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Additional file 1: Supplementary Material 1. SPIRIT Checklist.

Mixed methods systematic review

Additional file 4: Supplementary Material 4. Interview Consent Form Sample.

Additional file 3: Supplementary Material 3. Survey Consent Form Sample.

Additional file 2: Supplementary Material 2. Semi-structured interview guide.

The objective of this review is to summarize the evidence for the use of animal-associated interventions in emergency department and urgent care settings. More specifically, the review question to be answered is: “Are animal-assisted interventions (i.e., animal assisted therapy and animal-assisted activities) effective at improving patient, family, and healthcare provider experiences in the emergency department and ambulatory care settings?”

This project will look at the evidence around cannabis intoxication (i.e., acute poisoning) in children and youth.

This outlines a protocol for a scoping review of considerations when developing or adapting knowledge translation products for culturally and linguistically diverse communities.

Human beings are an active component of every terrestrial ecosystem on Earth. Although our local impact on the evolution of these ecosystems has been undeniable and extensively documented, it remains unclear precisely how our activities are altering them, in part because ecosystems are dynamic systems structured by complex, non-linear feedback processes and cascading effects. We argue that it is only by studying human–environment interactions over timescales that greatly exceed the lifespan of any individual human (i.e., the deep past or longue durée), we can hope to fully understand such processes and their implications. In this article, we identify some of the key challenges faced in integrating long-term datasets with those of other areas of sustainability science, and suggest some useful ways forward. Specifically, we (a) highlight the potential of the historical sciences for sustainability science, (b) stress the need to integrate theoretical frameworks wherein humans are seen as inherently entangled with the environment, and (c) propose formal computational modelling as the ideal platform to overcome the challenges of transdisciplinary work across large, and multiple, geographical and temporal scales. Our goal is to provide a manifesto for an integrated scientific approach to the study of socio-ecological systems over the long term.

Supplemental Material for Acute pediatric cannabis intoxication: A scoping review by Lindsay Gaudet, Kaitlin Hogue, Shannon Dawn Scott, Lisa Hartling and Sarah Elliott in Journal of Child Health Care

Supplemental Tables 1-3;Supplemental Figures 1-8

Human beings are an active component of every terrestrial ecosystem on Earth. Although our local impact on the evolution of these ecosystems has been undeniable and extensively documented, it remains unclear precisely how our activities are altering them, in part because ecosystems are dynamic systems structured by complex, non-linear feedback processes and cascading effects. We argue that it is only by studying human–environment interactions over timescales that greatly exceed the lifespan of any individual human (i.e., the deep past or longue durée), we can hope to fully understand such processes and their implications. In this article, we identify some of the key challenges faced in integrating long-term datasets with those of other areas of sustainability science, and suggest some useful ways forward. Specifically, we (a) highlight the potential of the historical sciences for sustainability science, (b) stress the need to integrate theoretical frameworks wherein humans are seen as inherently entangled with the environment, and (c) propose formal computational modelling as the ideal platform to overcome the challenges of transdisciplinary work across large, and multiple, geographical and temporal scales. Our goal is to provide a manifesto for an integrated scientific approach to the study of socio-ecological systems over the long term. 1. Introduction 2. The Importance of the Longue Durée 3. The Knotty Problem of Humans 4. Transdisciplinary Integration through Computational Modelling 4.1. Modelling as a Platform 4.2. Data Challenges 4.3. The Question of Scale 5. The (Im)practicalities of Transdisciplinarity 6. Concluding Remarks

Additional file 2.

Additional file 2.

Additional file 3.

Additional file 1: Appendix 1. Selection criteria for the systematic review. Description of data: Inclusion and exclusion criteria for the systematic review. Appendix 2. Initial search strategy for the systematic review (October 2016). Description of data: Initial search strategy for the systematic review. Appendix 3. Strategy for the Automated Full Search. Description of data: Strategy for the automated full search. Appendix 4. Seed articles for the PubMed Similar Articles and Scopus Citing References searches. Description of data: List of seed articles for the complementary search approaches. Appendix 5. Screening data by month. Description of data: Flow of records through the screening process each month. Appendix 6. Characteristics of the four new included trials. Description of data: Characteristics of the included studies. Appendix 7. Forest plots for the analysis of length of stay. Description of data: Forest plots for the length of stay analysis.

Additional file 1.

Additional file 2:. MEDLINE search strategy. The example search strategy to be used in the MEDLINE database.

Additional file 1:. PRISMA-ScR checklist. Completed checklist of recommended items to include in a systematic review.

Additional file 1.

Additional file 1. Scoping searches. Details of the scoping searches.

Additional file 3. Risk of bias categorization by quality score. This table shows how we categorized risk of bias for studies that measured methodological quality via a variety of different tools.

Additional file 2. Sources searched for each review. This table shows the sources searched for each review included in this study.

Additional file 2 Appendix A. 2 × 2 tables and performance metrics calculation for a systematic review and a rapid review.

Additional file 1. Retrospective Screening Simulations

Additional file 4. Missed studies for systematic reviews with meta-analyses. This table shows the studies that were classified as irrelevant via our semi-automated screening approach, yet were included in the meta-analyses in the included systematic reviews.

Additional file 5. Focused codes and supporting quotes for the properties of each tool. Focused codes and supporting quotes for the themes that emerged from the qualitative analysis, for each tool.

Additional file 4. 2 × 2 cross-tabulations for each review in each tool. 2 × 2 cross-tabulations for each review in each tool used to calculate the performance metrics.

Additional file 1. Screening exercise for the user experiences testing. Screening exercise instructions as presented to participants for the user experiences testing.

Additional file 1. SPIRIT 2013 Checklist: Recommended items to address in a clinical trial protocol and related documents*.

Additional file 2. User experiences survey. Details of the questions and response options on the user experiences survey.

Additional file 2. Schedule of the indirect calorimetry tests.

Data extraction guide for a descriptive analysis of non-Cochrane child-relevant systematic reviews. This file provides a detailed description of the data extracted for analysis. (PDF 423 kb)

Search strategy. This file documents the search strategy used to locate included studies (PDF 193 kb)

Section 164 of the Tax Administration Act 28 of 2011 (the TAA), previously contained in section 88 of the Income Tax Act 58 of 1962 (the Income Tax Act) and section 36 of the Value-Added Tax (VAT) Act 89 of 1991 (the VAT Act), provides that the payment of tax will not be automatically suspended until the resolution of a dispute regarding the liability for the said tax debt. This is known as the 'pay now argue later' principle. The objectives of this research were to analyse the development of the 'pay now argue later' principle in South African tax law, to provide an overview of the content and operation of section 164 of the TAA, to compare the principle and its purpose with civil debt enforcement procedures and, lastly, to test the principle against the Constitution of the Republic of South Africa, 1996 (the Constitution), specifically the right of access to courts. The underlying theme of this research is the recognition of taxpayers' rights in South Africa, specifically the interplay between the powers of the fiscus and the rights of taxpayers. In order to achieve the abovementioned objectives, this research examined the development of the 'pay now argue later' principle from its first appearance in section 88 of the Income Tax Act and section 36 of the VAT Act to its subsequent incorporation into the Tax Administration Bill 11 of 2011 and, ultimately, into section 164 of the TAA. It was concluded that the development of the 'pay now argue later' principle, from its first appearance in the Income Tax Act in 1962 and the VAT Act in 1993 until their repeal in 2011, was relatively minor save for in 2009, during which year there was a marked change in the structure of this principle with the inclusion of the so-called 'suspension rule'. This research provided a practical overview and understanding of the operation of the 'pay now argue later' principle in terms of section 164 of the TAA, specifically focusing on the suspension rule. This research further compared the 'pay now argue later' principle with civil debt enforcement procedures, specifically provisional sentence and summary judgment. It was concluded that the 'pay now argue later' principle is an exception to the ordinary rules governing civil debt enforcement proceedings. Lastly, this research placed the 'pay now argue later' principle under constitutional scrutiny, specifically whether its application infringes on the right of access to courts of taxpayers. It was found that the 'pay now argue later' principle infringes a taxpayer's right of access to courts, but this limitation is justified in terms of section 36 of the Constitution.

Historically, obese individuals were believed to have lower energy expenditure (EE) rates than nonobese individuals (normal and overweight), which, in the long term, would contribute to a positive energy balance and subsequent weight gain. The aim of this review was to critically appraise studies that compared measures of EE and its components, resting EE (REE), activity EE (AEE), and diet-induced thermogenesis (DIT), in obese and nonobese adults to elucidate whether obesity is associated with altered EE. Contrary to popular belief, research has shown that obese individuals have higher absolute REE and total EE. When body composition (namely the metabolically active component, fat-free mass) is taken into account, these differences between obese and nonobese individuals disappear, suggesting that EE in obese individuals is not altered. However, an important question is whether AEE is lower in obese individuals because of a decrease in overall physical activity or because of less energy expended while performing physical activity. AEE and DIT could be reduced in obese individuals, mostly because of unhealthy behavior (low physical activity, higher intake of fat). However, the current evidence does not support the hypothesis that obesity is sustained by lower daily EE or REE. Future studies, comparing EE between obese and nonobese and assessing potential physiologic abnormalities in obese individuals, should be able to better answer the question of whether these individuals have altered energy metabolism.

Mycobacterium tuberculosis uses the Type VII ESX secretion systems to transport proteins across its complex cell wall. ESX-5 has been implicated in M. tuberculosis virulence, but the regulatory mechanisms controlling ESX-5 secretion were unknown. Here we uncover a link between ESX-5 and the Pst/SenX3-RegX3 system that controls gene expression in response to phosphate availability. The DNA-binding response regulator RegX3 is normally activated by phosphate limitation. Deletion of pstA1, which encodes a Pst phosphate uptake system component, causes constitutive activation of RegX3. A ΔpstA1 mutant exhibited RegX3-dependent over-expression of esx-5 genes and hyper-secretion of the ESX-5 substrates EsxN and PPE41 when the bacteria were grown in phosphate-rich medium. In wild-type M. tuberculosis, phosphate limitation activated esx-5 transcription and secretion of both EsxN and PPE41, and this response required RegX3. Electrophoretic mobility shift assays revealed that RegX3 binds directly to a promoter within the esx-5 locus. Remarkably, phosphate limitation also induced secretion of EsxB, an effector of the virulence-associated ESX-1 secretion system, though this induction was RegX3 independent. Our work demonstrates that the Pst/SenX3-RegX3 system directly regulates ESX-5 secretion at the transcriptional level in response to phosphate availability and defines phosphate limitation as an environmental signal that activates ESX-5 secretion.

The incredible ability of planarian flatworms to regenerate from almost any type of injury has fascinated naturalists for centuries. Clearly, well-coordinated means of cellcell communication must be critical for this process to occur. This dissertation interrogated the roles of three conserved cell-cell signaling pathways during planarian regeneration: the Wnt, Hedgehog, and Notch pathways. Specifically, the Wnt pathway offered critical insights into discrete phases of the planarian wounding response and axial patterning. The Hh pathway was found to be involved in specification of the anteriorposterior axis, and its function is independent of cilia. Finally, the Notch pathway had numerous roles in planarians, including generation of cellular diversity in the mucociliary epidermis, regeneration of various sensory organs, and maintenance of midline identity. Cumulatively, we hope that this work serves as a useful foundation for future studies of the complex cell-cell signaling events underpinning the amazing regeneration biology of planarian flatworms.

This paper presents preliminary results from an ethnoarchaeological study of animal husbandry in the modern village of Bestansur, situated in the lower Zagros Mountains of Iraqi Kurdistan. This research explores how modern families use and manage their livestock within the local landscape and identifies traces of this use. The aim is to provide the groundwork for future archaeological investigations focusing on the nearby Neolithic site of Bestansur. This is based on the premise that modern behaviours can suggest testable patterns for past practices within the same functional and ecological domains. Semi-structured interviews conducted with villagers from several households provided large amounts of information on modern behaviours that helped direct data collection, and which also illustrate notable shifts in practices and use of the local landscape over time. Strontium isotope analysis of modern plant material demonstrates that a measurable variation exists between the alluvial floodplain and the lower foothills, while analysis of modern dung samples shows clear variation between sheep/goat and cow dung, in terms of numbers of faecal spherulites. These results are specific to the local environment of Bestansur and can be used for evaluating and contextualising archaeological evidence as well as providing modern reference material for comparative purposes.

A synthetic triterpenoid, 2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid (CDDO), has been reported to have anti-inflammatory properties and to decrease the interleukin-1 (IL-1)-induced expression of matrix metalloproteinase-1 (MMP-1) and MMP-13. We have shown previously that IL-1 induces expression of the inhibitor of NF-kappaB (IkappaB) family member Bcl-3, and that this contributes to MMP-1 expression. To quantify the effects of CDDO on IL-1-induced MMP-1, MMP-13 and Bcl-3 expression, we stimulated the chondrosarcoma cell line SW-1353 and human primary chondrocytes with IL-1, in the presence or absence of CDDO. Harvested RNA was subjected to quantitative real-time reverse-transcriptase polymerase chain reaction. In SW-1353 cells, 300 nM CDDO significantly decreased the induction of MMP-1 and MMP-13 by IL-1. In human primary chondrocytes, 300 nM CDDO inhibited the induction of these genes by IL-1 to an even greater extent. In both cell types, inhibition of MMP-1 required 24 hours of pretreatment with CDDO, whereas MMP-13 could be inhibited when CDDO and IL-1 were added simultaneously to culture. In human primary chondrocytes, IL-1-induced Bcl-3 expression was inhibited when cells were pretreated with CDDO. To determine whether the inhibitory effect of CDDO on MMP worked through inhibition of Bcl-3 gene expression, SW-1353 cells stably transfected with a Bcl-3 expression plasmid were treated with IL-1 and/or CDDO, and MMP gene expression was assayed. Overexpression of Bcl-3 increased MMP-1, but not MMP-13, mRNA levels. Furthermore, overexpressed Bcl-3 could sustain the CDDO-dependent inhibition of IL-1-induced MMP-1 expression. Our data demonstrate that CDDO inhibits IL-1-induced MMP-1 and MMP-13 expression in human chondrocytes. CDDO also inhibits the expression of Bcl-3, an IL-1-responsive gene that preferentially contributes to MMP-1 gene expression.

Adapting to blurred or sharpened images alters perceived blur of a focused image (M. A. Webster, M. A. Georgeson, & S. M. Webster, 2002). We asked whether blur adaptation results in (a) renormalization of perceived focus or (b) a repulsion aftereffect. Images were checkerboards or 2-D Gaussian noise, whose amplitude spectra had (log-log) slopes from -2 (strongly blurred) to 0 (strongly sharpened). Observers adjusted the spectral slope of a comparison image to match different test slopes after adaptation to blurred or sharpened images. Results did not show repulsion effects but were consistent with some renormalization. Test blur levels at and near a blurred or sharpened adaptation level were matched by more focused slopes (closer to 1/f) but with little or no change in appearance after adaptation to focused (1/f) images. A model of contrast adaptation and blur coding by multiple-scale spatial filters predicts these blur aftereffects and those of Webster et al. (2002). A key proposal is that observers are pre-adapted to natural spectra, and blurred or sharpened spectra induce changes in the state of adaptation. The model illustrates how norms might be encoded and recalibrated in the visual system even when they are represented only implicitly by the distribution of responses across multiple channels.

In 2004, the Social Sciences & Humanities Library at the University of California, San Diego (UCSD) implemented use of restaurant-style pagers for checking out Reserves Collection materials. Pagers are given to patrons when a desired reserves item is already in use. When the item is returned, the next patron is paged to the Circulation Desk to pick it up. The authors describe the UCSD Libraries’ process for initially implementing the pagers, explain the success they have seen with the pagers over the past four years, outline other libraries using similar pagers, and offer guidance for other institutions who might consider this innovative and user-friendly service enhancement.

The contributions of optical and neural factors to age-related losses in spatial vision are not fully understood. We used closed-loop adaptive optics to test the visual benefit of correcting monochromatic high-order aberrations (HOAs) on spatial vision for observers ranging in age from 18 to 81 years. Contrast sensitivity was measured monocularly using a two-alternative forced-choice (2AFC) procedure for sinusoidal gratings over 6 mm and 3 mm pupil diameters. Visual acuity was measured using a spatial 4AFC procedure. Over a 6 mm pupil, young observers showed a large benefit of AO at high spatial frequencies, whereas older observers exhibited the greatest benefit at middle spatial frequencies, plus a significantly larger increase in visual acuity. When age-related miosis is controlled, young and old observers exhibited a similar benefit of AO for spatial vision. An increase in HOAs cannot account for the complete senescent decline in spatial vision. These results may indicate a larger role of additional optical factors when the impact of HOAs is removed, but also lend support for the importance of neural factors in age-related changes in spatial vision. © ARVO.

Disclaimer: “UBC SEEDS provides students with the opportunity to share the findings of their studies, as well as their opinions, conclusions and recommendations with the UBC community. The reader should bear in mind that this is a student project/report and is not an official document of UBC. Furthermore readers should bear in mind that these reports may not reflect the current status of activities at UBC. We urge you to contact the research persons mentioned in a report or the SEEDS Coordinator about the current status of the subject matter of a project/report.”

Additional file 5. Impact of the missed study on the results of relevant meta-analyses in the Antipsychotics systematic review. This table shows the pooled effect estimates for relevant meta-analyses with and without the study by McCracken et al. (2002), which was incorrectly classified as irrelevant via our semi-automated screening approach.