Small mammal relationships with downed wood and antelope bitterbrush in ponderosa pine forests of central Oregon

Downed wood and antelope bitterbrush (Purshia tridentata) are often managed on federal ponderosa pine (Pinus ponderosa) forests in central Oregon to prevent catastrophic wildfires and provide wildlife habitat. However, although much is known regarding the roles of downed wood and bitterbrush in wildfire behavior, little is known regarding the relationships of small mammal populations with downed wood and bitterbrush in these pine forests east of the Cascade crest. This study had four primary objectives: 1) to test for differences in population parameters (i.e., density, reproductive condition, and survival) of common small mammals between forested areas with high and low downed wood volumes; 2) to test for differences in these small mammal population parameters between forested areas with high and low shrub cover; 3) to quantify relationships of small mammal population parameters with different habitat features, emphasizing downed wood volume bitterbrush cover, and total shrub cover and 4) to quantify relationships between small mammal population parameters and habitat features across seasons and years to assess temporal variability. Study units representing five replicates of three combinations of shrub cover and downed wood volume (high shrub cover/high downed wood volume, high shrub cover/low downed wood volume, low shrub cover/low downed wood volume) were selected in the Deschutes National Forest east of the crest of the Cascades Mountains in central Oregon. A total of 2,654 small mammals representing nine species were captured in live traps on the 15 study units during four sampling periods: early summer 2000 (June 25 to July 27), late summer 2000 (August 29 to September 30), fall 2000 (October 2 to October 28), and early summer 2001 (July 3 to August 4). Yellow-pine chipmunks (Tamias amoenus), golden-mantled ground squirrels (Spermophihis lateralis), and deer mice (Peromyscus maniculatus) comprised 98% of the captures. Golden-mantled ground squirrel survival and density were significantly higher on study units with high versus low downed wood volume. Yellow-pine chipmunk populations did not exhibit significant relationships with downed wood volume, but chipmunk density was higher on study units with high versus low shrub cover. Deer mouse populations failed to exhibit significant relationships with downed wood volume or shrub cover. For the three small mammal species, there was considerable variation among seasons, years, and locations for many of the population parameters examined. Results from this study suggest that managing downed wood and antelope bitterbrush in ponderosa pine forests of central Oregon may affect the small mammal community through changes in density and survival of golden-mantled ground squirrels and yellow-pine chipmunks. Such impacts on the small mammal community will, consequently, influence other aspects of forest ecology including fire behavior and shrub regeneration due to the consumption and dispersal of bitterbrush seeds by these chipmunks and ground squirrels

CEO Demographics and Accounting Fraud: Who is More Likely to Rationalize Illegal Acts?

This article proposes that key CEO demographic factors reflect alternative modes of rationalizing the choice to engage in and/or facilitate accounting fraud. Specifically the authors theorize that younger, less functionally experienced CEOs and CEOs without business degrees will be more likely to rationalize accounting fraud as an acceptable decision. Based on a sample of 312 fraud-committing and control firms, the study finds support for the authors’ predictions. It also finds that CEO stock options (a form of executive equity incentive) also predict fraud, and that this relationship is not moderated by CEO demographics. The study thus extends upper echelon theory by demonstrating how key demographic variables influence CEO decisions to rationalize accounting fraud

Characterization of Nursery Habitats used by Black Sea Bass and Summer Flounder in Chesapeake Bay and the Coastal Lagoons

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Computability, G\"odel's Incompleteness Theorem, and an inherent limit on the predictability of evolution

The process of evolutionary diversification unfolds in a vast genotypic space of potential outcomes. During the past century there have been remarkable advances in the development of theory for this diversification, and the theory's success rests, in part, on the scope of its applicability. A great deal of this theory focuses on a relatively small subset of the space of potential genotypes, chosen largely based on historical or contemporary patterns, and then predicts the evolutionary dynamics within this pre-defined set. To what extent can such an approach be pushed to a broader perspective that accounts for the potential open-endedness of evolutionary diversification? There have been a number of significant theoretical developments along these lines but the question of how far such theory can be pushed has not been addressed. Here a theorem is proven demonstrating that, because of the digital nature of inheritance, there are inherent limits on the kinds of questions that can be answered using such an approach. In particular, even in extremely simple evolutionary systems a complete theory accounting for the potential open-endedness of evolution is unattainable unless evolution is progressive. The theorem is closely related to G\"odel's Incompleteness Theorem and to the Halting Problem from computability theory.Comment: Journal of the Royal Society, Interface 201

Application of Optimal Control to CPMG Refocusing Pulse Design

We apply optimal control theory (OCT) to the design of refocusing pulses suitable for the CPMG sequence that are robust over a wide range of B0 and B1 offsets. We also introduce a model, based on recent progress in the analysis of unitary dynamics in the field of quantum information processing (QIP), that describes the multiple refocusing dynamics of the CPMG sequence as a dephasing Pauli channel. This model provides a compact characterization of the consequences and severity of residual pulse errors. We illustrate the methods by considering a specific example of designing and analyzing broadband OCT refocusing pulses of length 10 t180 that are constrained by the maximum instantaneous pulse power. We show that with this refocusing pulse, the CPMG sequence can refocus over 98% of magnetization for resonance offsets up to 3.2 times the maximum RF amplitude, even in the presence of +/- 10% RF inhomogeneity.Comment: 23 pages, 10 figures; Revised and reformatted version with new title and significant changes to Introduction and Conclusions section

Phylogenetic comparative analysis of electric communication signals in ghost knifefishes (Gymnotiformes: Apteronotidae)

Electrocommunication signals in electric fish are diverse, easily recorded and have well-characterized neural control. Two signal features, the frequency and waveform of the electric organ discharge (EOD), vary widely across species. Modulations of the EOD (i.e. chirps and gradual frequency rises) also function as active communication signals during social interactions, but they have been studied in relatively few species. We compared the electrocommunication signals of 13 species in the largest gymnotiform family, Apteronotidae. Playback stimuli were used to elicit chirps and rises. We analyzed EOD frequency and waveform and the production and structure of chirps and rises. Species diversity in these signals was characterized with discriminant function analyses, and correlations between signal parameters were tested with phylogenetic comparative methods. Signals varied markedly across species and even between congeners and populations of the same species. Chirps and EODs were particularly evolutionarily labile, whereas rises differed little across species. Although all chirp parameters contributed to species differences in these signals, chirp amplitude modulation, frequency modulation (FM) and duration were particularly diverse. Within this diversity, however, interspecific correlations between chirp parameters suggest that mechanistic trade-offs may shape some aspects of signal evolution. In particular, a consistent trade-off between FM and EOD amplitude during chirps is likely to have influenced the evolution of chirp structure. These patterns suggest that functional or mechanistic linkages between signal parameters (e.g. the inability of electromotor neurons increase their firing rates without a loss of synchrony or amplitude of action potentials) constrain the evolution of signal structure

De novo assembly of the cattle reference genome with single-molecule sequencing.

BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.ResultsWe present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.ConclusionsWe demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species

Hematopoietic Cell Transplantation in Patients With Primary Immune Regulatory Disorders (PIRD): A Primary Immune Deficiency Treatment Consortium (PIDTC) Survey.

Primary Immune Regulatory Disorders (PIRD) are an expanding group of diseases caused by gene defects in several different immune pathways, such as regulatory T cell function. Patients with PIRD develop clinical manifestations associated with diminished and exaggerated immune responses. Management of these patients is complicated; oftentimes immunosuppressive therapies are insufficient, and patients may require hematopoietic cell transplant (HCT) for treatment. Analysis of HCT data in PIRD patients have previously focused on a single gene defect. This study surveyed transplanted patients with a phenotypic clinical picture consistent with PIRD treated in 33 Primary Immune Deficiency Treatment Consortium centers and European centers. Our data showed that PIRD patients often had immunodeficient and autoimmune features affecting multiple organ systems. Transplantation resulted in resolution of disease manifestations in more than half of the patients with an overall 5-years survival of 67%. This study, the first to encompass disorders across the PIRD spectrum, highlights the need for further research in PIRD management

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought

Nurses' experiences of recruitment and migration from developing countries: a phenomenological approach

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