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Abstract The sequencing platform and workflow strongly influence microbial community analyses through potential errors at each step. Effective diagnostics and experimental controls are needed to validate data and improve reproducibility. This cross-laboratory study evaluates sources of variability and error at three main steps of a standardized amplicon sequencing workflow (DNA extraction, polymerase chain reaction [PCR], and sequencing) using Oxford Nanopore MinION to analyze agricultural soils and a simple mock community. Variability in sequence results occurs at each step in the workflow with PCR errors and differences in library size greatly influencing diversity estimates. Common bioinformatic diagnostics and the mock community are ineffective at detecting PCR abnormalities. This work outlines several diagnostic checks and techniques to account for sequencing depth and ensure accuracy and reproducibility in soil community analyses. These diagnostics and the inclusion of a reference soil can help ensure data validity and facilitate the comparison of multiple sequencing runs within and between laboratories.

Introduction Heterogeneity in reported outcomes of infants with oesophageal atresia (OA) with or without tracheo-oesophageal fistula (TOF) prevents effective data pooling. Core outcome sets (COS) have been developed for many conditions to standardise outcome reporting, facilitate meta-analysis and improve the relevance of research for patients and families. Our aim is to develop an internationally-agreed, comprehensive COS for OA-TOF, relevant from birth through to transition and adulthood.Methods and analysis A long list of outcomes will be generated using (1) a systematic review of existing studies on OA-TOF and (2) qualitative research with children (patients), adults (patients) and families involving focus groups, semistructured interviews and self-reported outcome activity packs. A two-phase Delphi survey will then be completed by four key stakeholder groups: (1) patients (paediatric and adult); (2) families; (3) healthcare professionals; and (4) researchers. Phase I will include stakeholders individually rating the importance and relevance of each long-listed outcome using a 9-point Likert scale, with the option to suggest additional outcomes not already included. During phase II, stakeholders will review summarised results from phase I relative to their own initial score and then will be asked to rescore the outcome based on this information. Responses from phase II will be summarised using descriptive statistics and a predefined definition of consensus for inclusion or exclusion of outcomes. Following the Delphi process, stakeholder experts will be invited to review data at a consensus meeting and agree on a COS for OA-TOF.Ethics and dissemination Ethical approval was sought through the Health Research Authority via the Integrated Research Application System, registration no. 297026. However, approval was deemed not to be required, so study sponsorship and oversight were provided by Alder Hey Children’s NHS Foundation Trust. The study has been prospectively registered with the COMET Initiative. The study will be published in an open access forum.

The inflection point is an important feature of sigmoidal height-diameter (H-D) models. It is often cited as one of the properties favoring sigmoidal model forms. However, there are very few studies analyzing the inflection points of H-D models. The goals of this study were to theoretically and empirically examine the behaviors of inflection points of six common H-D models with a regional dataset. The six models were the Wykoff (WYK), Schumacher (SCH), Curtis (CUR), Hossfeld IV (HOS), von Bertalanffy-Richards (VBR), and Gompertz (GPZ) models. The models were first fitted in their base forms with tree species as random effects and were then expanded to include functional traits and spatial distribution. The distributions of the estimated inflection points were similar between the two-parameter models WYK, SCH, and CUR, but were different between the three-parameter models HOS, VBR, and GPZ. GPZ produced some of the largest inflection points. HOS and VBR produced concave H-D curves without inflection points for 12.7% and 39.7% of the tree species. Evergreen species or decreasing shade tolerance resulted in larger inflection points. The trends in the estimated inflection points of HOS and VBR were entirely opposite across the landscape. Furthermore, HOS could produce concave H-D curves for portions of the landscape. Based on the studied behaviors, the choice between two-parameter models may not matter. We recommend comparing several three-parameter model forms for consistency in estimated inflection points before deciding on one. Believing sigmoidal models to have inflection points does not necessarily mean that they will produce fitted curves with one. Our study highlights the need to integrate analysis of inflection points into modeling H-D relationships.

Volume is an important attribute used in many forest management decisions. Data from 83 fixed-area plots located in central New Brunswick, Canada, are used to examine how different measures of stand-level diameter and height influence volume prediction using a stand-level variant of Honer’s (1967) volume equation. When density was included in the models (Volume=f(Diameter,Height,Density)) choice of diameter measure was more important than choice of height measure. When density was not included (Volume=f(Diameter,Height)), the opposite was true. For models with density included, moment-based estimators of stand diameter and height performed better than all other measures. For models without density, largest tree estimators of stand diameter and height performed better than other measures. The overall best equation used quadratic mean diameter, Lorey’s height, and density (root mean square error ​= ​5.26 ​m3⋅ha−1; 1.9 % relative error). The best equation without density used mean diameter of the largest trees needed to calculate a stand density index of 400 and the mean height of the tallest 400 trees per ha (root mean square error ​= ​32.08 ​m3⋅ha−1; 11.8 % relative error). The results of this study have some important implications for height subsampling and LiDAR-derived forest inventory analyses.

Abstract Background Concern has been growing in the academic literature and popular media about the licensing, introduction and adoption of surgical devices before full effectiveness and safety evidence is available to inform clinical practice. Our research will seek empirical survey evidence about the roles, responsibilities, and information and policy needs of the key stakeholders in the introduction into clinical practice of new surgical devices for pelvic floor surgery, in terms of the underlying ethical principals involved in the economic decision-making process, using the example of pelvic floor procedures. Methods/Design Our study involves three linked case studies using, as examples, selected pelvic floor surgery devices representing Health Canada device safety risk classes: low, medium and high risk. Data collection will focus on stakeholder roles and responsibilities, information and policy needs, and perceptions of those of other key stakeholders, in seeking and using evidence about new surgical devices when licensing and adopting them into practice. For each class of device, interviews will be used to seek the opinions of stakeholders. The following stakeholders and ethical and economic principles provide the theoretical framework for the study: Stakeholders - federal regulatory body, device manufacturers, clinicians, patients, health care institutions, provincial health departments, and professional societies. Clinical settings in two centres (in different provinces) will be included. Ethics - beneficence, non-maleficence, autonomy, justice. Economics - scarcity of resources, choices, opportunity costs. For each class of device, responses will be analysed to compare and contrast between stakeholders. Applied ethics and economic theory, analysis and critical interpretation will be used to further illuminate the case study material. Discussion The significance of our research in this new area of ethics will lie in providing recommendations for regulatory bodies, device manufacturers, clinicians, health care institutions, policy makers and professional societies, to ensure surgical patients receive sufficient information before providing consent for pelvic floor surgery. In addition, we shall provide a wealth of information for future study in other areas of surgery and clinical management, and provide suggestions for changes to health policy.

Background: Given the prevalence of women seeking surgical treatment for pelvic organ prolapse (POP), there is a need to understand women’s decision-making regarding uterine-preserving versus hysterectomy-based surgeries. Historically, hysterectomy-based surgeries have been the preferred treatment for pelvic organ prolapse; however, contemporary evidence supports uterine-preserving surgeries as equivalent. At present, the lack of information available to the general public and limited options presented at surgical consultation for pelvic organ prolapse may hinder women’s autonomy as they navigate surgical treatment. Objectives: To examine the factors affecting women’s decision-making processes regarding uterine-preserving or hysterectomy-based surgery for pelvic organ prolapse. Design: This is a qualitative study. Methods: We conducted semi-structured, qualitative interviews with women seeking surgery for pelvic organ prolapse to explore the factors affecting women’s decision-making between hysterectomy-based and uterine-preserving surgeries. Results: Women (n = 26) used clinical and personal factors to determine which surgery was best. Women noted that the lack of evidence (clinical and/or anecdotal) available to them hindered their decision-making, causing them to rely more on their own interpretations of the evidence, what they perceived to be “normal,” and what their surgeon recommended. Even with standardized discussion regarding the existing clinical equipoise between surgeries at the clinical consultation, some women still had misperceptions that hysterectomy-based surgery would convey the lowest risk of prolapse recurrence and be best for severe prolapse. Conclusion: There is a need for more transparency in discussions about prolapse and the factors affecting women’s decision-making for surgical repair of pelvic organ prolapse. Clinicians should be prepared to offer the option of hysterectomy-based or uterine-preserving surgeries and to clearly explain the clinical equipoise between these procedures.

Forest disturbances, such as an eastern spruce budworm (Choristoneura fumiferana) outbreak, impact the strength and persistence of forest carbon sinks. Salvage harvests are a typical management response to widespread tree mortality, but the decision to salvage mortality has large implications for the fate of carbon stocks (including forest carbon and harvested wood products) in the near and long terms. In this study, we created decision-support models for salvage harvesting based on carbon after an eastern spruce budworm outbreak. We used lasso regression to determine which stand characteristics (e.g., basal area) are the best predictors of carbon 40 years after an outbreak in both salvage and no salvage scenarios. We modeled carbon at year 40 for different treatment scenarios and discount rates. Treatment scenarios represent residual stand conditions that may be present when an outbreak occurs. Economic discount rates were applied to 40-year carbon values to account for near and long-term carbon storage aspects. We found that the volume and size of eastern spruce budworm host species are significant predictors of salvage preference based on carbon. We found overall that salvaging less volume is recommended to avoid major swings in carbon budgets and that discounting carbon values to apply weight to near or long-term sequestration greatly affects whether salvaging is preferred. Lasso models are constructed for the northeastern US, however, similar concepts may be applied beyond our study area and potentially for other insect outbreaks similar to spruce budworm, such as mountain pine beetle (Dendroctonus ponderosae) or hemlock woolly adelgid (Adelges tsugae). From a policy standpoint widespread salvaging could create a large carbon emissions deficit with the risk of not being fully replenished within a desired timeframe. Since salvaging is often financially driven, especially for private landowners, carbon market payments or incentives for not salvaging is a consideration for future policy.

Abstract Although remote sensing of lake surface water temperature has been ongoing for decades and has led to important discoveries regarding the warming of lake surface temperature in some regions, the ability to access and use remote sensing data is still primarily limited to remote sensing experts. Effective use of remote sensing data involves technical skills in coding (often in multiple programming languages), application of appropriate atmospheric corrections, and integrating spatially heterogeneous remote sensing data with in situ data obtained at specific geographic locations. To improve access to remote sensing data and broaden the understanding of changes in lake surface water temperature over the past four decades, we created lakeCoSTR (lake Collection 2 Surface Temperature Retrieval), a user‐friendly, cloud‐based script that gives ecologists lacking specialized training in remote sensing the ability to access the Landsat Collection 2 temperature estimates for lakes with a surface area of at least 0.4 ha. Additionally, if in situ data are provided, a paired dataset can be created within the tool. To demonstrate lakeCoSTR, we retrieved surface water temperature data for a lake with a long monitoring history, Lake Sunapee, NH, USA, and compared long‐term surface temperature trends between data obtained via lakeCoSTR and in situ measurements. When compared with Landsat Collection 1 temperature estimates derived from a single‐channel algorithm, the Landsat Collection 2 data from lakeCoSTR required no calibration to in situ data. This suggests that lakeCoSTR can be used to document temporal trends in lakes and to reprocess analyses that relied on Collection 1 data. From 1983 until 2020, remotely sensed surface water temperature estimates at Lake Sunapee increased by 0.07–0.09°C year−1 during July and August, a trend that agreed with long‐term in situ record. As climate change continues to impact freshwater systems, a better understanding of long‐term temperature data will be vital. Remotely sensed data, like those acquired using lakeCoSTR, may provide a window into temperature trends for lakes.

Quadratic mean diameter is the most frequently reported descriptor of the diameter distribution of forests. As such, it is often used as an indicator of forest stand structure, developmental stage, and ecological and economic potential. However, quadratic mean diameter can be heavily influenced by the presence or absence of large numbers of small stems in lower canopy strata, and it is also sensitive to left-truncation of the diameter distribution, making its interpretation across inventories with different protocols challenging. Here, we examine three alternative expressions of stand diameter: the arithmetic and quadratic mean diameter of the thickest 100 trees per hectare, and the basal area-weighted mean diameter. Using data from the United States Forest Inventory and Analysis program for New York and New England, these alternative expressions showed closer correlation with multiple stand structural variables than did quadratic mean diameter, including merchantable cubic and board foot volume per hectare, aboveground live tree carbon per hectare, and total number of live and dead standing trees greater than 40 ​cm diameter at breast height per hectare (previously proposed as an index of old-growth structure). Arithmetic and quadratic mean diameter of the thickest 100 trees per hectare showed nearly identical performance, and the strongest correlations across the board. We develop closed-form expressions for these variables when the diameter distribution is a Weibull, and illustrate their behavior relative to quadratic mean diameter for that situation. While the reasons for prevalence of quadratic mean diameter as an indicator remain valid, we suggest that these alternative measures should be more widely reported and analyzed to give a more informative depiction of stand structure and development in complex forests.

We analyzed over 8 decades of change in forest composition (represented by species proportion of basal area) and size class from more than 400 permanent plots located on the Bartlett Experimental Forest in the White Mountains of New Hampshire. These data represent one of the longest-term landscape-scale records of forest change based on permanent plots in North America. We analyzed the plots based on elevation class, land type indicating assumed successional direction (grouped into coniferous and deciduous), and inventory period within managed and unmanaged portions of the forest. An ongoing shift from small- to large-diameter stems is clear across all species, in response to the overall aging of the forest following exploitative harvesting in the 19th century. Major compositional changes include a continuing decline in shade-intolerant species (paper birch and aspen), along with the mid-tolerant yellow birch. An increase in red maple abundance through the early 1990s has leveled off or reversed. Among shade-tolerant species, increases in beech and red spruce were largely consistent with assumed land type on unmanaged plots, but heavy marking against diseased beech on managed plots restricted increase of that species. Sugar maple declined in abundance except where silvicultural intervention helped maintain it. By contrast, eastern hemlock showed a continuing expansion at all elevations below 600 m. The data continue to show little or no evidence of upward migration of species, despite evidence of recent regional change in climate. However, the BEF is poised for substantial changes when emerald ash borer and hemlock woolly adelgid, both of which are known to infest nearby areas, do arrive.

Introduction: Miscommunication during inter-unit handoffs between emergency and internal medicine physicians may jeopardize patient safety.  Our goal was to evaluate the impact of a structured communication strategy on the quality of admission handoffs. Methods: We conducted a mixed-methods, pre-test/post-test study at a 560-bed academic health center with 60,000 emergency department (ED) patient visits per year. Admission-handoff best practices were integrated into a modified SBAR format, resulting in the Situation, Background, Assessment, Responsibilities & Risk, Discussion & Disposition, Read-back & Record (SBAR-DR) model. Physician handoff conversations were recorded and transcribed for the 60 days before (n=110) and 60 days after (n=110) introduction of the SBAR-DR strategy. Transcriptions were scored by two blinded physicians using a 16-item scoring instrument. The primary outcome was the composite handoff quality score. We assessed physician perceptions via a post-intervention survey. Results: The composite quality score improved in the post-intervention phase (7.57 + 2.42 vs. 8.45 + 2.51, p=.0085). Three of the 16 individual scoring elements also improved, including time for questions (70.6% vs. 82.7%, p=.0344) and confirmation of disposition plan (41.8% vs. 62.7%, p=.0019). The majority of emergency and internal medicine physicians felt that the SBAR-DR model had a positive impact on patient safety and handoff efficiency.  Conclusion: Implementation of the SBAR-DR strategy resulted in improved verbal handoff quality. Agreement upon a clear disposition plan was the most improved element, which is of great importance in delineating responsibility of care and streamlining ED throughput. Future efforts should focus on nurturing broader physician buy-in to facilitate institution-wide implementation.

Alice Zeniter’s 2017 novel The Art of Losing, translated recently by Frank Wynne from French to English, explores how buried histories resurface and haunt generations to come, despite national efforts to ignore, if not minimalize, the enduring impacts of colonialism, independence struggles and exile. Set in contemporary France in the wake of the 2015 terrorist attacks, and loosely inspired by Zeniter’s own family history, the book follows Naïma, a young woman of Algerian decent who grapples with a largely unknown and misconstrued harki heritage. Drawing on Marianne Hirsch’s concept of postmemory, this article investigates intergenerational transmission of memory, trauma, and silence around themes such as war, exile and integration.

The pulp and paper industry in Indonesia is the tenth largest producer in the world, with Acacia and Eucalyptus as the main genera used for production; however, limited publications exist related to Eucalyptus growth models in Indonesia compared with other regions. Time-based models have been developed in which height, stand density, and basal area are predicted based on initial conditions and age. In contrast, a state-space approach utilizes the rate of change of these three state variables. Previous direct comparisons of these two approaches are generally limited. Consequently, the objective of this study was to compare two stand-level growth modeling approaches for Eucalyptus hybrid species on Sumatera (Sumatra) Island using both time-based and state-space methods. Our results indicate that dynamic models using either time-based or state-space approaches are adequate for predicting stand parameters to rotation age. A modified Bazukis matrix indicated that the behavior of both methods produced reliable predictions that were biologically reasonable in terms of stand development; however, the time-based approach provided better performance than the state-space approach on a variety of equivalence tests and goodness-of-fit statistics. Overall, the analysis highlights the advantages and disadvantages of these two commonly used, yet highly contrasting, stand-level growth modeling approaches, which need further consideration and evaluation. Key words: growth and yield, time-based model, state-space model, Eucalyptus hybrid clone, Indonesia. L'industrie des pates et papiers de l'Indonesie est le dixieme plus grand producteur au monde et utilise principalement les genres Acacia et Eucalyptus pour cette production; toutefois, il existe peu de publications traitant de modeles de croissance de l'eucalyptus en Indonesie comparativement a d'autres regions. Des modeles temporels ont ete mis au point dans lesquels la hauteur, la densite du peuplement et la surface terriere sont predites en fonction des conditions initiales et de l'age. En revanche, une approche par etats spatiaux utilise le taux de changement de ces trois variables d'etat. Les comparaisons directes de ces deux approches sont peu frequentes. Par consequent, l'objectif de cette etude etait de comparer deux approches de modelisation de la croissance a l'echelle du peuplement pour les especes d'eucalyptus hybrides de l'ile de Sumatera (Sumatra) en utilisant les methodes temporelles et d'etats spatiaux. Nos resultats indiquent que les modeles dynamiques utilisant des approches temporelles ou par etats spatiaux sont adequats pour predire les parametres des peuplements jusqu'a l'age d'exploitabilite. Une matrice modifiee de Bazukis indiquait que le comportement des deux methodes a produit des previsions fiables et biologiquement raisonnables en ce qui concerne le developpement des peuplements; cependant, l'approche temporelle etait superieure a l'approche par etats spatiaux dans le cas de plusieurs tests d'equivalence et de statistiques de validite d'ajustement. Dans l'ensemble, l'analyse met en evidence les avantages et les inconvenients de ces deux approches de modelisation de la croissance a l'echelle du peuplement qui sont couramment utilisees, tout en etant tres differentes, ce qui necessite un examen et une evaluation plus approfondis. [Traduit par la Redaction] Mots-cles : croissance et production, modele temporel, modele d'etats spatiaux, clone d'Eucalyptus hybride, Indonesie., Introduction The pulp and paper industry in Indonesia is the tenth largest producer in the world (Rini 2019). In 2018, Indonesia's paper production capacity was 16 million tonnes per year [...]

Using a two-phase sampling approach with systematic selection of large samples of covariates followed by a sampling with probability proportional to prediction (3P sampling) process to subsample field measures of the parameters of interest can be an efficient design to sample larger forest areas. To assist in obtaining predictions for each sample plot consistently and rapidly, we propose using a 360[degrees] spherical camera. In this study, three covariates derived from spherical images were evaluated: (i) basal area (P[BA]); (ii) sum of squared heights per hectare (P[SHT]); and (iii) stem fraction (P[SF]). These covariates were used to estimate volume. Sample simulations showed no biases in volume estimates for any of the three covariates. Overall, P[SF] had the lowest standard error percentages across different simulated sample sizes (10% for five subsamples to 2.5% for 50 subsamples), even though it had the lowest correlations with field volume (correlation = 0.30-0.31). This may be a result of the relatively consistent stand conditions within the study site. Based on our results, standard errors of 5% were obtainable with measurement fractions of about 25% of the number of image-based predictions when using P[SF] or P[BA] and 75% when using P[SHT]. Key words: 3P sampling, spherical image, stem fraction, photo point sampling, vertical point sampling. L'utilisation d'une approche d'echantillonnage en deux phases avec selection systematique de grands echantillons de covariables, suivie d'un processus d'echantillonnage avec probabilite proportionnelle a la prediction (echantillonnage 3P) pour sous-echantillonner les mesures sur le terrain des parametres d'interet, peut etre une conception efficace pour echantillonner de plus grandes regions forestieres. Nous proposons d'utiliser une camera spherique a 360[degrees], pour aider a obtenir des predictions pour chaque parcelle d'echantillonnage de maniere coherente et rapide. Dans cette etude, trois covariables derivees d'images spheriques ont ete evaluees : (i) la surface terriere (P[ST]); (ii) la somme de la hauteur des tiges au carre a l'hectare (P[SHT]); et (iii) la fraction des tiges (P[FT]). Ces covariables ont ete utilisees pour estimer le volume. Les simulations d'echantillonnage n'ont montre aucun biais dans l'estimation du volume pour aucune des trois covariables. Dans l'ensemble, P[FT] avait les pourcentages d'erreur-type les plus bas dans les differentes tailles d'echantillon simulees (10 % pour cinq sous-echantillons a 2,5 % pour 50 sous-echantillons), meme s'il avait les correlations les plus faibles avec le volume sur le terrain (correlation = 0,30-0,31). Cela peut etre le resultat des conditions de peuplement relativement uniformes dans le site d'etude. Sur la base de nos resultats, des erreurs-types de 5 % ont pu etre obtenues avec des intensites de mesure d'environ 25 % du nombre de predictions basees sur l'image lors de l'utilisation de P[FT] ou P[ST] et de 75 % lors de l'utilisation de P[SHT]. [Traduit par la Redaction] Mots-cles : echantillonnage 3P, image spherique, fraction des tiges, echantillonnage par points photographiques, echantillonnage par points verticaux., 1. Introduction In practice, forest inventory is designed to obtain estimates of forest conditions under time and cost constraints. Enhancing sampling efficiency is an important consideration in sample design (Freese [...]

Big basal area factor (big BAF) sampling is a widely used subsampling method to select measure-trees. Several studies have shown big BAF sampling to be an efficient sampling scheme. In this study, we use sector sampling (Smith et al. 2008, For. Sci. 54: 67-76) as an alternative subsample selection method. Based on some simulated mapped stands derived from three balsam fir (Abies balsamea (L.) Mill.) spacing trials in western Newfoundland, we show that sector subsampling is comparable to big BAF sampling in terms of estimated mean basal area ratios and their associated standard errors. Differences between big BAF sampling and sector sampling methods showed less than 1% difference across the three sites. As with big BAF sampling, changes in sample intensity had no significant (p < 0.05) effects on the accuracy of estimating mean biomass to basal area ratios and the resulting estimated mean biomasses per unit area. Key words: sector sampling, subsampling, basal area ratio estimation, sample efficiency, big BAF sampling, biomass estimation. L'echantillonnage par grand facteur de prisme (GFP) est une methode de sous-echantillonnage largement utilisee pour selectionner les arbres-etudes. Plusieurs etudes ont montre que l'echantillonnage par GFP est un plan d'echantillonnage efficace. Dans cette etude, nous utilisons l'echantillonnage sectoriel (Smith et al. 2008, For. Sci. 54: 67-76) comme methode alternative de selection des sous-echantillons. En se basant sur des peuplements cartographies simules issus de trois essais de degagement du sapin baumier (Abies balsamea (L.) Mill.) dans l'ouest de Terre-Neuve, nous montrons que le sous-echantillonnage sectoriel est comparable a un echantillonnage par GFP en termes d'estimation des ratios moyens de surface terriere et de leurs erreurs-types associees. Les comparaisons entre les methodes d'echantillonnage par GFP et par secteur montrent une difference de moins de 1 % entre les trois sites. Comme pour l'echantillonnage par GFP, les changements de densite de l'echantillon n'ont aucun effet significatif (p < 0,05) sur l'exactitude de l'estimation des ratios de la biomasse moyenne sur la surface terriere et sur les estimations de biomasses moyennes par unite de surface qui en resultent. [Traduit par la Redaction] Mots-cles : echantillonnage sectoriel, sous-echantillonnage, estimation du rapport de surface terriere, efficacite d'echantillonnage, echantillonnage par grand facteur de prisme, estimation de la biomasse., Introduction Many forest-level attributes such as volume, biomass, and carbon rely on individual tree measurements and allometric models (Kershaw et al. 2016). Direct measurement of these attributes is often impractical, [...]