub-labeling technique. (4) Finally, to yield fast and high-quality segmentations, we propose a specialized iterative inference algorithm, which locally adapts the field of view (FoV) for the network.ExperimentsWe compare our segmentation results against an analytical reference algorithm for root segmentation (RootForce) on a set of roots from Cassava plants and show qualitatively that an increased amount of root voxels and root branches can be segmented.ResultsOur findings show that with the proposed DCNN approach combined with the dynamic inference, much more, and especially fine, root structures can be detected than with a classical analytical reference method.ConclusionWe show that the application of the proposed DCNN approach leads to better and more robust root segmentation, especially for very small and thin roots

Directed evolution of an orthogonal nucleoside analog kinase via fluorescence-activated cell sorting

Nucleoside analogs (NAs) represent an important category of prodrugs for the treatment of viral infections and cancer, yet the biological potency of many analogs is compromised by their inefficient activation through cellular 2′-deoxyribonucleoside kinases (dNKs). We herein report the directed evolution and characterization of an orthogonal NA kinase for 3′-deoxythymidine (ddT), using a new FACS-based screening protocol in combination with a fluorescent analog of ddT. Four rounds of random mutagenesis and DNA shuffling of Drosophila melanogaster 2′-deoxynucleoside kinase, followed by FACS analysis, yielded an orthogonal ddT kinase with a 6-fold higher activity for the NA and a 20-fold kcat/KM preference for ddT over thymidine, an overall 10 000-fold change in substrate specificity. The contributions of individual amino acid substitutions in the ddT kinase were evaluated by reverse engineering, enabling a detailed structure–function analysis to rationalize the observed changes in performance. Based on our results, kinase engineering with fluorescent NAs and FACS should prove a highly versatile method for evolving selective kinase:NA pairs and for studying fundamental aspects of the structure–function relationship in dNKs