Multi-rotor unmanned aerial vehicles (UVAs) and high-resolution compact digital cameras: a promising new method for monitoring changes to surface karst resources

In the course of doctoral research, the authors required a quick and accurate means of documenting the real-time state of surface karst features at a variety of scales in remote and challenging field conditions. The main difficulty was finding an aerial platform that was 1) consistently effective; 2) versatile; and 3) relatively inexpensive. High resolution vertical images obtained during recreational use of a small multi-rotor unmanned aerial vehicle (UAV) seemed to have the potential to answer this need. Using five case studies, the authors examine the potential of these images for mapping, documenting, and monitoring changes to surface karst resources following forestry-related activities in the coastal temperate rainforest of British Columbia (B.C.). Possible applications, strengths and limitations of this technology are discussed. The authors conclude that mini quadcopter UAVs equipped with high-resolution compact digital cameras are a promising and cost-effective new tool for karst scientists and karst managers

Continuous variable polarization entanglement, experiment and analysis

We generate and characterise continuous variable polarization entanglement between two optical beams. We first produce quadrature entanglement, and by performing local operations we transform it into a polarization basis. We extend two entanglement criteria, the inseparability criteria proposed by Duan {\it et al.}\cite{Duan00} and the Einstein-Podolsky-Rosen paradox criteria proposed by Reid and Drummond\cite{Reid88}, to Stokes operators; and use them to charactise the entanglement. Our results for the Einstein-Podolsky-Rosen paradox criteria are visualised in terms of uncertainty balls on the Poincar\'{e} sphere. We demonstrate theoretically that using two quadrature entangled pairs it is possible to entangle three orthogonal Stokes operators between a pair of beams, although with a bound $\sqrt{3}$ times more stringent than for the quadrature entanglement.Comment: 12 pages, 13 figure

Persistent near real-time passive acoustic monitoring for baleen whales from a moored buoy: System description and evaluation

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Baumgartner, M. F., Bonnell, J., Van Parijs, S. M., Corkeron, P. J., Hotchkin, C., Ball, K., Pelletier, L., Partan, J., Peters, D., Kemp, J., Pietro, J., Newhall, K., Stokes, A., Cole, T. V. N., Quintana, E., & Kraus, S. D. Persistent near real-time passive acoustic monitoring for baleen whales from a moored buoy: System description and evaluation. Methods in Ecology and Evolution, 10(9), (2019): 1476-1489, doi: 10.1111/2041-210X.13244.1. Managing interactions between human activities and marine mammals often relies on an understanding of the real‐time distribution or occurrence of animals. Visual surveys typically cannot provide persistent monitoring because of expense and weather limitations, and while passive acoustic recorders can monitor continuously, the data they collect are often not accessible until the recorder is recovered. 2. We have developed a moored passive acoustic monitoring system that provides near real‐time occurrence estimates for humpback, sei, fin and North Atlantic right whales from a single site for a year, and makes those occurrence estimates available via a publicly accessible website, email and text messages, a smartphone/tablet app and the U.S. Coast Guard's maritime domain awareness software. We evaluated this system using a buoy deployed off the coast of Massachusetts during 2015–2016 and redeployed again during 2016–2017. Near real‐time estimates of whale occurrence were compared to simultaneously collected archived audio as well as whale sightings collected near the buoy by aerial surveys. 3. False detection rates for right, humpback and sei whales were 0% and nearly 0% for fin whales, whereas missed detection rates at daily time scales were modest (12%–42%). Missed detections were significantly associated with low calling rates for all species. We observed strong associations between right whale visual sightings and near real‐time acoustic detections over a monitoring range 30–40 km and temporal scales of 24–48 hr, suggesting that silent animals were not especially problematic for estimating occurrence of right whales in the study area. There was no association between acoustic detections and visual sightings of humpback whales. 4. The moored buoy has been used to reduce the risk of ship strikes for right whales in a U.S. Coast Guard gunnery range, and can be applied to other mitigation applications.We thank Annamaria Izzi, Danielle Cholewiak and Genevieve Davis of the NOAA NEFSC for assistance in developing the analyst protocol. We are grateful to the NOAA NEFSC aerial survey observers (Leah Crowe, Pete Duley, Jen Gatzke, Allison Henry, Christin Khan and Karen Vale) and the NEAq aerial survey observers (Angela Bostwick, Marianna Hagbloom and Paul Nagelkirk). Danielle Cholewiak and three anonymous reviewers provided constructive criticism on earlier drafts of the manuscript. Funding for this project was provided by the NOAA NEFSC, NOAA Advanced Sampling Technology Work Group, Environmental Security Technology Certification Program of the U.S. Department of Defense, the U.S. Navy's Living Marine Resources Program, Massachusetts Clean Energy Center and the Bureau of Ocean Energy Management. Funding from NOAA was facilitated by the Cooperative Institute for the North Atlantic Region (CINAR) under Cooperative Agreement NA14OAR4320158

Last millennium northern hemisphere summer temperatures from tree rings: Part I: The long term context

Large-scale millennial length Northern Hemisphere (NH) temperature reconstructions have been progressively improved over the last 20 years as new datasets have been developed. This paper, and its companion (Part II, Anchukaitis et al. in prep), details the latest tree-ring (TR) based NH land air temperature reconstruction from a temporal and spatial perspective. This work is the first product of a consortium called N-TREND (Northern Hemisphere Tree-Ring Network Development) which brings together dendroclimatologists to identify a collective strategy for improving large-scale summer temperature reconstructions. The new reconstruction, N-TREND2015, utilises 54 records, a significant expansion compared with previous TR studies, and yields an improved reconstruction with stronger statistical calibration metrics. N-TREND2015 is relatively insensitive to the compositing method and spatial weighting used and validation metrics indicate that the new record portrays reasonable coherence with large scale summer temperatures and is robust at all time-scales from 918 to 2004 where at least 3 TR records exist from each major continental mass. N-TREND2015 indicates a longer and warmer medieval period (∼900–1170) than portrayed by previous TR NH reconstructions and by the CMIP5 model ensemble, but with better overall agreement between records for the last 600 years. Future dendroclimatic projects should focus on developing new long records from data-sparse regions such as North America and eastern Eurasia as well as ensuring the measurement of parameters related to latewood density to complement ring-width records which can improve local based calibration substantially

Interconnected Microphysiological Systems for Quantitative Biology and Pharmacology Studies

Microphysiological systems (MPSs) are in vitro models that capture facets of in vivo organ function through use of specialized culture microenvironments, including 3D matrices and microperfusion. Here, we report an approach to co-culture multiple different MPSs linked together physiologically on re-useable, open-system microfluidic platforms that are compatible with the quantitative study of a range of compounds, including lipophilic drugs. We describe three different platform designs - "4-way", "7-way", and "10-way" - each accommodating a mixing chamber and up to 4, 7, or 10 MPSs. Platforms accommodate multiple different MPS flow configurations, each with internal re-circulation to enhance molecular exchange, and feature on-board pneumatically-driven pumps with independently programmable flow rates to provide precise control over both intra- and inter-MPS flow partitioning and drug distribution. We first developed a 4-MPS system, showing accurate prediction of secreted liver protein distribution and 2-week maintenance of phenotypic markers. We then developed 7-MPS and 10-MPS platforms, demonstrating reliable, robust operation and maintenance of MPS phenotypic function for 3 weeks (7-way) and 4 weeks (10-way) of continuous interaction, as well as PK analysis of diclofenac metabolism. This study illustrates several generalizable design and operational principles for implementing multi-MPS "physiome-on-a-chip" approaches in drug discovery.United States. Army Research Office (Grant W911NF-12-2-0039

Protection by the NDI1 Gene against Neurodegeneration in a Rotenone Rat Model of Parkinson's Disease

It is widely recognized that mitochondrial dysfunction, most notably defects in the NADH-quinone oxidoreductase (complex I), is closely related to the etiology of sporadic Parkinson's disease (PD). In fact, rotenone, a complex I inhibitor, has been used for establishing PD models both in vitro and in vivo. A rat model with chronic rotenone exposure seems to reproduce pathophysiological conditions of PD more closely than acute mouse models as manifested by neuronal cell death in the substantia nigra and Lewy body-like cytosolic aggregations. Using the rotenone rat model, we investigated the protective effects of alternative NADH dehydrogenase (Ndi1) which we previously demonstrated to act as a replacement for complex I both in vitro and in vivo. A single, unilateral injection of recombinant adeno-associated virus carrying the NDI1 gene into the vicinity of the substantia nigra resulted in expression of the Ndi1 protein in the entire substantia nigra of that side. It was clear that the introduction of the Ndi1 protein in the substantia nigra rendered resistance to the deleterious effects caused by rotenone exposure as assessed by the levels of tyrosine hydroxylase and dopamine. The presence of the Ndi1 protein also prevented cell death and oxidative damage to DNA in dopaminergic neurons observed in rotenone-treated rats. Unilateral protection also led to uni-directional rotation of the rotenone-exposed rats in the behavioral test. The present study shows, for the first time, the powerful neuroprotective effect offered by the Ndi1 enzyme in a rotenone rat model of PD

Transcriptomic links to muscle mass loss and declines in cumulative muscle protein synthesis during short-term disuse in healthy younger humans

Muscle disuse leads to a rapid decline in muscle mass, with reduced muscle protein synthesis (MPS) considered the primary physiological mechanism. Here, we employed a systems biology approach to uncover molecular networks and key molecular candidates that quantitatively link to the degree of muscle atrophy and/or extent of decline in MPS during short-term disuse in humans. After consuming a bolus dose of deuterium oxide (D2O; 3 mL.kg−1), eight healthy males (22 ± 2 years) underwent 4 days of unilateral lower-limb immobilization. Bilateral muscle biopsies were obtained post-intervention for RNA sequencing and D2O-derived measurement of MPS, with thigh lean mass quantified using dual-energy X-ray absorptiometry. Application of weighted gene co-expression network analysis identified 15 distinct gene clusters (“modules”) with an expression profile regulated by disuse and/or quantitatively connected to disuse-induced muscle mass or MPS changes. Module scans for candidate targets established an experimentally tractable set of candidate regulatory molecules (242 hub genes, 31 transcriptional regulators) associated with disuse-induced maladaptation, many themselves potently tied to disuse-induced reductions in muscle mass and/or MPS and, therefore, strong physiologically relevant candidates. Notably, we implicate a putative role for muscle protein breakdown-related molecular networks in impairing MPS during short-term disuse, and further establish DEPTOR (a potent mTOR inhibitor) as a critical mechanistic candidate of disuse driven MPS suppression in humans. Overall, these findings offer a strong benchmark for accelerating mechanistic understanding of short-term muscle disuse atrophy that may help expedite development of therapeutic interventions

Polarization squeezing and continuous-variable polarization entanglement

The Stokes-parameter operators and the associated Poincare sphere, which describe the quantum-optical polarization properties of light, are defined and their basic properties are reviewed. The general features of the Stokes operators are illustrated by evaluation of their means and variances for a range of simple polarization states. Some of the examples show polarization squeezing, in which the variances of one or more Stokes parameters are smaller than the coherent-state value. The main object of the paper is the application of these concepts to bright squeezed light. It is shown that a light beam formed by interference of two orthogonally-polarized quadrature-squeezed beams exhibits squeezing in some of the Stokes parameters. Passage of such a primary polarization-squeezed beam through suitable optical components generates a pair of polarization-entangled light beams with the nature of a two-mode squeezed state. The use of pairs of primary polarization-squeezed light beams leads to substantially increased entanglement and to the generation of EPR-entangled light beams. The important advantage of these nonclassical polarization states for quantum communication is the possibility of experimentally determining all of the relevant conjugate variables of both squeezed and entangled fields using only linear optical elements followed by direct detection.Comment: 27 pages, including 10 figure

Insights into hominid evolution from the gorilla genome sequence.

Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution