Montane Temperate-Boreal Forests Retain the Leaf Economic Spectrum Despite Intraspecific Variability

Trait-based analyses provide powerful tools for developing a generalizable, physiologically grounded understanding of how forest communities are responding to ongoing environmental changes. Key challenges lie in (1) selecting traits that best characterize the ecological performance of species in the community and (2) determining the degree and importance of intraspecific variability in those traits. Recent studies suggest that globally evident trait correlations (trait dimensions), such as the leaf economic spectrum, may be weak or absent at local scales. Moreover, trait-based analyses that utilize a mean value to represent a species may be misleading. Mean trait values are particularly problematic if species trait value rankings change along environmental gradients, resulting in species trait crossover. To assess how plant traits (1) covary at local spatial scales, (2) vary across the dominant environmental gradients, and (3) can be partitioned within and across taxa, we collected data on 9 traits for 13 tree species spanning the montane temperate—boreal forest ecotones of New York and northern New England. The primary dimension of the trait ordination was the leaf economic spectrum, with trait variability among species largely driven by differences between deciduous angiosperms and evergreen gymnosperms. A second dimension was related to variability in nitrogen to phosphorous levels and stem specific density. Levels of intraspecific trait variability differed considerably among traits, and was related to variation in light, climate, and tree developmental stage. However, trait rankings across species were generally conserved across these gradients and there was little evidence of species crossover. The persistence of the leaf economics spectrum in both temperate and high-elevation conifer forests suggests that ecological strategies of tree species are associated with trade-offs between resource acquisition and tolerance, and may be quantified with relatively few traits. Furthermore, the assumption that species may be represented with a single trait value may be warranted for some trait-based analyses provided traits were measured under similar light levels and climate conditions

Multiscale Controls on Natural Regeneration Dynamics after Partial Overstory Removal in Douglas-Fir Forests in Western Oregon, USA

We examined natural regeneration following operational-scale variable density retention treatments in 40-60 year old Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) forests at seven sites for a decade following treatment. Treatments included residual overstory densities of 300, 200, and 100 trees/ha, with leave islands and gaps of three sizes (0.1, 0.2, and 0.4 ha) and an untreated control (~600 trees/ha). Natural regeneration was influenced by factors from multiple spatial scales including broad-scale differences in overstory composition among sites, mesoscale variability in topographic position, and fine-scale variability in overstory and understory competition. High local basal area (BA) decreased the probability of seedling establishment, though some seedlings established even under high BA, particularly shade-tolerant western hemlock. In contrast, recruitment of saplings (> 1.37 m height) required lower residual overstory density (i.e., 100 trees/ha), especially for shade-intolerant Douglas-fir. Understory vegetation had little effect on saplings, but was negatively related to seedling densities, particularly when overstory density was low. Variable density prescriptions can take advantage of the importance of fine-scale variability to promote regeneration of desired species mixtures, though other factors such as site overstory species composition and variation in topographic position will also influence regeneration dynamics. Including heavy overstory removal or gap creation could facilitate rapid recruitment of saplings, especially for shade-intolerant Douglas-fir.Keywords: Seedling bank, Western hemlock, Thinning, Douglas-fir, Density managementKeywords: Seedling bank, Western hemlock, Thinning, Douglas-fir, Density managemen

Multi-scale spatial controls of understory vegetation in Douglas-fir–western hemlock forests of western Oregon, USA

Forest understory vegetation is influenced by broad-scale variation in climate, intermediate-scale variation in topography, disturbance and neighborhood interactions. However, little is known about how these multi-scale controls interact to influence observed spatial patterns. We examined relationships between the aggregated cover of understory plant species (%C[subscript U]) and multi-scale controls using a large-scale experiment including treatments of low (LS), moderate (MS) and variable (VS) disturbance severity replicated in second-growth Douglas-fir (Pseudotsuga meziesii)–western hemlock (Tsuga heterophylla) forests spanning climate and topographic gradients. We developed hierarchical models using a multi-step selection process, assessing changes residual spatial autocorrelation associated with progressively broader spatial scales of influence and interaction. To examine the role of plant traits in mediating multi-scale controls, we contrasted effects for early- (%C[subscript ES]) and late-seral (%C[subscript LS]) species cover. At neighborhood scales, decreases in %C[subscript U] with overstory density were accelerated with increases in the relative importance of hemlock in the overstory in the in all but the LS treatment. At intermediate scales, %C[subscript U] was lower in areas with higher potential radiation in undisturbed control treatments but that trend was reversed in the harvested, disturbed areas. When separated, effects of multi-scale controls differed between %C[subscript ES] and %C[subscript LS]. Rates of increases in %C[subscript ES] with reductions in density increased with disturbance severity and decreased with increases in %C[subscript LS]. At broader scales, %C[subscript ES] increased with climatic moisture deficit where potential radiation was high, and %C[subscript LS] low. Similarly to %C[subscript U], %C[subscript LS] was related to a three-way interaction between overstory density, disturbance and hemlock abundance. %C[subscript LS] declined with increases in climatic moisture deficit where overstory density and the relative abundance of hemlock was high, and decreased with local increases in %C[subscript ES]. Multi-scale controls explained a portion of the observed spatial autocorrelation for %C[subscript ES] but not %C[subscript LS], suggesting the spatial patterning of %C[subscript LS] is related primarily to unmeasured processes. Results show how understory responses to overstory density and disturbance severity vary across the landscape with moisture and potential radiation, at fine scales with neighborhood structure, and with species traits. Hence, understory responses to climate change likely depend on overstory composition and structure, disturbance and species traits

Forest Restoration Using Variable Density Thinning: Lessons from Douglas-Fir Stands in Western Oregon

A large research effort was initiated in the 1990s in western United States and Canada to investigate how the development of old-growth structures can be accelerated in young even-aged stands that regenerated following clearcut harvests, while also providing income and ecosystem services. Large-scale experiments were established to compare effects of thinning arrangements (e.g., spatial variability) and residual densities (including leave islands and gaps of various sizes). Treatment effects were context dependent, varying with initial conditions and spatial and temporal scales of measurement. The general trends were highly predictable, but most responses were spatially variable. Thus, accounting for initial conditions at neighborhood scales appears to be critical for efficient restoration. Different components of stand structure and composition responded uniquely to restoration thinnings. Achieving a wide range of structures and composition therefore requires the full suite of silvicultural treatments, from leave islands to variable density thinnings and creation of large gaps. Trade-offs among ecosystem services occurred as result of these contrasting responses, suggesting that foresters set priorities where and when different vegetation structures are most desirable within a stand or landscape. Finally, the results suggested that foresters should develop restoration approaches that include multiple treatments

Challenges facing gap-based silviculture and possible solutions for mesic northern forests in North America

Gap-based silvicultural systems were developed under the assumption that richness, and diversity of tree species and other biota positively respond to variation in size of harvest-created canopy gaps. However, varying gap size alone often does not meet diversity objectives and broader goals to address contemporary forest conditions. Recent research highlights the need to consider site factors and history, natural disturbance models, within-gap structure and recruitment requirements in addition to light resources for desired tree diversity. This synthesis brings together silvicultural developments and ecological literature on gap-based management, highlighting interactions with other factors such as microsite conditions, non-tree vegetation and more. We pose a revised concept for managers and researchers to use in prescriptions and studies focused on integrated overstory and understory manipulations that increase structural complexity within and around canopy openings

Analysis of IL12B Gene Variants in Inflammatory Bowel Disease

IL12B encodes the p40 subunit of IL-12, which is also part of IL-23. Recent genome-wide association studies identified IL12B and IL23R as susceptibility genes for inflammatory bowel disease (IBD). However, the phenotypic effects and potential gene-gene interactions of IL12B variants are largely unknow

The Interplay Between Host Genetic Variation, Viral Replication, and Microbial Translocation in Untreated HIV-Infected Individuals

Systemic immune activation, a major determinant of human immunodeficiency virus (HIV) disease progression, is the result of a complex interplay between viral replication, dysregulation of the immune system, and microbial translocation due to gut mucosal damage. Although human genetic variants influencing HIV load have been identified, it is unknown how much the host genetic background contributes to interindividual differences in other determinants of HIV pathogenesis such as gut damage and microbial translocation. Using samples and data from 717 untreated participants in the Swiss HIV Cohort Study and a genome-wide association study design, we searched for human genetic determinants of plasma levels of intestinal fatty acid-binding protein (I-FABP/FABP2), a marker of gut damage, and of soluble CD14 (sCD14), a marker of lipopolysaccharide bioactivity and microbial translocation. We also assessed the correlations between HIV load, sCD14, and I-FABP. Although we found no genome-wide significant determinant of the tested plasma markers, we observed strong associations between sCD14 and both HIV load and I-FABP, shedding new light on the relationships between processes that drive progression of untreated HIV infectio

The satisfactory growth and development at 2 years of age of the INTERGROWTH-21st Fetal Growth Standards cohort support its appropriateness for constructing international standards.

BACKGROUND: The World Health Organization recommends that human growth should be monitored with the use of international standards. However, in obstetric practice, we continue to monitor fetal growth using numerous local charts or equations that are based on different populations for each body structure. Consistent with World Health Organization recommendations, the INTERGROWTH-21st Project has produced the first set of international standards to date pregnancies; to monitor fetal growth, estimated fetal weight, Doppler measures, and brain structures; to measure uterine growth, maternal nutrition, newborn infant size, and body composition; and to assess the postnatal growth of preterm babies. All these standards are based on the same healthy pregnancy cohort. Recognizing the importance of demonstrating that, postnatally, this cohort still adhered to the World Health Organization prescriptive approach, we followed their growth and development to the key milestone of 2 years of age. OBJECTIVE: The purpose of this study was to determine whether the babies in the INTERGROWTH-21st Project maintained optimal growth and development in childhood. STUDY DESIGN: In the Infant Follow-up Study of the INTERGROWTH-21st Project, we evaluated postnatal growth, nutrition, morbidity, and motor development up to 2 years of age in the children who contributed data to the construction of the international fetal growth, newborn infant size and body composition at birth, and preterm postnatal growth standards. Clinical care, feeding practices, anthropometric measures, and assessment of morbidity were standardized across study sites and documented at 1 and 2 years of age. Weight, length, and head circumference age- and sex-specific z-scores and percentiles and motor development milestones were estimated with the use of the World Health Organization Child Growth Standards and World Health Organization milestone distributions, respectively. For the preterm infants, corrected age was used. Variance components analysis was used to estimate the percentage variability among individuals within a study site compared with that among study sites. RESULTS: There were 3711 eligible singleton live births; 3042 children (82%) were evaluated at 2 years of age. There were no substantive differences between the included group and the lost-to-follow up group. Infant mortality rate was 3 per 1000; neonatal mortality rate was 1.6 per 1000. At the 2-year visit, the children included in the INTERGROWTH-21st Fetal Growth Standards were at the 49th percentile for length, 50th percentile for head circumference, and 58th percentile for weight of the World Health Organization Child Growth Standards. Similar results were seen for the preterm subgroup that was included in the INTERGROWTH-21st Preterm Postnatal Growth Standards. The cohort overlapped between the 3rd and 97th percentiles of the World Health Organization motor development milestones. We estimated that the variance among study sites explains only 5.5% of the total variability in the length of the children between birth and 2 years of age, although the variance among individuals within a study site explains 42.9% (ie, 8 times the amount explained by the variation among sites). An increase of 8.9 cm in adult height over mean parental height is estimated to occur in the cohort from low-middle income countries, provided that children continue to have adequate health, environmental, and nutritional conditions. CONCLUSION: The cohort enrolled in the INTERGROWTH-21st standards remained healthy with adequate growth and motor development up to 2 years of age, which supports its appropriateness for the construction of international fetal and preterm postnatal growth standards

Critical Assessment of Metagenome Interpretation:A benchmark of metagenomics software

International audienceIn metagenome analysis, computational methods for assembly, taxonomic profilingand binning are key components facilitating downstream biological datainterpretation. However, a lack of consensus about benchmarking datasets andevaluation metrics complicates proper performance assessment. The CriticalAssessment of Metagenome Interpretation (CAMI) challenge has engaged the globaldeveloper community to benchmark their programs on datasets of unprecedentedcomplexity and realism. Benchmark metagenomes were generated from newlysequenced ~700 microorganisms and ~600 novel viruses and plasmids, includinggenomes with varying degrees of relatedness to each other and to publicly availableones and representing common experimental setups. Across all datasets, assemblyand genome binning programs performed well for species represented by individualgenomes, while performance was substantially affected by the presence of relatedstrains. Taxonomic profiling and binning programs were proficient at high taxonomicranks, with a notable performance decrease below the family level. Parametersettings substantially impacted performances, underscoring the importance ofprogram reproducibility. While highlighting current challenges in computationalmetagenomics, the CAMI results provide a roadmap for software selection to answerspecific research questions

Ten-year mortality, disease progression, and treatment-related side effects in men with localised prostate cancer from the ProtecT randomised controlled trial according to treatment received

Background The ProtecT trial reported intention-to-treat analysis of men with localised prostate cancer randomly allocated to active monitoring (AM), radical prostatectomy, and external beam radiotherapy. Objective To report outcomes according to treatment received in men in randomised and treatment choice cohorts. Design, setting, and participants This study focuses on secondary care. Men with clinically localised prostate cancer at one of nine UK centres were invited to participate in the treatment trial comparing AM, radical prostatectomy, and radiotherapy. Intervention Two cohorts included 1643 men who agreed to be randomised and 997 who declined randomisation and chose treatment. Outcome measurements and statistical analysis Analysis was carried out to assess mortality, metastasis and progression and health-related quality of life impacts on urinary, bowel, and sexual function using patient-reported outcome measures. Analysis was based on comparisons between groups defined by treatment received for both randomised and treatment choice cohorts in turn, with pooled estimates of intervention effect obtained using meta-analysis. Differences were estimated with adjustment for known prognostic factors using propensity scores. Results and limitations According to treatment received, more men receiving AM died of PCa (AM 1.85%, surgery 0.67%, radiotherapy 0.73%), whilst this difference remained consistent with chance in the randomised cohort (p = 0.08); stronger evidence was found in the exploratory analyses (randomised plus choice cohort) when AM was compared with the combined radical treatment group (p = 0.003). There was also strong evidence that metastasis (AM 5.6%, surgery 2.4%, radiotherapy 2.7%) and disease progression (AM 20.35%, surgery 5.87%, radiotherapy 6.62%) were more common in the AM group. Compared with AM, there were higher risks of sexual dysfunction (95% at 6 mo) and urinary incontinence (55% at 6 mo) after surgery, and of sexual dysfunction (88% at 6 mo) and bowel dysfunction (5% at 6 mo) after radiotherapy. The key limitations are the potential for bias when comparing groups defined by treatment received and changes in the protocol for AM during the lengthy follow-up required in trials of screen-detected PCa. Conclusions Analyses according to treatment received showed increased rates of disease-related events and lower rates of patient-reported harms in men managed by AM compared with men managed by radical treatment, and stronger evidence of greater PCa mortality in the AM group. Patient summary More than 95 out of every 100 men with low or intermediate risk localised prostate cancer do not die of prostate cancer within 10 yr, irrespective of whether treatment is by means of monitoring, surgery, or radiotherapy. Side effects on sexual and bladder function are better after active monitoring, but the risks of spreading of prostate cancer are more common