orchaRd 2.0 : an R package for visualising meta-analyses with orchard plots

1. Although meta-analysis has become an essential tool in ecology and evolution, reporting of meta-analytic results can still be much improved. To aid this, we have introduced the orchard plot, which presents not only overall estimates and their confidence intervals, but also shows corresponding heterogeneity (as prediction intervals) and individual effect sizes. 2. Here, we have added significant enhancements by integrating many new functionalities into orchaRd 2.0. This updated version allows the visualisation of heteroscedasticity (different variances across levels of a categorical moderator), marginal estimates (e.g. marginalising out effects other than the one visualised), conditional estimates (i.e. estimates of different groups conditioned upon specific values of a continuous variable) and visualisations of all types of interactions between two categorical/continuous moderators. 3. orchaRd 2.0 has additional functions which calculate key statistics from multilevel meta-analytic models such as $I^{2}$ and $R^{2}$. Importantly, orchaRd 2.0 contributes to better reporting by complying with PRISMA-EcoEvo (preferred reporting items for systematic reviews and meta-analyses in ecology and evolution). Taken together, orchaRd 2.0 can improve the presentation of meta-analytic results and facilitate the exploration of previously neglected patterns. 4. In addition, as a part of a literature survey, we found that graphical packages are rarely cited (~3%). We plea that researchers credit developers and maintainers of graphical packages, for example, by citations in a figure legend, acknowledging the use of relevant packages

Evidence for the protein leverage hypothesis in preschool children prone to obesity.

BACKGROUND & AIMS The protein leverage hypothesis (PLH) proposed that strict regulation of protein intake drives energy overconsumption and obesity when diets are diluted by fat and/or carbohydrates. Evidence about the PLH has been found in adults, while studies in children are limited. Thus, we aimed to test the PLH by assessing the role of dietary protein on macronutrients, energy intake, and obesity risk using data from preschool children followed for 1.3 years. METHODS 553 preschool children aged 2-6 years from the 'Healthy Start' project were included. EXPOSURES The proportion of energy intake from protein, fat, and carbohydrates collected from a 4-day dietary record. OUTCOMES Energy intake, BMI z-score, fat mass (FM) %, waist- (WHtR) and hip-height ratio (HHtR). Power function analysis was used to test the leverage of protein on energy intake. Mixture models were used to explore interactive associations of macronutrient composition on all these outcomes, with results visualized as response surfaces on the nutritional geometry. RESULTS Evidence for the PLH was confirmed in preschool children. The distribution of protein intake (% of MJ, IQR: 3.2) varied substantially less than for carbohydrate (IQR: 5.7) or fat (IQR: 6.3) intakes, suggesting protein intake is most tightly regulated. Absolute energy intake varied inversely with dietary percentage energy from protein (L = -0.14, 95% CI: -0.25, -0.04). Compared to children with high fat or carbohydrate intakes, children with high dietary protein intake (>20% of MJ) had a greater decrease in WHtR and HHtR over the 1.3-year follow-up, offering evidence for the PLH in prospective analysis. But no association was observed between macronutrient distribution and changes in BMI z-score or FM%. CONCLUSIONS In this study in preschool children, protein intake was the most tightly regulated macronutrient, and energy intake was an inverse function of dietary protein concentration, indicating the evidence for protein leverage. Increases in WHtR and HHtR were principally associated with the dietary protein dilution, supporting the PLH. These findings highlight the importance of protein in children's diets, which seems to have significant implications for childhood obesity risk and overall health

Dietary macronutrient composition impacts gene regulation in adipose tissue

Diet is a key lifestyle component that influences metabolic health through several factors, including total energy intake and macronutrient composition. While the impact of caloric intake on gene expression and physiological phenomena in various tissues is well described, the influence of dietary macronutrient composition on these parameters is less well studied. Here, we use the Nutritional Geometry framework to investigate the role of macronutrient composition on metabolic function and gene regulation in adipose tissue. Using ten isocaloric diets that vary systematically in their proportion of energy from fat, protein, and carbohydrates, we find that gene expression and splicing are highly responsive to macronutrient composition, with distinct sets of genes regulated by different macronutrient interactions. Specifically, the expression of many genes associated with Bardet-Biedl syndrome is responsive to dietary fat content. Splicing and expression changes occur in largely separate gene sets, highlighting distinct mechanisms by which dietary composition influences the transcriptome and emphasizing the importance of considering splicing changes to more fully capture the gene regulation response to environmental changes such as diet. Our study provides insight into the gene regulation plasticity of adipose tissue in response to macronutrient composition, beyond the already well-characterized response to caloric intake

Sucrose and starch intake contribute to reduced alveolar bone height in a rodent model of naturally occurring periodontitis

Funding: This research project was funded in part by the Strategic Research Excellence Initiative 2020 (SREI2020), University of Sydney to JE and the University of Sydney HMR + Implementation Funding Grant to VC, DLC and SS.Peer reviewedPublisher PD

Signaling Heterogeneity is Defined by Pathway Architecture and Intercellular Variability in Protein Expression.

Insulin's activation of PI3K/Akt signaling, stimulates glucose uptake by enhancing delivery of GLUT4 to the cell surface. Here we examined the origins of intercellular heterogeneity in insulin signaling. Akt activation alone accounted for ~25% of the variance in GLUT4, indicating that additional sources of variance exist. The Akt and GLUT4 responses were highly reproducible within the same cell, suggesting the variance is between cells (extrinsic) and not within cells (intrinsic). Generalized mechanistic models (supported by experimental observations) demonstrated that the correlation between the steady-state levels of two measured signaling processes decreases with increasing distance from each other and that intercellular variation in protein expression (as an example of extrinsic variance) is sufficient to account for the variance in and between Akt and GLUT4. Thus, the response of a population to insulin signaling is underpinned by considerable single-cell heterogeneity that is largely driven by variance in gene/protein expression between cells

Diagnóstico general y servicio prestado en la Cooperativa Agrícola Integral Unión de 4 Pinos R.L. Santiago Sacatepéquez, Guatemala C.A. y evaluación de Boscalid + Pyraclostrobin en la producción y prolongación de vida en anaquel del zucchini (Cucúrbita pepo L. subsp. pepo.)

La presente investigación se realizó en a Cooperativa Agrícola Integral Unión de 4 Pinos, R.L., Finca La Suiza, San Lucas Sacatepéquez, mediante el diagnóstico realizado en Finca La Suiza, área productora de Cooperativa Agrícola Integral Unión de 4 Pinos, determinando que la importancia de investigar el uso de nuevas tecnologías que aumenten la vida de anaquel del zucchini. La investigación consistió en la evaluación del efecto de los ingredientes activos Boscalid+Pyraclostrobin en la producción y prolongación de vida en anaquel del zucchini, para lo cual el ensayo fue dividido en dos etapas, la primera la producción en campo y la segunda el manejo postcosecha en planta empacadora. La primera parte fue realizada en Finca La Suiza, para lo cual se elaboró un plan de manejo fitosanitario, tomando como base el plan de manejo fitosanitario para el cultivo de zucchini Departamento Agrícola 2009, a la cual se incluyeron las aplicaciones de la estrobilurina (Boscalid+Pyraclostrobin) se evaluaron cuatro tratamientos, de los cuales uno era el testigo absoluto, dos tratamientos con 2 y 3 aplicaciones de la estrobilurina (Boscalid+Pyraclostrobin) en diferentes etapas fenológicas del cultivo y un cuarto tratamiento el manejo tradicional del Departamento Agrícola, asi como manejo postcosecha del producto, el cual fue sometido a un procedimiento de clasificación, lavado, desinfección, empaque y colocación en cuarto frio (4ºC) para determinar los días de vida en anaquel del zucchini

The older prisoner health and social care assessment and plan (OHSCAP) versus treatment as usual: a randomised controlled trial

From Springer Nature via Jisc Publications RouterHistory: received 2020-09-09, accepted 2021-10-11, registration 2021-10-12, pub-electronic 2021-11-10, online 2021-11-10, collection 2021-12Publication status: PublishedFunder: Service Delivery and Organisation Programme (GB); Grant(s): 12/5001Abstract: Background: Older people are the fastest-growing demographic group among prisoners in England and Wales and they have complex health and social care needs. Their care is frequently ad hoc and uncoordinated. No previous research has explored how to identify and appropriately address the needs of older adults in prison. We hypothesised that the Older prisoner Health and Social Care Assessment and Plan (OHSCAP) would significantly increase the proportion of met health and social care needs 3 months after prison entry, compared to treatment as usual (TAU). Methods: The study was a parallel randomised controlled trial (RCT) recruiting male prisoners aged 50 and over from 10 prisons in northern England. Participants received the OHSCAP or TAU. A clinical trials unit used minimisation with a random element as the allocation procedure. Data analysis was conducted blind to allocation status. The intervention group had their needs assessed using the OHSCAP tool and care plans were devised; processes that lasted approximately 30 min in total per prisoner. TAU included the standard prison health assessment and care. The intention to treat principle was followed. The trial was registered with the UK Clinical Research Network Portfolio (ISRCTN ID: 11841493) and was closed on 30 November 2016. Results: Data were collected between 28 January 2014 and 06 April 2016. Two hundred and forty nine older prisoners were assigned TAU of which 32 transferred prison; 12 were released; 2 withdrew and 1 was deemed unsafe to interview. Two hundred and fifty three 3 prisoners were assigned the OHSCAP of which 33 transferred prison; 11 were released; 6 withdrew and 1 was deemed unsafe to interview. Consequently, data from 202 participants were analysed in each of the two groups. There were no significant differences in the number of unmet needs as measured by the Camberwell Assessment of Needs – Forensic Short Version (CANFOR-S). The mean number of unmet needs for the OHSCAP group at follow-up was 2.03 (SD = 2.07) and 2.06 (SD = 2.11) for the TAU group (mean difference = 0.088; 95% CI − 0.276 to 0.449, p = 0.621). No adverse events were reported. Conclusion: The OHSCAP was fundamentally not implemented as planned, partly due to the national prison staffing crisis that ensued during the study period. Therefore, those receiving the OHSCAP did not experience improved outcomes compared to those who received TAU. Trial registration: Current Controlled Trials: ISRCTN11841493, 25/10/2012

Sexual dimorphism in trait variability and its eco-evolutionary and statistical implications

Biomedical and clinical sciences are experiencing a renewed interest in the fact that males and females differ in many anatomic, physiological, and behavioural traits. Sex differences in trait variability, however, are yet to receive similar recognition. In medical science, mammalian females are assumed to have higher trait variability due to estrous cycles (the ‘estrus-mediated variability hypothesis’); historically in biomedical research, females have been excluded for this reason. Contrastingly, evolutionary theory and associated data support the ‘greater male variability hypothesis’. Here, we test these competing hypotheses in 218 traits measured in >26,900 mice, using meta-analysis methods. Neither hypothesis could universally explain patterns in trait variability. Sex bias in variability was trait-dependent. While greater male variability was found in morphological traits, females were much more variable in immunological traits. Sex-specific variability has eco-evolutionary ramifications, including sex-dependent responses to climate change, as well as statistical implications including power analysis considering sex difference in variance.SRKZ and ML were supported by the Australian (ARC) Discovery Grant (DP180100818) awarded to SN. JM was supported by EMBL core funding and the NIH Common Fund (UM1-H G006370). AMS was supported by an ARC fellowship (DE180101520)

UK community Earth system modelling for CMIP6

We describe the approach taken to develop the UK’s first community Earth System model, UKESM1. This is a joint effort involving the Met Office and the Natural Environment Research Council (NERC), representing the UK academic community. We document our model development procedure and the subsequent UK submission to CMIP6, based on a traceable hierarchy of coupled physical and Earth system models. UKESM1 builds on the well‐established, world‐leading HadGEM models of the physical climate system and incorporates cutting‐edge new representations of aerosols, atmospheric chemistry, terrestrial carbon and nitrogen cycles, and an advanced model of ocean biogeochemistry. A high‐level metric of overall performance shows that both the physical model, HadGEM3‐GC3.1 and UKESM1 perform better than most other CMIP6 models so far submitted for a broad range of variables. We point to much more extensive evaluation performed in other papers in this special issue. The merits of not using any forced climate change simulations within our model development process are discussed. First results from HadGEM3‐GC3.1 and UKESM1 include the emergent climate sensitivity (5.5K and 5.4K respectively) which is high relative to the current range of CMIP5 models. The role of cloud microphysics and cloud‐aerosol interactions in driving the climate sensitivity, and the systematic approach taken to understand this role is highlighted in other papers in this special issue. We place our findings within the broader modelling landscape indicating how our understanding of key processes driving higher sensitivity in the two UK models seems to align with results from a number of other CMIP6 models

Forcings, feedbacks and climate sensitivity in HadGEM3‐GC3.1 and UKESM1

Climate forcing, sensitivity and feedback metrics are evaluated in both the UK’s physical climate model HadGEM3-GC3.1at low (-LL) and medium(-MM) resolution and the UK’s Earth System Model UKESM1. The Effective Climate Sensitivity (EffCS)to a doubling of CO2 is 5.5K for HadGEM3.1-GC3.1-LL and 5.4 K for UKESM1. The transient climate response is 2.5K and 2.8K respectively. Whilst the EffCS is larger than that seen in the previous generation of models, none of the model’s forcing or feedback processes are found to be atypical of models, though the cloud feedback is at the high end. The relatively large EffCS results from an unusual combination of a typical CO2 forcing with a relatively small feedback parameter. Compared to the previous UK climate model, HadGEM3-GC2.0, the EffCS has increased from 3.2K to 5.5K due to an increase in CO2 forcing, surface albedo feedback and mid-latitude cloud feedback. All changes are well understood and due to physical improvements in the model.At higher atmospheric and ocean resolution(HadGEM3-GC3.1-MM), there is a compensation between increased marine stratocumulous cloud feedback and reduced Antarctic sea-ice feedback. In UKESM1 a CO2 fertilization effect induces a land surface vegetation change and albedo radiative effect. Historical aerosol forcing in HadGEM3-GC3.1-LL is -1.1 Wm-2. In HadGEM3-GC3.1-LL historical simulations cloud feedback is found to be less positive than in abrupt-4xCO2, in agreement with atmosphere-only experiments forced with observed historical sea-surface-temperature and sea-ice variations. However variability in the coupled model’s historical sea-ice trends hampers accurate diagnosis of the model’s total historical feedback