Search

The data and code herein were used to write the associated article published by the Journal of Field Ornithology. The article describes which call types were most effective at trapping King Rails and how radio-tagged King Rails responded to audio playback. CSVs associated are named the same as the R file that use them. The code reproduces the three figures and all statistical analyses presented in the study. We also provide the full trapping (TrappingData.csv) and detectability (DetectionCF.csv) datasets.&nbsp

Coastal wetlands in the Laurentian Great Lakes undergo frequent, sometimes dramatic, physical changes at varying spatial and temporal scales. Changes in lake levels and the juxtaposition of vegetation and open water greatly influence biota that use coastal wetlands. Several regional studies have shown that changes in vegetation and lake levels lead to predictable changes in the composition of coastal wetland bird communities. We report new findings of wetland bird community changes at a broader scale, covering the entire Great Lakes basin. Our results indicate that water extent and interspersion increased in coastal wetlands across the Great Lakes between low (2013) and high (2018) lake-level years, although variation in the magnitude of change occurred within and among lakes. Increases in water extent and interspersion resulted in a general increase in marsh-obligate and marsh-facultative bird species richness. Species like American bittern (Botaurus lentiginosus), common gallinule (Gallinula galeata), American coot (Fulica americana), sora (Porzana carolina), Virginia rail (Rallus limicola), and pied-billed grebe (Podilymbus podiceps) were significantly more abundant during high water years. Lakes Huron and Michigan showed the greatest increase in water extent and interspersion among the five Great Lakes while Lake Michigan showed the greatest increase in marsh-obligate bird species richness. These results reinforce the idea that effective management, restoration, and assessment of wetlands must account for fluctuations in lake levels. Although high lake levels generally provide the most favorable conditions for wetland bird species, variation in lake levels and bird species assemblages create ecosystems that are both spatially and temporally dynamic.

The data and code provided here are associated with this manuscript: "Using radio-telemetry to validate eDNA as a tool for detecting a rare secretive marsh bird.' This study tests eDNA as a tool for detecting the presence of king rails (Rallus elegans).

The data and code provided here are associated with this manuscript. This study tests eDNA as a tool for detecting the presence of king rails (Rallus elegans).

Great Lakes coastal wetlands provide critical habitat and food resources for more species than any other Great Lakes ecosystem. Due to past and current anthropogenic disturbances, coastal wetland area has been reduced by >50% while remaining habitat is frequently degraded. Invasive mute swans have contributed to the degradation of coastal wetlands by removing submergent vegetation and competitively excluding native species from breeding areas and food resources. Despite current control practices, mute swan population estimates in Michigan are ~8000, comparable to population estimates in the entire Atlantic Flyway of North America. We collected local abiotic data and adjacent land cover data at 3 scales from 51 sites during 2010 and 2011 and conducted 2 mute swan detection surveys each year during the summer and fall. We developed a single-species, single-season occupancy-based habitat suitability model to determine current and potential mute swan habitat among Great Lakes coastal wetlands. We found mute swans occupied heterotrophic coastal wetlands adjacent to urban areas, which were high in ammonium and oxidation-reduction potential and low in nitrates, dissolved oxygen, and turbidity. Our model provides managers with a valuable tool for rapidly identifying mute swan habitat areas for control efforts, particularly the need for targeting mute swan populations in or near urbanized areas. Our model will also aid managers in monitoring areas that mute swans may invade and prioritizing coastal wetland areas for restoration efforts.

The attached data and scripts reproduce the CART and home range analysis conducted in the following study:King Rail (Rallus elegans) Microhabitat and Home Range Characteristics in the Great Lakes RegionKing Rail (Rallus elegans) Microhabitat and Home Range Characteristics in the Great Lakes Region.&nbsp

It has been predicted that 30-80% of archaeal genomes remain annotated as hypothetical proteins with no assigned gene function. Further, many archaeal organisms are difficult to grow or are unculturable. To overcome these technical and experimental hurdles, we have developed a high-throughput functional genomics screen that utilizes capillary electrophoresis (CE) to identify nucleic acid modifying enzymes based on activity rather than sequence homology. Here, we describe a functional genomics screening workflow to find DNA modifying enzyme activities encoded by the hyperthermophile Thermococcus kodakarensis (T. kodakarensis). Large DNA insert fosmid libraries representing a ∼5-fold average coverage of the T. kodakarensis genome were prepared in E. coli. RNA-seq showed a high fraction (84%) of T. kodakarensis genes were transcribed in E. coli despite differences in promoter structure and translational machinery. Our high-throughput screening workflow used fluorescently labeled DNA substrates directly in heat-treated lysates of fosmid clones with capillary electrophoresis detection of reaction products. Using this method, we identified both a new DNA endonuclease activity for a previously described RNA endonuclease (Nob1) and a novel AP lyase DNA repair enzyme family (termed 'TK0353') found only in a small subset of Thermococcales. The screening methodology described provides a fast and efficient way to explore the T. kodakarensis genome for a variety of nucleic acid modifying activities and may have implications for similar exploration of enzymes and pathways that underlie core cellular processes in other Archaea. IMPORTANCE This study provides a rapid, simple, high-throughput method to discover novel archaeal nucleic acid modifying enzymes by utilizing a fosmid genomic library, next-generation sequencing and capillary electrophoresis. The method described here provides details necessary to create 384-well fosmid library plates from Thermococcus kodakarensis genomic DNA, sequence 384-well fosmids plates using Illumina next generation sequencing and perform high-throughput functional read-out assays using capillary electrophoresis to identify a variety of nucleic acid modifying activities including DNA cleavage and ligation. We used this approach to identify a new DNA endonuclease activity for a previously described RNA endonuclease (Nob1) and identify a novel AP lyase enzyme (TK0353) that lacks sequence homology to known nucleic acid modifying enzymes.

Next generation ion therapy magnets both for gantry and for accelerator (synchrotron) are under investigation in a re-cently launched European collaboration that, in the frame of the Eu-ropean H2020 HITRIplus and I.FAST programmes, has obtained some funding for work packages on superconducting magnets. De-sign and technology of superconducting magnets will be developed for ion therapy synchrotron and -especially- gantry, taking as refer-ence beams of 430 MeV/nucleon ions (C-ions) with 1010 ions/pulse. The magnets are about 60-90 mm diameter, 4 to 5 T peak field with a field change of about 0.3 T/s and good field quality. The paper will illustrate the organization of the collaboration and the technical pro-gram. Various superconductor options (LTS, MgB2 or HTS) and different magnet shapes, like classical CosTheta or innovative Canted CosTheta (CCT), with curved multifunction (dipole and quadrupole), are under evaluation, CCT being the baseline. These studies should provide design inputs for a new superconducting gan-try design for existing facilities and, on a longer time scale, for a brand-new hadron therapy centre to be placed in the South East Eu-rope (SEEIIST project).

The faucet snail (Bithynia tentaculata) was introduced to the Great Lakes region in the late 1800s. Faucet snails alter native community dynamics and are an intermediate host for multiple trematode parasites that can be lethal to waterfowl when the snails are consumed. Although faucet snails have been established in the Great Lakes for over a century, their populations appear to have remained small for most of this period and their known distribution was limited to the lower Great Lakes, though basin-wide surveys were lacking until recently, so snails may have gone undetected. We compiled data from a five-year coastal wetland monitoring program spanning all of the Great Lakes, providing a basin-wide inventory of faucet snail populations and confirming the snail’s presence in every Great Lake. Further, we identified potential drivers of faucet snail occurrence and abundance (individuals per sampling replicate) across the basin and within individual lakes to identify factors that could lead to elevated risk of range expansion. Across the basin and within individual lakes, faucet snail occurrence was related to human recreational transport (proximity to a boat launch) and eutrophication (anthropogenic land-use, elevated nutrient concentrations). In addition, at sites where faucet snails occurred, they were most abundant at wetlands with surrounding forest cover, suggesting that the species can thrive in a range of environmental conditions. Our results suggest that limiting passive transport of faucet snails is vital to minimizing their spread to remote wetlands where the snails may thrive once established.

Traditionally, ecosystem monitoring, conservation, and restoration have been conducted in a piecemeal manner at the local scale without regional landscape context. However, scientifically driven conservation and restoration decisions benefit greatly when they are based on regionally determined benchmarks and goals. Unfortunately, required data sets rarely exist for regionally important ecosystems. Because of early recognition of the extreme ecological importance of Laurentian Great Lakes coastal wetlands, and the extensive degradation that had already occurred, significant investments in coastal wetland research, protection, and restoration have been made in recent decades and continue today. Continued and refined assessment of wetland condition and trends, and the evaluation of restoration practices are all essential to ensuring the success of these investments. To provide wetland managers and decision makers throughout the Laurentian Great Lakes basin with the optimal tools and data needed to make scientifically-based decisions, our regional team of Great Lakes wetland scientists developed standardized methods and indicators used for assessing wetland condition. From a landscape perspective, at the Laurentian Great Lakes ecosystem scale, we established a stratified random-site-selection process to monitor birds, anurans, fish, macroinvertebrates, vegetation, and physicochemical conditions of coastal wetlands in the US and Canada. Monitoring of approximately 200 wetlands per year began in 2011 as the Great Lakes Coastal Wetland Monitoring Program. In this paper, we describe the development, delivery, and expected results of this ongoing international, multi-disciplinary, multi-stakeholder, landscape-scale monitoring program as a case example of successful application of landscape conservation design.

Following decades of absence, the gray wolf (Canis lupus) has recolonized much of the northern Great Lakes region from Canada and remnant populations in northern Minnesota. The wolf population in Michigan’s Upper Peninsula may now be reaching saturation, with evidence that some dispersing individuals have traversed the Straits of Mackinac during ice-over winter conditions indicating potential recolonization of northern Lower Michigan. While previous research suggests suitable habitat exists in northern Lower Michigan to support a small wolf population, habitat availability at other hierarchical levels, including den habitat and the ability of individuals to disperse successfully among suitable habitat patches, has not been assessed. We evaluated the den habitat availability and landscape connectivity using a multi-scale modeling approach that integrates hierarchical habitat selection theory as well as spatial structure to assess whether corridors exist for wolves to successfully recolonize and raise pups in northern Lower Michigan. We used expert opinion, scientific literature, and geographical information systems to develop models of landscape suitability, resistance, and least-cost path analysis to identify dispersal corridors throughout the Upper and northern Lower Peninsulas of Michigan. Based on our models, the Upper Peninsula was almost entirely amenable to wolves for both denning and dispersing, particularly in the western portion of the peninsula. Our estimates indicate that over 1900 km2 of high quality den habitat exists in northern Lower Michigan, but landscape permeability between these habitat patches appeared relatively low relative to Upper Michigan. We delineated several corridors of high quality habitat in the Upper Peninsula that may facilitate dispersal in to Lower Michigan. Dispersal corridors were of moderate quality in northern Lower Michigan, representing higher mortality risk but potentially capable of promoting recolonization of high-quality habitat areas. Conservation efforts within these identified corridors may further increase the potential for successful recolonization and establishment of viable long-term breeding populations of gray wolves in northern Lower Michigan.

This validation study examines the PowerRef 3 as a method for measuring accommodation objectively. We assess agreement with refractive measurements obtained simultaneously by the Grand Seiko WAM-5500A autorefractor.Refractive measurements were recorded simultaneously using the PowerRef 3 and WAM-5500A in 32 noncyclopleged participants aged 15 to 46 years. Accommodative states were recorded for 10 seconds at six accommodative demands (5 diopters [D], 4 D, 3 D, 2.5 D, 2 D, and 0 D) while participants fixated a high-contrast Maltese cross. WAM-5500A measurements were converted to power in the vertical meridian for comparison with PowerRef 3 data. Dioptric difference values were computed, and agreement was assessed using Bland-Altman plots with 95% limits of agreement (LOA) and intraclass correlation coefficient analyses.The mean absolute dioptric differences measured 0.14 D or less across accommodative demands. Analyses showed an excellent intraclass correlation coefficient across the tested demands (0.93). Bland-Altman plots indicated a bias of -0.02 D with 95% LOA of -1.03 D to 0.99 D. The 95% LOA was smallest for the 3 D demand (-0.71 D to 0.64 D), and largest at 5 D demand (-1.51 D to 1.30 D).The mean dioptric differences between the PowerRef 3 and WAM-5500A autorefractor were small and not clinically significant. While some variability in agreement was observed depending on the tested demand, the PowerRef 3 demonstrated good agreement with the WAM-5500A.The PowerRef 3 may be used to obtain objective measures of accommodation both monocularly and binocularly and provides a more flexible method, especially in pediatric populations.

Larus delawarensis (Ring-billed Gull) populations have increased >4% annually in the Great Lakes region since 2003. Gull–human interactions and conflicts have similarly increased, particularly concerning human health and safety issues related to gull feces deposited at recreational beaches. During June–August 2013, we conducted a radiotelemetry study of Ring-billed Gulls in a Lake Michigan coastal region to determine patterns of habitat use and movement between recreational beaches and human infrastructure by gulls. Of 14 individuals relocated, we found Ring-billed Gulls selected recreational beaches and landfill sites and avoided agricultural fields. We found 5 of 14 gulls made a minimum of 2 roundtrips between beaches and landfills over the study period. Gulls may serve as transport vectors for bacteria and other pathogens from human-waste sites to areas of probable human contact and concentration, such as public recreational beaches. As such, pathogen distribution and connectivity within a landscape could be established, maintained, and enhanced by gull movements. Managers may need to implement exclusion tools for gulls at both of these sites to maintain human-health standards.

VI$_{3}$ is a ferromagnet with planar honeycomb sheets of bonded V$^{3+}$ ions held together by van der Waals forces. We apply neutron spectroscopy to measure the two dimensional ($J/J_{c} \approx 17$) magnetic excitations in the ferromagnetic phase, finding two energetically gapped ($\Delta \approx k_{B} T_{c} \approx$ 55 K) and dispersive excitations. We apply a multi-level spin wave formalism to describe the spectra in terms of two coexisting domains hosting differing V$^{3+}$ orbital ground states built from contrasting distorted octahedral environments. This analysis fits a common nearest neighbor in-plane exchange coupling ($J$=-8.6 $\pm$ 0.3 meV) between V$^{3+}$ sites. The distorted local crystalline electric field combined with spin-orbit coupling provides the needed magnetic anisotropy for spatially long-ranged two-dimensional ferromagnetism in VI$_{3}$., Comment: (main text - 7 pages, 4 figures; supplementary information - 13 pages, 9 figures, to be published in Phys. Rev. B)

Materials based on the cubic perovskite unit cell continue to provide the basis for technologically important materials with two notable recent examples being lead-based relaxor piezoelectrics and lead-based organic-inorganic halide photovoltaics. These materials carry considerable disorder, arising from site substitution in relaxors and molecular vibrations in the organic-inorganics, yet much of our understanding of these systems derives from the initial classic work of Prof. Roger A. Cowley, who applied both theory and neutron scattering methods while at Chalk River Laboratories to the study of lattice vibrations in SrTiO$_{3}$. Neutron scattering continues to play a vital role in characterizing lattice vibrations in perovskites owing to the simple cross section and the wide range of energy resolutions achievable with current neutron instrumentation. We discuss the dynamics that drive the phase transitions in the relaxors and organic-inorganic lead-halides in terms of neutron scattering and compare them to those in phase transitions associated with a ``central peak" and also a soft mode. We review some of the past experimental work on these materials and present new data from high-resolution time-of-flight backscattering spectroscopy taken on organic-inorganic perovskites. We will show that the structural transitions in disordered lead-based perovskites are driven by a broad frequency band of excitations., 23 pages, 9 figures, submitted as part of a special issue of JPCM on X-ray and Neutron Scattering and dedicated to the memory of Prof. R. A. Cowley

We investigate the hypothesis of dynamic tetragonal domains occurring in cubic ${\mathrm{CH}}_{3}{\mathrm{NH}}_{3}{\mathrm{PbI}}_{3}$ using high-resolution neutron spectroscopy to study a fully deuterated single crystal. The $R$-point scattering above the 327.5 K cubic-tetragonal phase transition is always resolution limited in energy and therefore inconsistent with dynamic-domain predictions. This behavior is instead consistent with the central peak phenomenon observed in other perovskites. The scattering may originate from small, static, tetragonal-phase domains nucleating about crystal defects, and the temperature dependence demonstrates the transition is first order.

Contamination of recreational beaches due to fecal waste from gulls complicates beach monitoring and may pose a risk to public health. Gulls that feed at human waste sites may ingest human fecal microorganisms associated with that waste. If these gulls also visit beaches, they may serve as vectors, transporting fecal microorganisms to the beach where they may subsequently contaminate sand and water. In this study, samples collected from landfills, treated wastewater storage lagoons, and public beaches demonstrated a spatial and temporal overlap of markers for gull and human-associated microorganisms. In addition, markers for gull, fecal indicator bacteria, and the human-associated marker, HF183, were detected in gull feces and cloacae samples. Further, HF183 was detected in cloacae samples from gulls that were documented by radio-telemetry traveling between human waste sites and public beaches. This study highlights the potential for gulls that visit human waste sites to disperse human-associated microorganisms in the beach landscape.

The organic-inorganic lead-halide perovskites are composed of organic molecules imbedded in an inorganic framework. The compounds with general formula ${\mathrm{CH}}_{3}{\mathrm{NH}}_{3}\mathrm{Pb}{X}_{3}$ ($\mathrm{MAPb}{X}_{3}$) display large photovoltaic efficiencies for halogens $X=\mathrm{Cl}$, Br, and I in a wide variety of sample geometries and preparation methods. The organic cation and inorganic framework are bound by hydrogen bonds that tether the molecules to the halide anions, and this has been suggested to be important to the optoelectronic properties. We have studied the effects of this bonding using time-of-flight neutron spectroscopy to measure the molecular dynamics in ${\mathrm{CH}}_{3}{\mathrm{NH}}_{3}{\mathrm{PbCl}}_{3}$ (${\mathrm{MAPbCl}}_{3}$). Low-energy/high-resolution neutron backscattering reveals thermally activated molecular dynamics with a characteristic temperature of $\ensuremath{\sim}95$ K. At this same temperature, higher-energy neutron spectroscopy indicates the presence of an anomalous broadening in energy (reduced lifetime) associated with the molecular vibrations. By contrast, neutron powder diffraction shows that a spatially long-range structural phase transitions occurs at 178 K (cubic $\ensuremath{\rightarrow}$ tetragonal) and 173 K (tetragonal $\ensuremath{\rightarrow}$ orthorhombic). The large difference between these two temperature scales suggests that the molecular and inorganic lattice dynamics in ${\mathrm{MAPbCl}}_{3}$ are actually decoupled. With the assumption that underlying physical mechanisms do not change with differing halogens in the organic-inorganic perovskites, we speculate that the energy scale most relevant to the photovoltaic properties of the lead-halogen perovskites is set by the lead-halide bond, not by the hydrogen bond.

The acoustic phonons in the organic-inorganic lead halide perovskites have been reported to have anomalously short lifetimes over a large part of the Brillouin zone. The resulting shortened mean free paths of the phonons have been implicated as the origin of the low thermal conductivity. We apply neutron spectroscopy to show that the same acoustic phonon energy linewidth broadening (corresponding to shortened lifetimes) occurs in the fully inorganic ${\mathrm{CsPbBr}}_{3}$ by comparing the results on the organic-inorganic ${\mathrm{CH}}_{3}{\mathrm{NH}}_{3}{\mathrm{PbCl}}_{3}$. We investigate the critical dynamics near the three zone boundaries of the cubic $Pm\overline{3}m$ Brillouin zone of ${\mathrm{CsPbBr}}_{3}$ and find energy and momentum broadened dynamics at momentum points where the Cs-site ($A$-site) motions contribute to the cross section. Neutron diffraction is used to confirm that both the Cs and Br sites have unusually large thermal displacements with an anisotropy that mirrors the low temperature structural distortions. The presence of an organic molecule is not necessary to disrupt the low-energy acoustic phonons at momentum transfers located away from the zone center in the lead halide perovskites and such damping may be driven by the large displacements or possibly disorder on the $A$ site.

Short-range polar orders in the relaxor ferroelectric material PbMg$_{1/3}$Nb$_{2/3}$O$_3$-$28\%$PbTiO$_3$ (PMN-28PT) have been studied using neutron diffuse scattering. An external electric field along [110] direction can affect the diffuse scattering in the low temperature rhombohedral/monoclinic phase. Diffuse scattering intensities associated with [110] short-range polarizations are partially suppressed, while those arising from [1$\bar{1}$0] polarizations are enhanced. On the other hand, short-range polar orders along other equivalent $\langle110\rangle$ directions, i.e. [101],[10$\bar{1}$], [011], and [01$\bar{1}$] directions, are virtually unaffected by the field. Our results, combined with previous work, strongly suggest that most part of short-range polar orders in PMN-$x$PT relaxor systems are robust in the low temperature phase, where they couple strongly to ferroelectric polarizations of the surrounding ferroelectric domains, and would only respond to an external field indirectly through ferroelectric domain rotation., 5 pages, 4 figures, 2 tables. submitted to Phys. Rev. B

We present a study on a micromechanical bending actuator, which is intended for creating fluid flow by a fish-like, undulatory motion. This motion pattern describes an ascending wave traveling along the actuator and is capable to shed vortices into the surrounding fluid, forming a vortex wake. A segmented electrode at the top of the bending actuator enables the undulatory excitation. It turns out, that undulation creates slightly higher mass flow than resonant oscillations in the structure’s first eigenmode. At the same time, undulation needs less energy for generating equal mass flow, and, hence, is more efficient compared to resonant motion.

The emerging lab-on-chip technology for in-situ medical use and environmental surveillance brought with it the demand for new, micro-scale actuator designs specialized in energy-efficient fluid transport, supporting the development of lightweight and mobile systems. In this work, we present the simulation-based design of a novel, integrated micro-fluidic actuator intended for mobile applications. The design is laid-out to be compatible with standard semiconductor manufacturing processes in order to enable mass-production at low cost per unit. The development of the device is supported and accelerated by a dedicated fully energy-coupled finite element model (FEM). The FE model takes into account the fluid-solid interaction in addition to the electro-mechanical interrelations, therefore reproducing the full device behavior in reaction to electrical input signals. In the end, we discuss several design parameters exhibiting space for improvement compared to the chosen standard values, as identified by the FEM simulations.