Recent studies have shown the importance of subtropical forests as terrestrial carbon sinks and also their vulnerability to human disturbances and climate change. The Semi-deciduous Atlantic Forest ...presents large extensions replaced by productive uses, such as tree plantations, and forest remnants showing high levels of structural heterogeneity. No studies have performed carbon stock densities estimations in different pools in the region. We wonder how changes in forest structure and forest replacement by pine plantations affect ecosystem carbon stock densities in different pools and fluxes. We performed carbon estimates based on field data and compared closed (CF) and open (OF) canopy natural forest patches and Pinus taeda plantations at harvest age (PP). Structural changes in the natural forest had a profound effect on the ecosystem by halving the forest carbon stock while pulp-intended pine plantations reached the carbon stock of closed forest at harvest age. Main changes from CF to OF were a 55% decrease in the carbon of biomass and a 42% decrease in SOC. Instead, carbon stock density in biomass of PP was similar to CF but the carbon in fallen deadwood was 78% lower while in the litter layer was double; the SOC at 0–5 cm depth was 31% lower in PP than CF. Our study shows that structural changes in the natural forest halve the forest carbon stock while pulp-intended pine plantations can reach the closed forest carbon stock at harvest age. However, PP do not seem to be effective for carbon storage in the long term because of regular harvesting and clearing and their short-life products. Therefore, to effectively store the forest carbon, arresting deforestation, replacement and degradation of the original forest is crucial.
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•Biomass carbon in pine plantations almost equals closed forest at the harvest age.•Biomass carbon is about 50% lower in open-canopy forests than in closed ones.•Soil organic carbon at 0–5 cm depth is highest in closed-canopy forest patches.
Mammals exhibit marked interindividual variations in their gut microbiota, but it remains unclear if this is primarily driven by host genetics or by extrinsic factors like dietary intake. To address ...this, we examined the effect of dietary perturbations on the gut microbiota of five inbred mouse strains, mice deficient for genes relevant to host-microbial interactions (MyD88−/−, NOD2−/−, ob/ob, and Rag1−/−), and >200 outbred mice. In each experiment, consumption of a high-fat, high-sugar diet reproducibly altered the gut microbiota despite differences in host genotype. The gut microbiota exhibited a linear dose response to dietary perturbations, taking an average of 3.5 days for each diet-responsive bacterial group to reach a new steady state. Repeated dietary shifts demonstrated that most changes to the gut microbiota are reversible, while also uncovering bacteria whose abundance depends on prior consumption. These results emphasize the dominant role that diet plays in shaping interindividual variations in host-associated microbial communities.
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•Diet reproducibly alters the gut microbiota of mice with diverse genotypes•The gut microbiota exhibits a linear dose response to dietary perturbations•Postperturbation, most bacterial taxa reach a new steady state in 3 days•Most changes are reversible, but some taxa reflect prior diets (hysteresis)
Diet-induced manipulation of gut microbes holds therapeutic potential, but the reproducibility of effects across individuals remains unknown. Carmody et al. show that diet reproducibly alters the gut microbiota despite differences in host genotype. Although most bacteria respond rapidly and consistently to repeated dietary shifts, some exhibit dependence on past diet.
Using a state-of-the-art semi analytic model for galaxy formation, we investigated in detail the effects of black hole (BH) accretion triggered by disk instabilities (DI) in isolated galaxies on the ...evolution of the AGN population. Specifically, we took on, developed, and expanded the Hopkins & Quataert (2011, MNRAS, 411, 1027) model for the mass inflow following disk perturbations, based on a physical description of nuclear inflows and tested against aimed N-body simulations. We compared the evolution of AGN due to such a DI accretion mode with that arising in a scenario where galaxy interactions (IT mode) produce the sudden destabilization of large quantities of gas feeding the AGN; this constitutes the standard AGN feeding mode implemented in the earliest versions of most semi-analytic models. To study the maximal contribution of DI to the evolution of the AGN population, we extended and developed the DI model to assess the effects of changing the assumed disk surface density profile, and to obtain lower limits for the nuclear star formation rates associated to the DI accretion mode. We obtained the following results: i) For AGN with luminosity M1450 ≳ − 26, the DI mode can provide the BH accretion needed to match the observed AGN luminosity functions up to z ≈ 4.5. In such a luminosity range and redshift, it constitutes a viable candidate mechanism to fuel AGN, and can compete with the IT scenario as the main driver of cosmological evolution of the AGN population. ii) The DI scenario cannot provide the observed abundance of high-luminosity QSO with M1450 ≤ −26 AGN, as well as the abundance of high-redhshift z ≳ 4.5 QSO with M1450 ≤ −24. As found in our earliest works, the IT scenario provides an acceptable match to the observed luminosity functions up to z ≈ 6. iii) The dispersion of the distributions of Eddington ratio λ for low- and intermediate-luminosity AGN (bolometric LAGN = 1043−1045 erg s-1) is predicted to be much smaller in the DI scenario compared to the IT mode. iv) The above conclusions concerning the DI mode are robust with respect to the explored variants of the DI model. We discuss the physical origin of our findings. Finally, we discuss how it is possible to pin down the dominant fueling mechanism of AGN in the low-intermediate luminosity range M1450 ≳ −26 where the DI and the IT modes are both viable candidates as the main drivers of the AGN evolution. We show that an interesting discriminant could be provided by the fraction of AGN with high Eddington ratios λ ≥ 0.5, since it increases with luminosity in the IT case, while the opposite is true in the DI scenario.
Genetic variation modulates protein expression through both transcriptional and post-transcriptional mechanisms. To characterize the consequences of natural genetic diversity on the proteome, here we ...combine a multiplexed, mass spectrometry-based method for protein quantification with an emerging outbred mouse model containing extensive genetic variation from eight inbred founder strains. By measuring genome-wide transcript and protein expression in livers from 192 Diversity outbred mice, we identify 2,866 protein quantitative trait loci (pQTL) with twice as many local as distant genetic variants. These data support distinct transcriptional and post-transcriptional models underlying the observed pQTL effects. Using a sensitive approach to mediation analysis, we often identified a second protein or transcript as the causal mediator of distant pQTL. Our analysis reveals an extensive network of direct protein-protein interactions. Finally, we show that local genotype can provide accurate predictions of protein abundance in an independent cohort of collaborative cross mice.
Advances in the diagnostic and therapeutic management of patients with bloodstream infections (BSIs) have been achieved in the last years, improving clinical outcome. However, mortality associated ...with some pathogens, such as Staphylococcus aureus and Enterococcus spp., is still high. In addition, the spread of antibiotic resistance, mainly among Gram-negative bacteria, reduces treatment options in some circumstances. Therefore, interest in new drugs, combination regimens and optimal dosing schedules is rising.
Our aim is to summarize the current evidence on available antibiotic regimens for patients with bacterial BSI, focusing on drug choice, combination regimens and optimal dosing schedules. We selected bacteria that are difficult to manage because of virulence factors (i.e. methicillin-susceptible S. aureus), tolerance to antibiotic activity (i.e. Enterococcus faecalis), and/or susceptibility patterns (i.e. methicillin-resistant S. aureus, vancomycin-resistant enterococci, carbapenem-resistant Enterobacteriaceae, multidrug-resistant Pseudomonas aeruginosa and carbapenem-resistant Acinetobacter baumannii).
MEDLINE search with English language and publication in the last 5 years as limits.
The literature gaps on the use of new drugs, the uncertainties regarding the use of combination regimens, and the need to optimize dosing schedules in some circumstances (e.g. augmented renal clearance, renal replacement therapy, high inoculum BSI sources, and isolation of bacteria showing high MICs) have been revised.
The JAX Diversity Outbred population is a new mouse resource derived from partially inbred Collaborative Cross strains and maintained by randomized outcrossing. As such, it segregates the same ...allelic variants as the Collaborative Cross but embeds these in a distinct population architecture in which each animal has a high degree of heterozygosity and carries a unique combination of alleles. Phenotypic diversity is striking and often divergent from phenotypes seen in the founder strains of the Collaborative Cross. Allele frequencies and recombination density in early generations of Diversity Outbred mice are consistent with expectations based on simulations of the mating design. We describe analytical methods for genetic mapping using this resource and demonstrate the power and high mapping resolution achieved with this population by mapping a serum cholesterol trait to a 2-Mb region on chromosome 3 containing only 11 genes. Analysis of the estimated allele effects in conjunction with complete genome sequence data of the founder strains reduced the pool of candidate polymorphisms to seven SNPs, five of which are located in an intergenic region upstream of the Foxo1 gene.
► Biological and separation process performance has been evaluated at 33°C, 70days SRT, and variable HRT. ► Almost 90% of COD removal was achieved with low effluent volatile fatty acid concentrations ...(<20mgL−1). ► The observed methane yield was quite low due to the low influent COD/SO4–S ratio and SRB and MA competition. ► No irreversible fouling problems were detected, even for high total solid concentrations. ► A flux of 10 LMH and MLTS above 22gL−1 (sub-critical conditions) led to a low TMP (<0.1bar).
The aim of this study was to assess the effect of several operational variables on both biological and separation process performance in a submerged anaerobic membrane bioreactor pilot plant that treats urban wastewater. The pilot plant is equipped with two industrial hollow-fibre ultrafiltration membrane modules (PURON® Koch Membrane Systems, 30m2 of filtration surface each). It was operated under mesophilic conditions (at 33°C), 70days of SRT, and variable HRT ranging from 20 to 6h. The effects of the influent COD/SO4–S ratio (ranging from 2 to 12) and the MLTS concentration (ranging from 6 to 22gL−1) were also analysed. The main performance results were about 87% of COD removal, effluent VFA below 20mgL−1 and biogas methane concentrations over 55% v/v. Methane yield was strongly affected by the influent COD/SO4–S ratio. No irreversible fouling problems were detected, even for MLTS concentrations above 22gL−1.
We present CloudNeo, a cloud-based computational workflow for identifying patient-specific tumor neoantigens from next generation sequencing data. Tumor-specific mutant peptides can be detected by ...the immune system through their interactions with the human leukocyte antigen complex, and neoantigen presence has recently been shown to correlate with anti T-cell immunity and efficacy of checkpoint inhibitor therapy. However computing capabilities to identify neoantigens from genomic sequencing data are a limiting factor for understanding their role. This challenge has grown as cancer datasets become increasingly abundant, making them cumbersome to store and analyze on local servers. Our cloud-based pipeline provides scalable computation capabilities for neoantigen identification while eliminating the need to invest in local infrastructure for data transfer, storage or compute. The pipeline is a Common Workflow Language (CWL) implementation of human leukocyte antigen (HLA) typing using Polysolver or HLAminer combined with custom scripts for mutant peptide identification and NetMHCpan for neoantigen prediction. We have demonstrated the efficacy of these pipelines on Amazon cloud instances through the Seven Bridges Genomics implementation of the NCI Cancer Genomics Cloud, which provides graphical interfaces for running and editing, infrastructure for workflow sharing and version tracking, and access to TCGA data.
The CWL implementation is at: https://github.com/TheJacksonLaboratory/CloudNeo. For users who have obtained licenses for all internal software, integrated versions in CWL and on the Seven Bridges Cancer Genomics Cloud platform (https://cgc.sbgenomics.com/, recommended version) can be obtained by contacting the authors.
jeff.chuang@jax.org.
Supplementary data are available at Bioinformatics online.
Abstract
The degradation of spatial resolution in star-forming regions, observed at large distances (d ≳ 1 kpc) with Herschel, can lead to estimates of the physical parameters of the detected compact ...sources (clumps), which do not necessarily mirror the properties of the original population of cores. This paper aims at quantifying the bias introduced in the estimation of these parameters by the distance effect. To do so, we consider Herschel maps of nearby star-forming regions taken from the Herschel Gould Belt survey, and simulate the effect of increased distance to understand what amount of information is lost when a distant star-forming region is observed with Herschel resolution. In the maps displaced to different distances we extract compact sources, and we derive their physical parameters as if they were original Herschel infrared Galactic Plane Survey maps of the extracted source samples. In this way, we are able to discuss how the main physical properties change with distance. In particular, we discuss the ability of clumps to form massive stars: we estimate the fraction of distant sources that are classified as high-mass stars-forming objects due to their position in the mass versus radius diagram, that are only ‘false positives’. We also give a threshold for high-mass star formation
$M>1282 \ \left(\frac{r}{ \mathrm{pc}}\right)^{1.42} {\rm M}_{{\odot }}$
. In conclusion, this paper provides the astronomer dealing with Herschel
maps of distant star-forming regions with a set of prescriptions to partially recover the character of the core population in unresolved clumps.
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