Univariate and multivariate methods are commonly used to explore the spatial and temporal dynamics of ecological communities, but each has limitations, including oversimplification or ion of ...communities. Rank abundance curves (RACs) potentially integrate these existing methodologies by detailing species‐level community changes. Here, we had three goals: first, to simplify analysis of community dynamics by developing a coordinated set of R functions, and second, to demystify the relationships among univariate, multivariate, and RACs measures, and examine how each is influenced by the community parameters as well as data collection methods. We developed new functions for studying temporal changes and spatial differences in RACs in an update to the R package library(“codyn”), alongside other new functions to calculate univariate and multivariate measures of community dynamics. We also developed a new approach to studying changes in the shape of RAC curves. The R package update presented here increases the accessibility of univariate and multivariate measures of community change over time and difference over space. Next, we use simulated and real data to assess the RAC and multivariate measures that are output from our new functions, studying (1) if they are influenced by species richness and evenness, temporal turnover, and spatial variability and (2) how the measures are related to each other. Lastly, we explore the use of the measures with an example from a long‐term nutrient addition experiment. We find that the RAC and multivariate measures are not sensitive to species richness and evenness and that all the measures detail unique aspects of temporal change or spatial differences. We also find that species reordering is the strongest correlate of a multivariate measure of compositional change and explains most community change observed in long‐term nutrient addition experiment. Overall, we show that species reordering is potentially an understudied determinant of community changes over time or differences between treatments. The functions developed here should enhance the use of RACs to further explore the dynamics of ecological communities.
WMAP precision data enables accurate testing of cosmological models. We find that the emerging standard model of cosmology, a flat Lambda-dominated universe seeded by nearly scale-invariant adiabatic ...Gaussian fluctuations, fits the WMAP data. With parameters fixed only by WMAP data, we can fit finer scale CMB measurements and measurements of large scle structure (galaxy surveys and the Lyman alpha forest). This simple model is also consistent with a host of other astronomical measurements. We then fit the model parameters to a combination of WMAP data with other finer scale CMB experiments (ACBAR and CBI), 2dFGRS measurements and Lyman alpha forest data to find the model's best fit cosmological parameters: h=0.71+0.04-0.03, Omega_b h^2=0.0224+-0.0009, Omega_m h^2=0.135+0.008-0.009, tau=0.17+-0.06, n_s(0.05/Mpc)=0.93+-0.03, and sigma_8=0.84+-0.04. WMAP's best determination of tau=0.17+-0.04 arises directly from the TE data and not from this model fit, but they are consistent. These parameters imply that the age of the universe is 13.7+-0.2 Gyr. The data favors but does not require a slowly varying spectral index. By combining WMAP data with other astronomical data sets, we constrain the geometry of the universe, Omega_tot = 1.02 +- 0.02, the equation of state of the dark energy w < -0.78 (95% confidence limit assuming w >= -1), and the energy density in stable neutrinos, Omega_nu h^2 < 0.0076 (95% confidence limit). For 3 degenerate neutrino species, this limit implies that their mass is less than 0.23 eV (95% confidence limit). The WMAP detection of early reionization rules out warm dark matter.
We present full sky microwave maps in five bands (23 to 94 GHz) from the WMAP first year sky survey. Calibration errors are <0.5% and the low systematic error level is well specified. The 2<l<900 ...anisotropy power spectrum is cosmic variance limited for l<354 with a signal-to-noise ratio >1 per mode to l=658. The temperature-polarization cross-power spectrum reveals both acoustic features and a large angle correlation from reionization. The optical depth of reionization is 0.17 +/- 0.04, which implies a reionization epoch of 180+220-80 Myr (95% CL) after the Big Bang at a redshift of 20+10-9 (95% CL) for a range of ionization scenarios. This early reionization is incompatible with the presence of a significant warm dark matter density. The age of the best-fit universe is 13.7 +/- 0.2 Gyr old. Decoupling was 379+8-7 kyr after the Big Bang at a redshift of 1089 +/- 1. The thickness of the decoupling surface was dz=195 +/- 2. The matter density is Omega_m h^2 = 0.135 +0.008 -0.009, the baryon density is Omega_b h^2 = 0.0224 +/- 0.0009, and the total mass-energy of the universe is Omega_tot = 1.02 +/- 0.02. The spectral index of scalar fluctuations is fit as n_s = 0.93 +/- 0.03 at wavenumber k_0 = 0.05 Mpc^-1, with a running index slope of dn_s/d ln k = -0.031 +0.016 -0.018 in the best-fit model. This flat universe model is composed of 4.4% baryons, 22% dark matter and 73% dark energy. The dark energy equation of state is limited to w<-0.78 (95% CL). Inflation theory is supported with n_s~1, Omega_tot~1, Gaussian random phases of the CMB anisotropy, and superhorizon fluctuations. An admixture of isocurvature modes does not improve the fit. The tensor-to-scalar ratio is r(k_0=0.002 Mpc^-1)<0.90 (95% CL).
Autophagy is a membrane-trafficking mechanism that delivers cytoplasmic constituents into the lysosome/vacuole for bulk protein degradation. This mechanism is involved in the preservation of ...nutrients under starvation condition as well as the normal turnover of cytoplasmic component. Aberrant autophagy has been reported in several neurodegenerative disorders, hepatitis, and myopathies. Here, we generated conditional knockout mice of Atg7, an essential gene for autophagy in yeast. Atg7 was essential for ATG conjugation systems and autophagosome formation, amino acid supply in neonates, and starvation-induced bulk degradation of proteins and organelles in mice. Furthermore, Atg7 deficiency led to multiple cellular abnormalities, such as appearance of concentric membranous structure and deformed mitochondria, and accumulation of ubiquitin-positive aggregates. Our results indicate the important role of autophagy in starvation response and the quality control of proteins and organelles in quiescent cells.
The asteroid impact near the Russian city of Chelyabinsk on 15 February 2013 was the largest airburst on Earth since the 1908 Tunguska event, causing a natural disaster in an area with a population ...exceeding one million. Because it occurred in an era with modern consumer electronics, field sensors, and laboratory techniques, unprecedented measurements were made of the impact event and the meteoroid that caused it. Here, we document the account of what happened, as understood now, using comprehensive data obtained from astronomy, planetary science, geophysics, meteorology, meteoritics, and cosmochemistry and from social science surveys. A good understanding of the Chelyabinsk incident provides an opportunity to calibrate the event, with implications for the study of near-Earth objects and developing hazard mitigation strategies for planetary protection.
Neonatal hypoxic/ischemic (H/I) brain injury causes neurological impairment, including cognitive and motor dysfunction as well as seizures. However, the molecular mechanisms regulating neuron death ...after H/I injury are poorly defined and remain controversial. Here we show that Atg7, a gene essential for autophagy induction, is a critical mediator of H/I-induced neuron death. Neonatal mice subjected to H/I injury show dramatically increased autophagosome formation and extensive hippocampal neuron death that is regulated by both caspase-3-dependent and -independent execution. Mice deficient in Atg7 show nearly complete protection from both H/I-induced caspase-3 activation and neuron death indicating that Atg7 is critically positioned upstream of multiple neuronal death executioner pathways. Adult H/I brain injury also produces a significant increase in autophagy, but unlike neonatal H/I, neuron death is almost exclusively caspase-3-independent. These data suggest that autophagy plays an essential role in triggering neuronal death execution after H/I injury and Atg7 represents an attractive therapeutic target for minimizing the neurological deficits associated with H/I brain injury.
Defining codominance in plant communities Gray, Jesse E.; Komatsu, Kimberly J.; Smith, Melinda D.
The New phytologist,
June 2021, 2021-06-00, 20210601, Letnik:
230, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Summary
Species dominance and biodiversity in plant communities have received considerable attention and characterisation. However, species codominance, while often alleged, is seldom defined or ...quantified. Codominance is a common phenomenon and is likely to be an important driver of community structure, ecosystem function and the stability of both. Here we review the use of the term ‘codominance’ and find inconsistencies in its use, suggesting that the scientific community currently lacks a universal understanding of codominance. We address this issue by: (1) qualitatively defining codominance as mostly shared abundance that is distinctively isolated within a subset of a community, and (2) presenting a novel metric for quantifying the degree to which relative abundances are shared among a codominant subset of plant species, while also accounting for the remaining species within a plant community. Using both simulated and real‐world data, we then demonstrate the process of applying the codominance metric to compare communities and to generate a quantitatively defensible subset of species to consider codominant within a community. We show that our metric effectively distinguishes the degree of codominance between four types of grassland ecosystems as well as simulated ecosystems with varying degrees of abundance sharing among community members. Overall, we make the case that increased research focusses on the conditions under which codominance occurs and the consequences for species coexistence, community structure and ecosystem function that would considerably advance the fields of community and ecosystem ecology.
Summary
We developed an en bloc lymphadenectomy method in the upper mediastinum with a single-port mediastinoscopic cervical approach. This study was designed to evaluate the safety and efficacy of ...single-port mediastinoscope-assisted transhiatal esophagectomy for thoracic esophageal cancer. The perioperative outcomes of 60 patients with thoracic esophageal cancer who underwent this operation between March 2014 and June 2016 were retrospectively analyzed. The upper mediastinal dissection including lymphadenectomy along the left recurrent laryngeal nerve, using a left cervical approach, was performed with a single-port mediastinoscopic technique, which was used to improve the visibility and handling in the deep mediastinum around the aortic arch. The lymphadenectomy along the right recurrent laryngeal nerve was performed under direct vision using a right cervical approach. Bilateral cervical approaches were followed by hand-assisted laparoscopic transhiatal esophagectomy with en bloc lymphadenectomy in the middle and lower mediastinum. Tumors were mainly located in the middle thoracic esophagus (n = 33), and most tumors were squamous cell carcinoma (n = 58). Pretreatment diagnoses were stage I, 19; II, 13; III, 24; IV, 4. Preoperative chemotherapy was performed for 40 patients. The median operation time and blood loss were 363 minutes and 235 mL, respectively. There were two patients who underwent conversion to thoracotomy. Perioperative complications were evaluated and graded according to the Clavien-Dindo (CD) and the Esophagectomy Complications Consensus Group (ECCG) classifications. Postoperatively, pneumonia was observed in four patients (CD, Grade II, 2; Grade IIIb, 2), although vocal cord palsy was more frequent (ECCG, Type I, 12; Type III, 8). The median number of thoracic lymph nodes resected was 21, and the R0 resection rate was 95%. Single-port mediastinoscope-assisted transhiatal esophagectomy is feasible, in terms of perioperative outcomes, for a radical surgery for thoracic esophageal cancer, although its safety needs to be further demonstrated.
We examined plasma microRNA (miRNA) concentrations from patients with gastric cancers (GCs) to assess their clinical application for diagnosing and monitoring diseases.
We initially investigated the ...appropriateness of plasma miRNA assay, and then compared plasma miRNA results with the expressions in cancer tissues from eight GC patients, and also compared plasma miRNAs between pre- and post-operative paired samples from 10 GC patients. Then, plasma miRNAs (miR-17-5p, miR-21, miR-106a, miR-106b and let-7a) were analysed in 69 GC patients and 30 healthy volunteers in total.
The initial analysis showed that miRNAs were stable and detectable in all plasma samples, and the plasma miRNA levels reflected the tumour miRNAs in most cases. The levels of these miRNAs were significantly reduced in post-operative samples. In large-scale analysis, the plasma concentrations of miRNAs (miR-17-5p, miR-21, miR-106a, miR-106b) were significantly higher in GC patients than controls (P=0.05, 0.006, 0.008 and <0.001 respectively), whereas let-7a was lower in GC patients (P=0.002). The values of the area under the receiver-operating characteristic curve were 0.721 for the miR-106b assay and 0.879 for the miR-106a/let-7a ratio assay.
Detection of circulating miRNAs might provide new complementary tumour markers for GC.
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