Analysis of red spruce (Picea rubens) regeneration in Pocahontas, Randolph, and Tucker counties, West Virginia

Three red spruce communities in the Central Appalachians of West Virginia were accessed temporally over a period of 10 to 11 years and by forest zones (i.e. hardwood, ecotone, red spruce zones). These communities experienced an increasing density of red spruce over time across all forest zones. Red spruce was successfully establishing and expanding across the ecotone into the hardwood forest zone. The greatest increase of red spruce was seen in the more disturbed and earlier successional sites, whereas the less disturbed red spruce community experienced the least change. The red spruce populations in this study were thriving and increasing the density of red spruce seedlings, advanced regeneration and trees across the spruce-hardwood ecotone as well as under the surrounding hardwood canopy. Red spruce seedling densities were found to be greater with increased cover of bryophytes and coarse woody debris, while densities are reduced with increasing cover of Dryopteris spp

The role of sampling methodology and site selection on myxomycete data from the Neotropics

Myxomycete sporocarps are practical units that can be used to study the effect of environmental issues such as climate change, urbanization, and natural disasters on microorganisms. Recent scientific literature lacks empirical approaches to understand the impacts of sampling design and site selection on the data obtained in myxomycete field surveys. The present investigation was designed to generate useful data for the evaluation of methodological approaches. Myxomycetes were studied for two years in a tropical premontane wet forest in Costa Rica using two different sampling strategies and several collecting sites to evaluate potential differences in the results. Field collections were used to generate the dataset due to their usefulness for monitoring purposes. Sampling strategies had a smaller impact on the reported structure and composition of obtained species assemblages than site selection, but a combination of both clearly maximized the effort and provided the best results during the field surveys. Functional variables of the forest with direct influence on the myxomycete life cycle such as tree diameter and leaf litter depth impacted the results synergically. Simulations of surveys at two different levels of effort were compared with total yearly efforts and results showed that revisiting sampling sites maximized the field effort. Results demonstrated that the variability of sporocarp production in tropical forests should be considered in the design of long-term field experiments on myxomycetes.Universidad de Costa Rica/[570-B8-006]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ingeniería::Instituto Investigaciones en Ingeniería (INII)UCR::Sedes Regionales::Sede del Atlántico::Recinto de Paraíso::Finca Experimental Interdisciplinaria de Modelos Agroecológicos (FEIMA

Generation of myxomycete data from three discrete experiments using moist chamber cultures in a Neotropical forest

The moist chamber technique is widely used in ecological research on myxomycetes. However, limited assessments on the usefulness of the technique have been carried out using empirical data. In the present study, three discrete experiments were carried out in a tropical forest in Costa Rica with the main objective of providing meaningful parameters for the design of future studies in similar environments. All three experiments showed that results could be maximized for representativeness by designing studies that purposedly target ecological components of the studied system. In a comparison of recorded data at three heights above the forest ground, a significantly higher number of records and species were observed in the higher vertical partitions, suggesting that collecting research material from the ground, in this ecological setting, reduces the probability of recording the highest species diversity. However, the ground level was associated with a high number of records and species within the genus Didymium, offering relevant information for studies targeting this genus. Similarly, based on effort, results from the present study suggest that a collecting effort designed to record system variability represents a superior cost-benefit situation for synecological studies than a more intense effort designed only for a limited spatial or temporal space, which in turn would reduce the ecological significance of the resultant dataUniversidad de Costa Rica/[570-B8-006]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ingeniería::Instituto Investigaciones en Ingeniería (INII)UCR::Sedes Regionales::Sede del Atlántico::Recinto de Paraíso::Finca Experimental Interdisciplinaria de Modelos Agroecológicos (FEIMA

Can the location of the isolation laboratory affect the generation of myxomycete data using moist chambers? An experiment in the Neotropics

The moist chamber technique, as it is used in myxomycete research, is an extremely useful method to optimize project resources. However, as it occurs with any laboratory-based protocol, the usefulness of this technique should be evaluated using contextual elements, most of which, are lacking in the literature. The present study evaluated the results obtained using the moist chamber technique with the same substrate material, synchronously, in two different laboratories in Costa Rica. Using climate data obtained at both isolation localities and microclimate data obtained directly from the moist chambers, an analysis of differences in results was attempted. Even though variations in results are intrinsic to biological surveys, the results presented herein suggested that some recorded differences could have been linked to the air humidity and the temperature of the moist chamber culture. Even though the two laboratories were only 30 km apart, an average difference of 8.5% in the values of the diversity indices was observed. Also, between 15% and 19% of the species recorded in the total dataset were only observed in one laboratory. In this manner, the present study is useful to keep in mind that myxomycete results using the moist chamber technique, can be extremely influenced by variables that are usually not considered in the general application of the protocol. Perhaps it is time to work on an optimized version of such useful technique.Universidad de Costa Rica/[731-B7-721]/UCR/Costa RicaUniversidad de Costa Rica/[570-B8-006]/UCR/Costa RicaUCR::Sedes Regionales::Sede del Atlántico::Recinto de Paraíso::Finca Experimental Interdisciplinaria de Modelos Agroecológicos (FEIMA)UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ingeniería::Instituto Investigaciones en Ingeniería (INII)UCR::Vicerrectoría de Docencia::Ingeniería::Facultad de Ingeniería::Escuela de Ingeniería de BiosistemasUCR::Sedes Regionales::Sede del Caribe::Recinto Limó

Mixomicetos em ecótonos florestais de bosques temperados e tropicais

Ecotones are interesting portions of forests where microorganisms can be studied for monitoring and diversity purposes. Given the faster life cycle of these organisms, their study in such a context is important to develop models that allow us to understand adaptive microbial dynamics. The main objective of this study was to evaluate the dynamics of myxomycetes present in the leaf litter layer in different geographical locations representing both temperate and tropical systems, using an experimental approach within the ecotones produced by sharp forest edges. Employing the moist chamber technique and three ecological indicators (species richness, diversity, and number of records, as a proxy for abundance) associated with the reproductive phase of the life cycle of myxomycetes, the present study summarized the potential effect of both temperate and tropical ecotones on the distribution of these organisms. Data from 26 locations in six countries showed that all indicators were higher in temperate than in tropical forests and that most differences could be explained by ecological effects. The overall influence of the ecotone on myxomycetes was opposite in temperate and tropical forests, but the data collected for both types of forests showed similarities that could be explained by comparable mathematical models. These results suggested that, with the methods used herein, ecotones do affect ecological patterns of myxomycetes, but the intensity and directionality of such an effect differ depending on the forest type involved.Los ecotonos son porciones interesantes del bosque donde los microorganismos pueden ser estudiados para efectos de monitoreo de la diversidad. Debido a su ciclo de vida rápido, estos organismos pueden ser importantes modelos para comprender la dinámica adaptativa microbiana. El objetivo principal de esta investigación fue evaluar la dinámica de los mixomicetes presentes en la capa de hojarasca en diferentes sitios asociados con sistemas templados y tropicales, por medio de una estrategia experimental, dentro de los ecotonos producidos por los bordes boscosos marcados. Con el uso de la técnica de cámara húmeda y con base en tres indicadores ecológicos (riqueza de especies, diversidad y número de registros, como una aproximación de abundancia) asociados con la fase reproductiva del ciclo de vida de los mixomicetes, el presente estudio resume el efecto potencial de ecotonos templados y tropicales en la distribución de estos organismos. Los datos de 26 sitios en seis países mostraron que todos los indicadores fueron más altos en ecotonos templados y que la mayoría de las diferencias pueden ser explicadas por efectos ecológicos. La influencia de estos sobre los mixomicetes fue opuesta en bosques templados y tropicales, pero los datos acumulados para ambos tipos de bosque mostraron similitudes que pueden ser explicadas por modelos matemáticos comparables. Estos resultados sugieren que, con los métodos usados acá, los ecotonos afectan los patrones ecológicos de los mixomicetes, pero la intensidad y la direccionalidad de tal efecto depende del tipo de bosque.Os ecótonos são parcelas interessantes da floreta em que os micro-organismos podem ser estudados com o objetivo de monitoramento da diversidade. Devido ao seu rápido ciclo de vida, estes organismos podem ser importantes modelos para a compreensão da dinâmica adaptativa microbiana. O principal objetivo desta pesquisa foi avaliar a dinâmica dos mixomicetos presentes na camada de folhagem em diferentes lugares associados aos sistemas temperados e tropicais, mediante uma estratégia experimental, dentro dos ecótonos produzidos pelas margens arborizadas marcadas. Com a utilização da técnica de câmara úmida e com base em três indicadores ecológicos (riqueza de espécies, diversidade e número de registros, como uma aproximação de abundância) associados à fase reprodutiva do ciclo de vida dos mixomicetos, o presente estudo resume o efeito potencial de ecótonos temperados e tropicais na distribuição destes organismos. Os dados de 26 locais em seis países mostraram que todos os indicadores foram mais altos em ecótonos temperados e que a maioria das diferenças podem ser explicadas por efeitos ecológicos. A influência destes sobre os mixomicetos foi oposta em florestas temperados e tropicais, porém os dados acumulados para ambos os tipos de florestas mostraram semelhanças que podem ser explicadas por modelos matemáticos comparáveis. Tais resultados sugerem que, com os métodos usados aqui, os ecótonos afetam os padrões ecológicos dos mixomicetos, mas a intensidade e a direcionalidade de tal efeito depende do tipo de floresta.Universidad de Costa Rica/[731-B5-062]/UCR/Costa RicaUniversidad de Costa Rica/[731-B7-721]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ingeniería::Instituto Investigaciones en Ingeniería (INII)UCR::Vicerrectoría de Docencia::Ingeniería::Facultad de Ingeniería::Escuela de Ingeniería de Biosistema

Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine

Translating whole exome sequencing (WES) for prospective clinical use may impact the care of cancer patients; however, multiple innovations are necessary for clinical implementation. These include: (1) rapid and robust WES from formalin-fixed paraffin embedded (FFPE) tumor tissue, (2) analytical output similar to data from frozen samples, and (3) clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival FFPE tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a “long tail” of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15/16 patients. In one patient, previously undetected findings guided clinical trial enrollment leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine

Gamma-ray and radio properties of six pulsars detected by the fermi large area telescope

We report the detection of pulsed γ-rays for PSRs J0631+1036, J0659+1414, J0742-2822, J1420-6048, J1509-5850, and J1718-3825 using the Large Area Telescope on board the Fermi Gamma-ray Space Telescope (formerly known as GLAST). Although these six pulsars are diverse in terms of their spin parameters, they share an important feature: their γ-ray light curves are (at least given the current count statistics) single peaked. For two pulsars, there are hints for a double-peaked structure in the light curves. The shapes of the observed light curves of this group of pulsars are discussed in the light of models for which the emission originates from high up in the magnetosphere. The observed phases of the γ-ray light curves are, in general, consistent with those predicted by high-altitude models, although we speculate that the γ-ray emission of PSR J0659+1414, possibly featuring the softest spectrum of all Fermi pulsars coupled with a very low efficiency, arises from relatively low down in the magnetosphere. High-quality radio polarization data are available showing that all but one have a high degree of linear polarization. This allows us to place some constraints on the viewing geometry and aids the comparison of the γ-ray light curves with high-energy beam models

X-ray Polarization of the Eastern Lobe of SS 433

How astrophysical systems translate the kinetic energy of bulk motion into the acceleration of particles to very high energies is a pressing question. SS 433 is a microquasar that emits TeV gamma-rays indicating the presence of high-energy particles. A region of hard X-ray emission in the eastern lobe of SS 433 was recently identified as an acceleration site. We observed this region with the Imaging X-ray Polarimetry Explorer and measured a polarization degree in the range 38% to 77%. The high polarization degree indicates the magnetic field has a well ordered component if the X-rays are due to synchrotron emission. The polarization angle is in the range -12 to +10 degrees (east of north) which indicates that the magnetic field is parallel to the jet. Magnetic fields parallel to the bulk flow have also been found in supernova remnants and the jets of powerful radio galaxies. This may be caused by interaction of the flow with the ambient medium.Comment: 8 pages, accepted in the Astrophysical Journal Letter

First X-ray polarization measurement confirms the low black-hole spin in LMC X-3

X-ray polarization is a powerful tool to investigate the geometry of accreting material around black holes, allowing independent measurements of the black hole spin and orientation of the innermost parts of the accretion disk. We perform the X-ray spectro-polarimetric analysis of an X-ray binary system in the Large Magellanic Cloud, LMC X-3, that hosts a stellar-mass black hole, known to be persistently accreting since its discovery. We report the first detection of the X-ray polarization in LMC X-3 with the Imaging X-ray Polarimetry Explorer, and find the average polarization degree of 3.2% +- 0.6% and a constant polarization angle -42 deg +- 6 deg over the 2-8 keV range. Using accompanying spectroscopic observations by NICER, NuSTAR, and the Neil Gehrels Swift observatories, we confirm previous measurements of the black hole spin via the X-ray continuum method, a ~ 0.2. From polarization analysis only, we found consistent results with low black-hole spin, with an upper limit of a < 0.7 at a 90% confidence level. A slight increase of the polarization degree with energy, similar to other black-hole X-ray binaries in the soft state, is suggested from the data but with a low statistical significance.Comment: 14 pages, 8 figures, submitted to Ap

The first X-ray polarimetric observation of the black hole binary LMC X-1

We report on an X-ray polarimetric observation of the high-mass X-ray binary LMC X-1 in the high/soft state, obtained by the Imaging X-ray Polarimetry Explorer (IXPE) in October 2022. The measured polarization is below the minimum detectable polarization of 1.1 per cent (at the 99 per cent confidence level). Simultaneously, the source was observed with the NICER, NuSTAR and SRG/ART-XC instruments, which enabled spectral decomposition into a dominant thermal component and a Comptonized one. The low 2-8 keV polarization of the source did not allow for strong constraints on the black-hole spin and inclination of the accretion disc. However, if the orbital inclination of about 36 degrees is assumed, then the upper limit is consistent with predictions for pure thermal emission from geometrically thin and optically thick discs. Assuming the polarization degree of the Comptonization component to be 0, 4, or 10 per cent, and oriented perpendicular to the polarization of the disc emission (in turn assumed to be perpendicular to the large scale ionization cone orientation detected in the optical band), an upper limit to the polarization of the disc emission of 1.0, 0.9 or 0.9 per cent, respectively, is found (at the 99 per cent confidence level).Comment: 12 pages, 9 figures, 4 tables. Accepted for publication in MNRA