Topology of the three-qubit space of entanglement types

The three-qubit space of entanglement types is the orbit space of the local unitary action on the space of three-qubit pure states, and hence describes the types of entanglement that a system of three qubits can achieve. We show that this orbit space is homeomorphic to a certain subspace of R^6, which we describe completely. We give a topologically based classification of three-qubit entanglement types, and we argue that the nontrivial topology of the three-qubit space of entanglement types forbids the existence of standard states with the convenient properties of two-qubit standard states.Comment: 9 pages, 3 figures, v2 adds a referenc

Identifying Highly Connected Counties Compensates for Resource Limitations when Evaluating National Spread of an Invasive Pathogen

Surveying invasive species can be highly resource intensive, yet near-real-time evaluations of invasion progress are important resources for management planning. In the case of the soybean rust invasion of the United States, a linked monitoring, prediction, and communication network saved U.S. soybean growers approximately $200 M/yr. Modeling of future movement of the pathogen (Phakopsora pachyrhizi) was based on data about current disease locations from an extensive network of sentinel plots. We developed a dynamic network model for U.S. soybean rust epidemics, with counties as nodes and link weights a function of host hectarage and wind speed and direction. We used the network model to compare four strategies for selecting an optimal subset of sentinel plots, listed here in order of increasing performance: random selection, zonal selection (based on more heavily weighting regions nearer the south, where the pathogen overwinters), frequency-based selection (based on how frequently the county had been infected in the past), and frequency-based selection weighted by the node strength of the sentinel plot in the network model. When dynamic network properties such as node strength are characterized for invasive species, this information can be used to reduce the resources necessary to survey and predict invasion progress

Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon

<p>Abstract</p> <p>Background</p> <p>Several recent studies have demonstrated the use of Roche 454 sequencing technology for <it>de novo </it>transcriptome analysis. Low error rates and high coverage also allow for effective SNP discovery and genetic diversity estimates. However, genetically diverse datasets, such as those sourced from natural populations, pose challenges for assembly programs and subsequent analysis. Further, estimating the effectiveness of transcript discovery using Roche 454 transcriptome data is still a difficult task.</p> <p>Results</p> <p>Using the Roche 454 FLX Titanium platform, we sequenced and assembled larval transcriptomes for two butterfly species: the Propertius duskywing, <it>Erynnis propertius </it>(Lepidoptera: Hesperiidae) and the Anise swallowtail, <it>Papilio zelicaon </it>(Lepidoptera: Papilionidae). The Expressed Sequence Tags (ESTs) generated represent a diverse sample drawn from multiple populations, developmental stages, and stress treatments.</p> <p>Despite this diversity, > 95% of the ESTs assembled into long (> 714 bp on average) and highly covered (> 9.6× on average) contigs. To estimate the effectiveness of transcript discovery, we compared the number of bases in the hit region of unigenes (contigs and singletons) to the length of the best match silkworm (<it>Bombyx mori</it>) protein--this "ortholog hit ratio" gives a close estimate on the amount of the transcript discovered relative to a model lepidopteran genome. For each species, we tested two assembly programs and two parameter sets; although CAP3 is commonly used for such data, the assemblies produced by Celera Assembler with modified parameters were chosen over those produced by CAP3 based on contig and singleton counts as well as ortholog hit ratio analysis. In the final assemblies, 1,413 <it>E. propertius </it>and 1,940 <it>P. zelicaon </it>unigenes had a ratio > 0.8; 2,866 <it>E. propertius </it>and 4,015 <it>P. zelicaon </it>unigenes had a ratio > 0.5.</p> <p>Conclusions</p> <p>Ultimately, these assemblies and SNP data will be used to generate microarrays for ecoinformatics examining climate change tolerance of different natural populations. These studies will benefit from high quality assemblies with few singletons (less than 26% of bases for each assembled transcriptome are present in unassembled singleton ESTs) and effective transcript discovery (over 6,500 of our putative orthologs cover at least 50% of the corresponding model silkworm gene).</p

A brain-spinal interface (BSI) system-on-chip (SoC) for closed-loop cortically-controlled intraspinal microstimulation

This paper reports on a fully miniaturized brain-spinal interface system for closed-loop cortically-controlled intraspinal microstimulation (ISMS). Fabricated in AMS 0.35 µm two-poly four-metal complementary metal–oxide–semiconductor technology, this system-on-chip measures ~ 3.46 mm × 3.46 mm and incorporates two identical 4-channel modules, each comprising a spike-recording front-end, embedded digital signal processing (DSP) unit, and programmable stimulating back-end. The DSP unit is capable of generating multichannel trigger signals for a wide array of ISMS triggering patterns based on real-time discrimination of a programmable number of intracortical neural spikes within a pre-specified time-bin duration via thresholding and user-adjustable time–amplitude windowing. The system is validated experimentally using an anesthetized rat model of a spinal cord contusion injury at the T8 level. Multichannel neural spikes are recorded from the cerebral cortex and converted in real time into electrical stimuli delivered to the lumbar spinal cord below the level of the injury, resulting in distinct patterns of hindlimb muscle activation

A cautionary tale of pyridoxine toxicity in cystathionine beta‐synthase deficiency detected by two‐tier newborn screening highlights the need for clear pyridoxine dosing guidelines

Classic homocystinuria is due to deficiency of cystathionine beta‐synthase (CBS), a pyridoxine‐dependent enzyme that, depending on the molecular variants, may be co‐factor responsive. Elevated methionine is often used as the primary analyte to detect CBS deficiency (CBSD) on newborn screening (NBS), but is limited by increased detection of other biochemical disorders with less clear clinical significance such as methionine aminotransferase (MAT) I/III heterozygotes. Our state has implemented a two‐tier NBS algorithm for CBSD that successfully reduced the number of MATI/III heterozygotes, yet effectively detected a mild, co‐factor responsive form of CBSD. After initial diagnosis, newborns with CBSD often undergo a pyridoxine challenge with high‐dose pyridoxine to determine responsiveness. Here we describe our NBS‐identified patient with a mild form of pyridoxine responsive CBSD who developed respiratory failure and rhabdomyolysis consistent with pyridoxine toxicity during a pyridoxine challenge. This case highlights the need for weight‐based dosing and duration recommendations for pyridoxine challenge in neonates.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/163455/2/ajmga61815.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163455/1/ajmga61815_am.pd

An atomic boson sampler

A boson sampler implements a restricted model of quantum computing. It is defined by the ability to sample from the distribution resulting from the interference of identical bosons propagating according to programmable, non-interacting dynamics. Here, we demonstrate a new combination of tools for implementing boson sampling using ultracold atoms in a two-dimensional, tunnel-coupled optical lattice. These tools include fast and programmable preparation of large ensembles of nearly identical bosonic atoms ($99.5^{+0.5}_{-1.6}\;\%$ indistinguishability) by means of rearrangement with optical tweezers and high-fidelity optical cooling, propagation for variable evolution time in the lattice with low loss ($5.0(2)\;\%$, independent of evolution time), and high fidelity detection of the atom positions after their evolution (typically $99.8(1)\;\%$). With this system, we study specific instances of boson sampling involving up to $180$ atoms distributed among $\sim 1000$ sites in the lattice. Direct verification of a given boson sampling distribution is not feasible in this regime. Instead, we introduce and perform targeted tests to determine the indistinguishability of the prepared atoms, to characterize the applied family of single particle unitaries, and to observe expected bunching features due to interference for a large range of atom numbers. When extended to interacting systems, our work demonstrates the core capabilities required to directly assemble ground and excited states in simulations of various Hubbard models.Comment: 20 pages, 7 figures (main text and methods); 8 pages, 2 figures (supplemental materials

Dating the Cryptococcus gattii Dispersal to the North American Pacific Northwest.

The emergence of Cryptococcus gattii, previously regarded as a predominantly tropical pathogen, in the temperate climate of the North American Pacific Northwest (PNW) in 1999 prompted several questions. The most prevalent among these was the timing of the introduction of this pathogen to this novel environment. Here, we infer tip-dated timing estimates for the three clonal C.&nbsp;gattii populations observed in the PNW, VGIIa, VGIIb, and VGIIc, based on whole-genome sequencing of 134 C.&nbsp;gattii isolates and using Bayesian evolutionary analysis by sampling trees (BEAST). We estimated the nucleotide substitution rate for each lineage (1.59 × 10-8, 1.59 × 10-8, and 2.70 × 10-8, respectively) to be an order of magnitude higher than common neutral fungal mutation rates (2.0 × 10-9), indicating a microevolutionary rate (e.g., successive clonal generations in a laboratory) in comparison to a species' slower, macroevolutionary rate (e.g., when using fossil records). The clonal nature of the PNW C.&nbsp;gattii emergence over a narrow number of years would therefore possibly explain our higher mutation rates. Our results suggest that the mean time to most recent common ancestor for all three sublineages occurred within the last 60 to 100&nbsp;years. While the cause of C.&nbsp;gattii dispersal to the PNW is still unclear, our research estimates that the arrival is neither ancient nor very recent (i.e., &lt;25 years ago), making a strong case for an anthropogenic introduction. IMPORTANCE The recent emergence of the pathogenic fungus Cryptococcus gattii in the Pacific Northwest (PNW) resulted in numerous investigations into the epidemiological and enzootic impacts, as well as multiple genomic explorations of the three primary molecular subtypes of the fungus that were discovered. These studies lead to the general conclusion that the subtypes identified likely emerged out of Brazil. Here, we conducted genomic dating analyses to determine the ages of the various lineages seen in the PNW and propose hypothetical causes for the dispersal events. Bayesian evolutionary analysis strongly suggests that these independent fungal populations in the PNW are all 60 to 100 years old, providing a timing that is subsequent to the opening of the Panama Canal, which allowed for more direct shipping between Brazil and the western North American coastline, a possible driving event for these fungal translocation events

Lack of Toluene-Induced Dominant Lethals in Rats

Author Institution: Department of Biology, Central State UniversityThe mutagenic potential of toluene was investigated with the dominant lethal mutation assay. Male Sprague Dawley rats (8-10 wk old) were injected intraperitoneally for 5 consecutive days with 346 and 692 mg per kg body weight of toluene in corn oil. To analyze for the effect of toluene on several germ cell stages, each male was mated with one untreated, virgin female per week for up to 7 weeks. Females were sacrificed 14 to 17 d after insemination for analysis of their uterine contents. The total number of implantations and the number of dead and living embryos per pregnant female were determined. From these data the dominant lethal mutation index was calculated. There was no significant effect of toluene on the number of implantations (total, dead, or alive) per pregnant female per week. The different stages of spermatogenesis from late primary spermatocyte to fully mature sperm were not affected by the action of toluene as measured by the dominant lethal mutation assay. The dominant lethal mutation indices were small positive and negative percentages, suggesting that toluene did not induce dominant lethal mutations in the germ cells of male Sprague Dawley rats under the conditions tested

A Neural Region of Abstract Working Memory

■ Over 350 years ago, Descartes proposed that the neural basis of consciousness must be a brain region in which sen-sory inputs are combined. Using fMRI, we identified at least one such area for working memory, the limited information held in mind, described by William James as the trailing edge of consciousness. Specifically, a region in the left intraparietal sulcus was found to demonstrate load-dependent activity for either visual stimuli (colored squares) or a combination of vi-sual and auditory stimuli (spoken letters). This result was repli-cated across two experiments with different participants and methods. The results suggest that this brain region, previously well known for working memory of visually presented materials, actually holds or refers to information from more than one modality.