Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest ...carbon cycle--particularly net primary productivity and carbon storage--increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree's total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to undertand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.
The widespread use of immune checkpoint inhibitors (ICIs) has revolutionised treatment of multiple cancer types. However, selecting patients who may benefit from ICI remains challenging. Artificial ...intelligence (AI) approaches allow exploitation of high-dimension oncological data in research and development of precision immuno-oncology.
We conducted a systematic literature review of peer-reviewed original articles studying the ICI efficacy prediction in cancer patients across five data modalities: genomics (including genomics, transcriptomics, and epigenomics), radiomics, digital pathology (pathomics), and real-world and multimodality data.
A total of 90 studies were included in this systematic review, with 80% published in 2021-2022. Among them, 37 studies included genomic, 20 radiomic, 8 pathomic, 20 real-world, and 5 multimodal data. Standard machine learning (ML) methods were used in 72% of studies, deep learning (DL) methods in 22%, and both in 6%. The most frequently studied cancer type was non-small-cell lung cancer (36%), followed by melanoma (16%), while 25% included pan-cancer studies. No prospective study design incorporated AI-based methodologies from the outset; rather, all implemented AI as a post hoc analysis. Novel biomarkers for ICI in radiomics and pathomics were identified using AI approaches, and molecular biomarkers have expanded past genomics into transcriptomics and epigenomics. Finally, complex algorithms and new types of AI-based markers, such as meta-biomarkers, are emerging by integrating multimodal/multi-omics data.
AI-based methods have expanded the horizon for biomarker discovery, demonstrating the power of integrating multimodal data from existing datasets to discover new meta-biomarkers. While most of the included studies showed promise for AI-based prediction of benefit from immunotherapy, none provided high-level evidence for immediate practice change. A priori planned prospective trial designs are needed to cover all lifecycle steps of these software biomarkers, from development and validation to integration into clinical practice.
FlyBase (http://flybase.org) is the leading database and web portal for genetic and genomic information on the fruit fly Drosophila melanogaster and related fly species. Whether you use the fruit fly ...as an experimental system or want to apply Drosophila biological knowledge to another field of study, FlyBase can help you successfully navigate the wealth of available Drosophila data. Here, we review the FlyBase web site with novice and less-experienced users of FlyBase in mind and point out recent developments stemming from the availability of genome-wide data from the modENCODE project. The first section of this paper explains the organization of the web site and describes the report pages available on FlyBase, focusing on the most popular, the Gene Report. The next section introduces some of the search tools available on FlyBase, in particular, our heavily used and recently redesigned search tool QuickSearch, found on the FlyBase homepage. The final section concerns genomic data, including recent modENCODE (http://www.modencode.org) data, available through our Genome Browser, GBrowse.
Background
Individuals with Down syndrome (DS) appear to perform at a level that is commensurate with developmental expectations on simple tasks of selective attention. In this study, we examine how ...their selective attention is impacted by target changes that unfold over both time and space. This increased complexity reflects an attempt at greater ecological validity in an experimental task, as a steppingstone for better understanding attention among persons with DS in real‐world environments.
Methods
A modified flanker task was used to assess visual temporal and spatial filtering among persons with DS (n = 14) and typically developing individuals (n = 14) matched on non‐verbal mental age (mental age = 8.5 years). Experimental conditions included varying the stimulus onset asynchronies between the onset of the target and flankers, the distances between the target and flankers, and the similarity of the target and flankers.
Results
Both the participants with DS and the typically developing participants showed slower reaction times and lower accuracy rates when the flankers appeared closer in time and/or space to the target.
Conclusion
No group differences were found on a broad level, but the findings suggest that dynamic stimuli may be processed differently by those with DS. Implications of the findings are discussed in relation to the developmental approach to intellectual disability originally articulated by Ed Zigler.
Fungal decay of heart wood creates hollows and areas of reduced wood density within the stems of living trees known as stem rot. Although stem rot is acknowledged as a source of error in forest ...aboveground biomass (AGB) estimates, there are few data sets available to evaluate the controls over stem rot infection and severity in tropical forests. Using legacy and recent data from 3180 drilled, felled, and cored stems in mixed dipterocarp forests in Sarawak, Malaysian Borneo, we quantified the frequency and severity of stem rot in a total of 339 tree species, and related variation in stem rot with tree size, wood density, taxonomy, and species' soil association, as well as edaphic conditions. Predicted stem rot frequency for a 50 cm tree was 53 % of felled, 39 % of drilled, and 28 % of cored stems, demonstrating differences among methods in rot detection ability. The percent stem volume infected by rot, or stem rot severity, ranged widely among trees with stem rot infection (0.1-82.8 %) and averaged 9 % across all trees felled. Tree taxonomy explained the greatest proportion of variance in both stem rot frequency and severity among the predictors evaluated in our models. Stem rot frequency, but not severity, increased sharply with tree diameter, ranging from 13 % in trees 10-30 cm DBH to 54 % in stems ≥ 50 cm DBH across all data sets. The frequency of stem rot increased significantly in soils with low pH and cation concentrations in topsoil, and stem rot was more common in tree species associated with dystrophic sandy soils than with nutrient-rich clays. When scaled to forest stands, the maximum percent of stem biomass lost to stem rot varied significantly with soil properties, and we estimate that stem rot reduces total forest AGB estimates by up to 7 % relative to what would be predicted assuming all stems are composed strictly of intact wood. This study demonstrates not only that stem rot is likely to be a significant source of error in forest AGB estimation, but also that it strongly covaries with tree size, taxonomy, habitat association, and soil resources, underscoring the need to account for tree community composition and edaphic variation in estimating carbon storage in tropical forests.
Reflux scintigraphy is often used to diagnose gastro-esophageal reflux disease (GERD). However, the efficacy of this study remains controversial. Our aim was to determine the role of reflux ...scintigraphy in diagnosing GERD by comparing it to 24 h combined pH-impedance study as the gold standard.
Adult patients who presented for investigations of reflux symptoms were prospectively recruited into the study. All patients underwent high resolution esophageal manometry and those with major motor disorders of the esophagus were excluded. Eligible patients immediately underwent reflux scintigraphy following insertion of the pH-impedance catheter.
Thirty patients were included in the study. Using a total acid exposure time (AET) of >4.2% as the reference for abnormal acid reflux, reflux scintigraphy had a sensitivity and specificity of 62.5 and 68.2%, respectively, in detecting acid reflux. When compared to AET >6%, reflux scintigraphy had a sensitivity and specificity of 66.7 and 62.5%, respectively, and a positive predictive value of 30.8% and a negative predictive value of 88.2%. There were no associations between outcomes of reflux scintigraphy and total AET (p = .46), total (acid or non-acid) reflux events (p = 0.11), proximal AET (p = .33) or the number of proximal reflux episodes (p = .75) on 24 h pH-impedance study.
Reflux scintigraphy has limited role in diagnosing GERD when compared to 24 h combined pH-impedance monitoring.
Neuromedin U (NMU) is a hypothalamic neuropeptide with important roles in several metabolic processes, recently suggested as potential therapeutic target for obesity. We analysed the associations ...between NMU gene variants and haplotypes and body mass index (BMI) in a large sample of European children.
From a large European multi-center study on childhood obesity, 4,528 children (2.0-9.9 years, mean age 6.0±1.8 SD; boys 52.2%) were randomly selected, stratifying by age, sex and country, and genotyped for tag single nucleotide polymorphisms (SNPs; rs6827359, T:C; rs12500837, T:C; rs9999653,C:T) of NMU gene, then haplotypes were inferred. Regression models were applied to estimate the associations between SNPs or haplotypes and BMI as well as other anthropometric measures. BMI was associated with all NMU SNPs (p<0.05). Among five haplotypes inferred, the haplotype carrying the minor alleles (CCT, frequency = 22.3%) was the only associated with lower BMI values (beta = -0.16, 95%CI:-0.28,-0.04, p = 0.006; z-score, beta = -0.08, 95%CI:-0.14,-0.01, p = 0.019) and decreased risk of overweight/obesity (OR = 0.81, 95%CI:0.68,0.97, p = 0.020) when compared to the most prevalent haplotype (codominant model). Similar significant associations were also observed using the same variables collected after two years' time (BMI, beta = -0.25, 95%CI:-0.41,-0.08, p = 0.004; z-score, beta = -0.10, 95%CI:-0.18,-0.03, p = 0.009; overweight/obesity OR = 0.81, 95%CI:0.66,0.99, p = 0.036). The association was age-dependent in girls (interaction between CCT haplotypes and age, p = 0.008), more evident between 7 and 9 years of age. The CCT haplotype was consistently associated with lower levels of fat mass, skinfold thickness, hip and arm circumferences both at T0 and at T1, after adjustment for multiple testing (FDR-adjusted p<0.05).
This study shows an association between a NMU haplotype and anthropometric indices, mainly linked to fat mass, which appears to be age- and sex-specific in children. Genetic variations within or in linkage with this haplotype should be investigated to identify functional variants responsible for the observed phenotypic variation.
Highlights • Cognitive processing was compared in higher and lower fit pre-adolescents. • Response preparation, prior to perception, in higher fit pre-adolescents had larger prefrontal activity. • ...Aerobic fitness related to increases in brain activity in early perceptual processing and response accuracy. • Aerobic fitness related to increases in proactive motor control in the prefrontal cortex of pre-adolescents.
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