Lidar-derived canopy architecture predicts brown creeper occupancy of two western coniferous forests

In western conifer-dominated forests where the abundance of old-growth stands is decreasing, species such as the Brown Creeper (Certhia americana) may be useful as indicator species for monitoring the health of old-growth systems because they are strongly associated with habitat characteristics associated with old growth and are especially sensitive to forest management. Light detection and ranging (lidar) is useful for acquiring fine-resolution, three-dimensional data on vegetation structure across broad areas. We evaluated Brown Creeper occupancy of forested landscapes by using lidar-derived canopy metrics in two coniferous forests in Idaho. Density of the upper canopy was the most important variable for predicting Brown Creeper occupancy, although mean height and height variability were also included in the top models. The upper canopy was twice as dense and the mean height was almost 50% higher at occupied than at unoccupied sites. Previous studies have found indicators of canopy density to be important factors for Brown Creeper habitat; however, this represents the first time that lidar data have been used to examine this relationship empirically through the mapping of the upper canopy density that cannot be continuously quantified by field-based methods or passive remote sensing. Our model’s performance was classified as “good” by multiple criteria. We were able to map probabilities of Brown Creeper occupancy in ~50 000 ha of forest, probabilities that can be used at the local, forest-stand, and landscape scales, and illustrate the potential utility of lidar-derived data for studies of avian distributions in forested landscapes.En los bosques dominados por coníferas del oeste, donde está disminuyendo la abundancia de rodales maduros, las especies como Certhia americana pueden ser útiles como especies indicadoras para monitorear la salud de los sistemas maduros debido a que están fuertemente asociadas con las características del hábitat vinculadas con el bosque maduro y son especialmente sensibles al manejo del bosque. El sistema de detección y alcance de luz (denominado lidar, un acrónimo del inglés “light detection and ranging”) es útil para adquirir datos tridimensionales de alta resolución de la estructura de la vegetación a través de grandes áreas. Evaluamos la ocupación de C. americana de paisajes boscosos usando métricas del dosel derivadas de lidar en dos bosques de coníferas en Idaho. La densidad del dosel alto fue la variable más importante para predecir la ocupación de C. americana, aunque la altura media y la variabilidad de la altura también fueron incluidas en los mejores modelos. El dosel alto fue dos veces más denso y la altura media fue casi 50% más alta en los sitios ocupados que en los sitios desocupados. Estudios previos han encontrado que los indicadores de densidad del dosel son factores importantes del hábitat de C. americana; sin embargo, esto representa la primera vez que datos de lidar han sido usados para examinar esta relación de modo empírico a través del mapeo de la densidad del dosel alto, de un modo continuo que no puede ser cuantificado por métodos basados en trabajo de campo o muestreo remoto pasivo. El desempeño de nuestro modelo fue clasificado como “bueno” por múltiples criterios. Fuimos capaces de mapear las probabilidades de ocupación de C. americana en ~50 000 ha de bosque, probabilidades que pueden ser usadas a las escalas local, de rodal de bosque y de paisaje, y que ilustran la utilidad potencial de los datos derivados de lidar para estudios de distribución de aves en paisajes boscosos.Keywords: Brown Creeper, Certhia americana, mapping, habitat, forest, occupancy, lida

Evaluating GEDI data fusions for continuous characterizations of forest wildlife habitat

Continuous characterizations of forest structure are critical for modeling wildlife habitat as well as for assessing trade-offs with additional ecosystem services. To overcome the spatial and temporal limitations of airborne lidar data for studying wide-ranging animals and for monitoring wildlife habitat through time, novel sampling data sources, including the space-borne Global Ecosystem Dynamics Investigation (GEDI) lidar instrument, may be incorporated within data fusion frameworks to scale up satellite-based estimates of forest structure across continuous spatial extents. The objectives of this study were to: 1) investigate the value and limitations of satellite data sources for generating GEDI-fusion models and 30 m resolution predictive maps of eight forest structure measures across six western U.S. states (Colorado, Wyoming, Idaho, Oregon, Washington, and Montana); 2) evaluate the suitability of GEDI as a reference data source and assess any spatiotemporal biases of GEDI-fusion maps using samples of airborne lidar data; and 3) examine differences in GEDI-fusion products for inclusion within wildlife habitat models for three keystone woodpecker species with varying forest structure needs. We focused on two fusion models, one that combined Landsat, Sentinel-1 Synthetic Aperture Radar, disturbance, topographic, and bioclimatic predictor information (combined model), and one that was restricted to Landsat, topographic, and bioclimatic predictors (Landsat/topo/bio model). Model performance varied across the eight GEDI structure measures although all representing moderate to high predictive performance (model testing R2 values ranging from 0.36 to 0.76). Results were similar between fusion models, as well as for map validations for years of model creation (2019–2020) and hindcasted years (2016–2018). Within our wildlife case studies, modeling encounter rates of the three woodpecker species using GEDI-fusion inputs yielded AUC values ranging from 0.76–0.87 with observed relationships that followed our ecological understanding of the species. While our results show promise for the use of remote sensing data fusions for scaling up GEDI structure metrics of value for habitat modeling and other applications across broad continuous extents, further assessments are needed to test their performance within habitat modeling for additional species of conservation interest as well as biodiversity assessments

Modeling Denitrification : Can We Report What We Don't Know?

Funding Information: This study is the products of a workshop funded by the Deutsche Forschungsgemeinschaft through the research unit DFG‐FOR 2337: Denitrification in Agricultural Soils: Integrated Control and Modelling at Various Scales (DASIM), and by the German Federal Ministry of Education and Research (BMBF) under the “Make our Planet Great Again—German Research Initiative”, Grant 306060, implemented by the German Academic Exchange Service (DAAD). This work was supported by the European Union's Horizon 2020 research and innovation programme project VERIFY (grant agreement no. 776810). We would like to thank the contribution of all workshop participants of the II. DASIM Modeler Workshop. Publisher Copyright: © 2023. The Authors.Peer reviewedPublisher PD

The nuclear receptors of Biomphalaria glabrata and Lottia gigantea: Implications for developing new model organisms

© 2015 Kaur et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedNuclear receptors (NRs) are transcription regulators involved in an array of diverse physiological functions including key roles in endocrine and metabolic function. The aim of this study was to identify nuclear receptors in the fully sequenced genome of the gastropod snail, Biomphalaria glabrata, intermediate host for Schistosoma mansoni and compare these to known vertebrate NRs, with a view to assessing the snail's potential as a invertebrate model organism for endocrine function, both as a prospective new test organism and to elucidate the fundamental genetic and mechanistic causes of disease. For comparative purposes, the genome of a second gastropod, the owl limpet, Lottia gigantea was also investigated for nuclear receptors. Thirty-nine and thirty-three putative NRs were identified from the B. glabrata and L. gigantea genomes respectively, based on the presence of a conserved DNA-binding domain and/or ligand-binding domain. Nuclear receptor transcript expression was confirmed and sequences were subjected to a comparative phylogenetic analysis, which demonstrated that these molluscs have representatives of all the major NR subfamilies (1-6). Many of the identified NRs are conserved between vertebrates and invertebrates, however differences exist, most notably, the absence of receptors of Group 3C, which includes some of the vertebrate endocrine hormone targets. The mollusc genomes also contain NR homologues that are present in insects and nematodes but not in vertebrates, such as Group 1J (HR48/DAF12/HR96). The identification of many shared receptors between humans and molluscs indicates the potential for molluscs as model organisms; however the absence of several steroid hormone receptors indicates snail endocrine systems are fundamentally different.The National Centre for the Replacement, Refinement and Reduction of Animals in Research, Grant Ref:G0900802 to CSJ, LRN, SJ & EJR [www.nc3rs.org.uk]

Hyperbolic and semi-hyperbolic surface codes for quantum storage

We show how a hyperbolic surface code could be used for overhead-efficient quantum storage. We give numerical evidence for a noise threshold of 1.3% for the {4, 5}-hyperbolic surface code in a phenomenological noise model (as compared with 2.9% for the toric code). In this code family, parity checks are of weight 4 and 5, while each qubit participates in four different parity checks. We introduce a family of semi-hyperbolic codes that interpolate between the toric code and the {4, 5}-hyperbolic surface code in terms of encoding rate and threshold. We show how these hyperbolic codes outperform the toric code in terms of qubit overhead for a target logical error probability. We show how Dehn twists and lattice code surgery can be used to read and write individual qubits to this quantum storage medium

Evaluating carbon storage, timber harvest, and habitat possibilities for a Western Cascades (USA) forest landscape

Forest policymakers and managers have long sought ways to evaluate the capability of forest landscapes to jointly produce timber, habitat, and other ecosystem services in response to forest management. Currently, carbon is of particular interest as policies for increasing carbon storage on federal lands are being proposed. However, a challenge in joint production analysis of forest management is adequately representing ecological conditions and processes that influence joint production relationships. We used simulation models of vegetation structure, forest sector carbon, and potential wildlife habitat to characterize landscape-level joint production possibilities for carbon storage, timber harvest, and habitat for seven wildlife species across a range of forest management regimes. We sought to (1) characterize the general relationships of production possibilities for combinations of carbon storage, timber, and habitat, and (2) identify management variables that most influence joint production relationships. Our 160 000-ha study landscape featured environmental conditions typical of forests in the Western Cascade Mountains of Oregon (USA). Our results indicate that managing forests for carbon storage involves trade-offs among timber harvest and habitat for focal wildlife species, depending on the disturbance interval and utilization intensity followed. Joint production possibilities for wildlife species varied in shape, ranging from competitive to complementary to compound, reflecting niche breadth and habitat component needs of species examined. Managing Pacific Northwest forests to store forest sector carbon can be roughly complementary with habitat for Northern Spotted Owl, Olive-sided Flycatcher, and red tree vole. However, managing forests to increase carbon storage potentially can be competitive with timber production and habitat for Pacific marten, Pileated Woodpecker, and Western Bluebird, depending on the disturbance interval and harvest intensity chosen. Our analysis suggests that joint production possibilities under forest management regimes currently typical on industrial forest lands (e.g., 40- to 80-yr rotations with some tree retention for wildlife) represent but a small fraction of joint production outcomes possible in the region. Although the theoretical boundaries of the production possibilities sets we developed are probably unachievable in the current management environment, they arguably define the long-term potential of managing forests to produce multiple ecosystem services within and across multiple forest ownerships

Development and analysis of the Soil Water Infiltration Global database.

In this paper, we present and analyze a novel global database of soil infiltration measurements, the Soil Water Infiltration Global (SWIG) database. In total, 5023 infiltration curves were collected across all continents in the SWIG database. These data were either provided and quality checked by the scientists who performed the experiments or they were digitized from published articles. Data from 54 different countries were included in the database with major contributions from Iran, China, and the USA. In addition to its extensive geographical coverage, the collected infiltration curves cover research from 1976 to late 2017. Basic information on measurement location and method, soil properties, and land use was gathered along with the infiltration data, making the database valuable for the development of pedotransfer functions (PTFs) for estimating soil hydraulic properties, for the evaluation of infiltration measurement methods, and for developing and validating infiltration models. Soil textural information (clay, silt, and sand content) is available for 3842 out of 5023 infiltration measurements (~76%) covering nearly all soil USDA textural classes except for the sandy clay and silt classes. Information on land use is available for 76% of the experimental sites with agricultural land use as the dominant type (~40%). We are convinced that the SWIG database will allow for a better parameterization of the infiltration process in land surface models and for testing infiltration models. All collected data and related soil characteristics are provided online in *.xlsx and *.csv formats for reference, and we add a disclaimer that the database is for public domain use only and can be copied freely by referencing it. Supplementary data are available at https://doi.org/10.1594/PANGAEA.885492 (Rahmati et al., 2018). Data quality assessment is strongly advised prior to any use of this database. Finally, we would like to encourage scientists to extend and update the SWIG database by uploading new data to it

Cloning retinoid and peroxisome proliferator-activated nuclear receptors of the Pacific oyster and in silico binding to environmental chemicals

This is the final version of the article. Available from Public Library of Science via the DOI in this record.Disruption of nuclear receptors, a transcription factor superfamily regulating gene expression in animals, is one proposed mechanism through which pollution causes effects in aquatic invertebrates. Environmental pollutants have the ability to interfere with the receptor's functions through direct binding and inducing incorrect signals. Limited knowledge of invertebrate endocrinology and molecular regulatory mechanisms, however, impede the understanding of endocrine disruptive effects in many aquatic invertebrate species. Here, we isolated three nuclear receptors of the Pacific oyster, Crassostrea gigas: two isoforms of the retinoid X receptor, CgRXR-1 and CgRXR-2, a retinoic acid receptor ortholog CgRAR, and a peroxisome proliferator-activated receptor ortholog CgPPAR. Computer modelling of the receptors based on 3D crystal structures of human proteins was used to predict each receptor's ability to bind to different ligands in silico. CgRXR showed high potential to bind and be activated by 9-cis retinoic acid and the organotin tributyltin (TBT). Computer modelling of CgRAR revealed six residues in the ligand binding domain, which prevent the successful interaction with natural and synthetic retinoid ligands. This supports an existing theory of loss of retinoid binding in molluscan RARs. Modelling of CgPPAR was less reliable due to high discrepancies in sequence to its human ortholog. Yet, there are suggestions of binding to TBT, but not to rosiglitazone. The effect of potential receptor ligands on early oyster development was assessed after 24h of chemical exposure. TBT oxide (0.2μg/l), all-trans retinoic acid (ATRA) (0.06 mg/L) and perfluorooctanoic acid (20 mg/L) showed high effects on development (>74% abnormal developed D-shelled larvae), while rosiglitazone (40 mg/L) showed no effect. The results are discussed in relation to a putative direct (TBT) disruption effect on nuclear receptors. The inability of direct binding of ATRA to CgRAR suggests either a disruptive effect through a pathway excluding nuclear receptors or an indirect interaction. Our findings provide valuable information on potential mechanisms of molluscan nuclear receptors and the effects of environmental pollution on aquatic invertebrates.The study was funded by the Centre for Environment, Fisheries and Aquaculture Science (Cefas; https://www.cefas.co.uk) and by the University of Exeter (http://www.exeter.ac.uk)

David Rice Atchison, Southern Spokesman: 1844-1855

Missouri Senator David Rice Atchison represented one of the most radical southern factions in Congress. He accomplished his greatest feat in 1854 by securing passage of the Kansas-Nebraska Act. When he returned home to face re-election, he lost in Missouri\u27s General Assembly. This work examined the electoral returns of Missouri General Assembly elections in 1848, 1850, and 1854 in an effort to determine Atchison\u27s power base, how this power base changed in his critical re-election, and how certain critical issues damaged his candidacy. It examined the circumstances and internal strife occuring within the Missouri Democratic Party. Missourians rejected fanaticism on both sides, the North and South. Their desire to avoid the slavery issue sealed the fate of David Rice Atchison\u27s political career