The effects of landscape modifications on the long-term persistence of animal populations

Background: The effects of landscape modifications on the long-term persistence of wild animal populations is of crucial importance to wildlife managers and conservation biologists, but obtaining experimental evidence using real landscapes is usually impossible. To circumvent this problem we used individual-based models (IBMs) of interacting animals in experimental modifications of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of four species with contrasting life-history characteristics: skylark (Alauda arvensis), vole (Microtus agrestis), a ground beetle (Bembidion lampros) and a linyphiid spider (Erigone atra). This allows us to quantify the population implications of experimental modifications of landscape configuration and composition. Methodology/Principal Findings: Starting with a real agricultural landscape, we progressively reduced landscape complexity by (i) homogenizing habitat patch shapes, (ii) randomizing the locations of the patches, and (iii) randomizing the size of the patches. The first two steps increased landscape fragmentation. We assessed the effects of these manipulations on the long-term persistence of animal populations by measuring equilibrium population sizes and time to recovery after disturbance. Patch rearrangement and the presence of corridors had a large effect on the population dynamics of species whose local success depends on the surrounding terrain. Landscape modifications that reduced population sizes increased recovery times in the short-dispersing species, making small populations vulnerable to increasing disturbance. The species that were most strongly affected by large disturbances fluctuated little in population sizes in years when no perturbations took place. Significance: Traditional approaches to the management and conservation of populations use either classical methods of population analysis, which fail to adequately account for the spatial configurations of landscapes, or landscape ecology, which accounts for landscape structure but has difficulty predicting the dynamics of populations living in them. Here we show how realistic and replicable individual-based models can bridge the gap between non-spatial population theory and non-dynamic landscape ecology. A major strength of the approach is its ability to identify population vulnerabilities not detected by standard population viability analyses

A de Finetti Representation Theorem for Quantum Process Tomography

In quantum process tomography, it is possible to express the experimenter's prior information as a sequence of quantum operations, i.e., trace-preserving completely positive maps. In analogy to de Finetti's concept of exchangeability for probability distributions, we give a definition of exchangeability for sequences of quantum operations. We then state and prove a representation theorem for such exchangeable sequences. The theorem leads to a simple characterization of admissible priors for quantum process tomography and solves to a Bayesian's satisfaction the problem of an unknown quantum operation.Comment: 10 page

Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks

Genetic circuits require many regulatory parts in order to implement signal processing or execute algorithms in cells. A potentially scalable approach is to use dCas9, which employs small guide RNAs (sgRNAs) to repress genetic loci via the programmability of RNA:DNA base pairing. To this end, we use dCas9 and designed sgRNAs to build transcriptional logic gates and connect them to perform computation in living cells. We constructed a set of NOT gates by designing five synthetic Escherichia coli σ[subscript 70] promoters that are repressed by corresponding sgRNAs, and these interactions do not exhibit crosstalk between each other. These sgRNAs exhibit high on‐target repression (56‐ to 440‐fold) and negligible off‐target interactions (< 1.3‐fold). These gates were connected to build larger circuits, including the Boolean‐complete NOR gate and a 3‐gate circuit consisting of four layered sgRNAs. The synthetic circuits were connected to the native E. coli regulatory network by designing output sgRNAs to target an E. coli transcription factor (malT). This converts the output of a synthetic circuit to a switch in cellular phenotype (sugar utilization, chemotaxis, phage resistance).United States. Defense Advanced Research Projects Agency (CLIO N66001‐12‐C‐4016)National Institutes of Health (U.S.) (GM095765)National Institute of General Medical Sciences (U.S.) (Grant P50 GMO98792)Synthetic Biology Engineering Research Center (EEC0540879)United States. Defense Advanced Research Projects Agency (Ginkgo BioWorks. CLIO N66001‐12‐C‐4018)United States. Office of Naval Research. Multidisciplinary University Research Initiative (Grant N00014‐13‐1‐0074)United States. Office of Naval Research. Multidisciplinary University Research Initiative (Boston University. Award 4500000552)United States. Air Force Office of Scientific Research (FA9550‐11‐C‐0028)American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowship (32 CFR 168a

Patterns of Intron Gain and Loss in Fungi

Little is known about the patterns of intron gain and loss or the relative contributions of these two processes to gene evolution. To investigate the dynamics of intron evolution, we analyzed orthologous genes from four filamentous fungal genomes and determined the pattern of intron conservation. We developed a probabilistic model to estimate the most likely rates of intron gain and loss giving rise to these observed conservation patterns. Our data reveal the surprising importance of intron gain. Between about 150 and 250 gains and between 150 and 350 losses were inferred in each lineage. We discuss one gene in particular (encoding 1-phosphoribosyl-5-pyrophosphate synthetase) that displays an unusually high rate of intron gain in multiple lineages. It has been recognized that introns are biased towards the 5′ ends of genes in intron-poor genomes but are evenly distributed in intron-rich genomes. Current models attribute this bias to 3′ intron loss through a poly-adenosine-primed reverse transcription mechanism. Contrary to standard models, we find no increased frequency of intron loss toward the 3′ ends of genes. Thus, recent intron dynamics do not support a model whereby 5′ intron positional bias is generated solely by 3′-biased intron loss

Periodic Adaptive Stabilization of Rapidly Time-Varying Linear Systems

This is a post-peer-review, pre-copyedit version of an article published in Mathematics of Control, Signals, and Systems. The final authenticated version is available online at: http://dx.doi.org/https://doi.org/10.1007/s00498-019-0236-6Adaptive control deals with systems that have unknown and/or time-varying parameters. Most techniques are proven for the case in which any time variation is slow, with results for systems with fast time variations limited to those for which the time variation is of a known form or for which the plant has stable zero dynamics. In this paper, a new adaptive controller design methodology is proposed in which the time variation can be rapid and the plant may have unstable zero dynamics. Under the structural assumptions that the plant is relative degree one and that the plant uncertainty is a single scalar variable, as well as some mild regularity assumptions, it is proven that the closed-loop system is exponentially stable under fast parameter variations with persistent jumps. The proposed controller is nonlinear and periodic, and in each period the parameter is estimated and an appropriate stabilizing control signal is applied.C. Nielsen and D. E. Miller: Research supported by a grant from the Natural Sciences and Engineering Research Council of Canada

Using digital time-lapse cameras to monitor species-specific understorey and overstorey phenology in support of wildlife habitat assessment

Critical to habitat management is the understanding of not only the location of animal food resources, but also the timing of their availability. Grizzly bear (Ursus arctos) diets, for example, shift seasonally as different vegetation species enter key phenological phases. In this paper, we describe the use of a network of seven ground-based digital camera systems to monitor understorey and overstorey vegetation within species-specific regions of interest. Established across an elevation gradient in western Alberta, Canada, the cameras collected true-colour (RGB) images daily from 13 April 2009 to 27 October 2009. Fourth-order polynomials were fit to an RGB-derived index, which was then compared to field-based observations of phenological phases. Using linear regression to statistically relate the camera and field data, results indicated that 61% (r 2?= 0.61, df = 1, F?= 14.3, p?= 0.0043) of the variance observed in the field phenological phase data is captured by the cameras for the start of the growing season and 72% (r 2?= 0.72, df = 1, F?= 23.09, p?= 0.0009) of the variance in length of growing season. Based on the linear regression models, the mean absolute differences in residuals between predicted and observed start of growing season and length of growing season were 4 and 6 days, respectively. This work extends upon previous research by demonstrating that specific understorey and overstorey species can be targeted for phenological monitoring in a forested environment, using readily available digital camera technology and RGB-based vegetation indices

TCT-749 The Impact of Race and Gender on Procedural Outcomes After Alcohol Septal Ablation for Symptomatic Hypertrophic Obstructive Cardiomyopathy

Digitalitzat per Artypla

Alternative fidelity measure for quantum states

We propose an alternative fidelity measure (namely, a measure of the degree of similarity) between quantum states and benchmark it against a number of properties of the standard Uhlmann-Jozsa fidelity. This measure is a simple function of the linear entropy and the Hilbert-Schmidt inner product between the given states and is thus, in comparison, not as computationally demanding. It also features several remarkable properties such as being jointly concave and satisfying all of "Jozsa's axioms". The trade-off, however, is that it is supermultiplicative and does not behave monotonically under quantum operations. In addition, new metrics for the space of density matrices are identified and the joint concavity of the Uhlmann-Jozsa fidelity for qubit states is established.Comment: 12 pages, 3 figures. v2 includes minor changes, new references and new numerical results (Sec. IV

Stochastic priming and spatial cues orchestrate heterogeneous clonal contribution to mouse pancreas organogenesis

The pancreas arises from a small population of cells but how individual cells contribute to organ formation is unclear. Here, the authors deconstruct pancreas organogenesis into clonal units, showing that single progenitors give rise to heterogeneous multi-lineage and endocrinogenic single-lineage clones

On quantum coding for ensembles of mixed states

We consider the problem of optimal asymptotically faithful compression for ensembles of mixed quantum states. Although the optimal rate is unknown, we prove upper and lower bounds and describe a series of illustrative examples of compression of mixed states. We also discuss a classical analogue of the problem.Comment: 23 pages, LaTe