Mean and median bias reduction in generalized linear models

Kosmidis, Ioannis; Pagui, Euloge Clovis Kenne; Sartori, Nicola

doi:10.1007/s11222-019-09860-6

Cited by 219 publications

(255 citation statements)

References 36 publications

(53 reference statements)

Supporting

Mentioning

252

Contrasting

Order By: Relevance

“…Logistic models fitted with small samples have been shown to give biased estimates (Nemes et al . ); this was recognised and bias‐corrected estimates were reported (Kosmidis, ) with P values from likelihood‐ratio tests comparing sequentially reduced models.…”

Section: Methodsmentioning

confidence: 99%

Benefits of higher resistance‐training volume are related to ribosome biogenesis

Hammarström

Øfsteng

Koll

et al. 2020

The Journal of Physiology

117

View full text Add to dashboard Cite

Key points For individuals showing suboptimal adaptations to resistance training, manipulation of training volume is a potential measure to facilitate responses. This remains unexplored. Here, 34 untrained individuals performed contralateral resistance training with moderate and low volume for 12 weeks. Moderate volume led to larger increases in muscle cross‐sectional area, strength and type II fibre‐type transitions. These changes coincided with greater activation of signalling pathways controlling muscle growth and greater induction of ribosome synthesis. Out of 34 participants, thirteen displayed clear benefit of MOD on muscle hypertrophy and sixteen showed clear benefit of MOD on muscle strength gains. This coincided with greater total RNA accumulation in the early phase of the training period, suggesting that ribosomal biogenesis regulates the dose–response relationship between training volume and muscle hypertrophy. These results demonstrate that there is a dose‐dependent relationship between training volume and outcomes. On the individual level, benefits of higher training volume were associated with increased ribosomal biogenesis. Abstract Resistance‐exercise volume is a determinant of training outcomes. However not all individuals respond in a dose‐dependent fashion. In this study, 34 healthy individuals (males n = 16, 23.6 (4.1) years; females n = 18, 22.0 (1.3) years) performed moderate‐ (3 sets per exercise, MOD) and low‐volume (1 set, LOW) resistance training in a contralateral fashion for 12 weeks (2–3 sessions per week). Muscle cross‐sectional area (CSA) and strength were assessed at Weeks 0 and 12, along with biopsy sampling (m. vastus lateralis). Muscle biopsies were also sampled before and 1 h after the fifth session (Week 2). MOD resulted in larger increases in muscle CSA (5.2 (3.8)% versus 3.7 (3.7)%, P < 0.001) and strength (3.4–7.7% difference, all P < 0.05. This coincided with greater reductions in type IIX fibres from Week 0 to Week 12 (MOD, −4.6 percentage points; LOW −3.2 percentage points), greater phosphorylation of S6‐kinase 1 (p85 S6K1Thr412, 19%; p70 S6K1Thr389, 58%) and ribosomal protein S6Ser235/236 (37%), greater rested‐state total RNA (8.8%) and greater exercise‐induced c‐Myc mRNA expression (25%; Week 2, all P < 0.05). Thirteen and sixteen participants, respectively, displayed clear benefits in response to MOD on muscle hypertrophy and strength. Benefits were associated with greater accumulation of total RNA at Week 2 in the MOD leg, with every 1% difference increasing the odds of MOD benefit by 7.0% (P = 0.005) and 9.8% (P = 0.002). In conclusion, MOD led to greater functional and biological adaptations than LOW. Associations between dose‐dependent total RNA accumulation and increases in muscle mass and strength point to ribosome biogenesis as a determinant of dose‐dependent training responses.

show abstract

Section: Methodsmentioning

confidence: 99%

Benefits of higher resistance‐training volume are related to ribosome biogenesis

Hammarström

Øfsteng

Koll

et al. 2020

The Journal of Physiology

117

View full text Add to dashboard Cite

show abstract

“…In a greenhouse, we secured colonized or uncolonized (for paired controls) 2% ME agar plugs to healthy leaves using Parafilm (Bemis Company, Inc., Oshkosh, WI, USA; Sinclair and Dhingra ). We censused leaves for symptoms within one week, and compared the proportion of diseased leaves for each isolate to its paired control using bias‐reduced generalized linear models (brglm function; Kosmidis ), with binomial errors and probit link functions (Appendix : Table S4).…”

Section: Methodsmentioning

confidence: 99%

Foliar pathogens are unlikely to stabilize coexistence of competing species in a California grassland

Spear

Mordecai

2018

Ecology

View full text Add to dashboard Cite

Pathogen infection is common in wild plants and animals, and may regulate their populations. If pathogens have narrow host ranges and increase with the density of their favored hosts, they may promote host species diversity by suppressing common species to the benefit of rare species. Yet, because many pathogens infect multiple co-occurring hosts, they may not strongly respond to the relative abundance of a single host species. Are natural communities dominated by specialized pathogens that respond to the relative abundance of a specific host or by pathogens with broad host ranges and limited responses to the relative abundance of single host? The answer determines the potential for pathogens to promote host coexistence, as often hypothesized, or to have negligible or even negative effects on host coexistence. We lack a systematic understanding of the impacts, identities, and host ranges of pathogens in natural communities. Here we characterize a community of foliar fungal pathogens and evaluate their host specificity and fitness impacts in a California grassland community of native and exotic species. We found that most of the commonly isolated fungal pathogens were multi-host, with intermediate to low specialization. The amount of pathogen damage each host experienced was independent of host species local relative abundance. Despite pathogen sharing among the host species, fungal communities slightly differed in composition across host species. Plants with high pathogen damage tended to have lower seed production but the relationship was weak, suggesting limited fitness impacts. Moreover, seed production was not dependent on the local relative abundance of each plant species, suggesting that stabilizing coexistence mechanisms may operate at larger spatial scales in this community. Because foliar pathogens in this grassland community are multi-host and have small fitness impacts, they are unlikely to promote negative frequency dependence or plant species coexistence in this system. Still, given that pathogen community composition differentiates across host species, some more subtle feedbacks between host relative abundance and pathogen community composition, damage, and fitness impacts are possible, which could, in turn, promote either coexistence or competitive exclusion.

show abstract

“…Analyses and plotting was performed using the “lme4” (Bates et al. ), “brglm” (Kosmidis ), “vegan” (Oksanen et al. ), “MuMIn” (Barton ) and “ggplot2” (Wickham ) packages in R (R Core Team ).…”

Section: Methodsmentioning

confidence: 99%

Short‐ and long‐term effects of habitat fragmentation differ but are predicted by response to the matrix

Evans

Banks

Driscoll

et al. 2017

Ecology

View full text Add to dashboard Cite

Habitat loss and fragmentation are major threats to biodiversity and ecosystem processes. Our current understanding of the impacts of habitat loss and fragmentation is based largely on studies that focus on either short-term or long-term responses. Short-term responses are often used to predict long-term responses and make management decisions. The lack of studies comparing short- and long-term responses to fragmentation means we do not adequately understand when and how well short-term responses can be extrapolated to predict long-term responses, and when or why they cannot. To address this gap, we used data from one of the world's longest-running fragmentation experiments, The Wog Wog Habitat Fragmentation Experiment. Using data for carabid beetles, we found that responses in the long term (more than 22 yr post-fragmentation ≈22 generations) often contrasted markedly with those in the short term (5 yr post-fragmentation). The total abundance of all carabids, species richness and the occurrence of six species declined in the short term in the fragments but increased over the long term. The occurrence of three species declined initially and continued to decline, whilst another species was positively affected initially but decreased in the long term. Species' responses to the matrix that surrounds the fragments strongly predicted both the direction (increase/decline in occurrence) and magnitude of their responses to fragmentation. Additionally, species' responses to the matrix were somewhat predicted by their preferences for different types of native habitat (open vs. shaded). Our study highlights the degree of the matrix's influence in fragmented landscapes, and how this influence can change over time. We urge caution in using short-term responses to forecast long-term responses in cases where the matrix (1) impacts species' responses to fragmentation (by isolating them, creating new habitat or altering fragment habitat) and (2) is likely to change through time.

show abstract

Mean and median bias reduction in generalized linear models

Cited by 219 publications

References 36 publications

Benefits of higher resistance‐training volume are related to ribosome biogenesis

Benefits of higher resistance‐training volume are related to ribosome biogenesis

Foliar pathogens are unlikely to stabilize coexistence of competing species in a California grassland

Short‐ and long‐term effects of habitat fragmentation differ but are predicted by response to the matrix

Contact Info

Product

Resources

About