bluuebunny/crossref_metadata_2025_split huggingface dataset:
Connecting theory and data to understand recombination rate evolution
Authors: Dapper Amy L. , Payseur Bret A. 
Published: November 2017

Meiotic recombination is necessary for successful gametogenesis in most sexually reproducing organisms and is a fundamental genomic parameter, influencing the efficacy of selection and the fate of new mutations. The molecular and evolutionary functions of recombination should impose strong selective constraints on the range of recombination rates. Yet, variation in recombination rate is observed on a variety of genomic and evolutionary scales. In the past decade, empirical studies have described variation in recombination rate within genomes, between individuals, between sexes, between populations and between species. At the same time, theoretical work has provided an increasingly detailed picture of the evolutionary advantages to recombination. Perhaps surprisingly, the causes of natural variation in recombination rate remain poorly understood. We argue that empirical and theoretical approaches to understand the evolution of recombination have proceeded largely independently of each other. Most models that address the evolution of recombination rate were created to explain the evolutionary advantage of recombination rather than quantitative differences in rate among individuals. Conversely, most empirical studies aim to describe variation in recombination rate, rather than to test evolutionary hypotheses. In this Perspective, we argue that efforts to integrate the rich bodies of empirical and theoretical work on recombination rate are crucial to moving this field forward. We provide new directions for the development of theory and the production of data that will jointly close this gap.This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.
Background selection as null hypothesis in population genomics: insights and challenges fromDrosophilastudies
Authors: Comeron Josep M. 
Published: November 2017

The consequences of selection at linked sites are multiple and widespread across the genomes of most species. Here, I first review the main concepts behind models of selection and linkage in recombining genomes, present the difficulty in parametrizing these models simply as a reduction in effective population size (Ne) and discuss the predicted impact of recombination rates on levels of diversity across genomes. Arguments are then put forward in favour of using a model of selection and linkage with neutral and deleterious mutations (i.e. the background selection model, BGS) as a sensible null hypothesis for investigating the presence of other forms of selection, such as balancing or positive. I also describe and compare two studies that have generated high-resolution landscapes of the predicted consequences of selection at linked sites inDrosophila melanogaster. Both studies show that BGS can explain a very large fraction of the observed variation in diversity across the whole genome, thus supporting its use as null model. Finally, I identify and discuss a number of caveats and challenges in studies of genetic hitchhiking that have been often overlooked, with several of them sharing a potential bias towards overestimating the evidence supporting recent selective sweeps to the detriment of a BGS explanation. One potential source of bias is the analysis of non-equilibrium populations: it is precisely because models of selection and linkage predict variation inNeacross chromosomes that demographic dynamics are not expected to be equivalent chromosome- or genome-wide. Other challenges include the use of incomplete genome annotations, the assumption of temporally stable recombination landscapes, the presence of genes under balancing selection and the consequences of ignoring non-crossover (gene conversion) recombination events.This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.
Subtle individual variation in indeterminate growth leads to major variation in survival and lifetime reproductive output in a long‐lived reptile
Authors: Armstrong Doug P. , Keevil Matthew G. , Rollinson Njal , Brooks Ronald J. 
Published: November 2017

Abstract

The consequences of individual variation in life‐history traits have been well studied due to their importance in evolutionary ecology. However, a trait that has received little empirical attention is the rate of indeterminate growth. In long‐lived ectotherms, subtle variation in growth after maturity could have major effects over the animals’ lifetimes.

These effects are difficult to measure due to the challenges involved in reliably estimating individual variation in the face of environmental stochasticity, and the need to account for trade‐offs among growth, reproduction and survival. However, modelling advances have made such analysis possible if long‐term high‐quality datasets are available.

We used an integrated state‐space modelling framework to reveal relationships between indeterminate growth, reproduction and survival in a population of North American snapping turtles (Chelydra serpentina) using a 41‐year dataset for 298 adult females.

A hierarchical version of the von Bertalanffy model fitted to data on carapace lengths showed substantial individual variation in growth trajectories, and hierarchical models fitted to clutch‐mass data and recapture histories showed that reproductive output and survival probability increased with size. Integration of these models revealed no detectable trade‐offs—i.e., individual growth parameters were not correlated with size‐specific survival or reproduction rates, and individual variation in reproductive output did not affect the size‐specific survival rate. Consequently, individual variation in growth parameters was estimated to result in >2‐fold variation in post‐maturity life expectancy and >4‐fold variation in expected lifetime reproductive output.

These results illustrate that indeterminate growth can have major fitness consequences in long‐lived species. We suggest that the individual variation in growth rates reflects variation in environments experienced during development or later life. An understanding of this variation may be essential for predicting the population dynamics of long‐lived species under threat and identifying the most important environments to protect.

A plain language summary is available for this article.
Time domain electromagnetic‐induced polarisation: extracting more induced polarisation information from grounded source time domain electromagnetic data
Authors: Kang Seogi , Oldenburg Douglas W. 
Published: November 2017

ABSTRACTElectrical induced polarisation surveys are used to detect chargeable materials in the earth. For interpretation of time domain electrical‐induced polarisation data a common procedure is to first invert the direct current data (electric current on time) to recover conductivity and then invert the induced polarisation data (current off‐time) to recover chargeability. This direct current‐induced polarisation inversion procedure assumes that the off time data are free of secondary electromagnetic induction effects. To comply with this, early time data are often discarded or not recorded. For mid‐time data, an electromagnetic decoupling technique, which removes electromagnetic induction in the observations, needs to be implemented. Usually, responses from a half‐space or a layered earth are subtracted. Recent capability in three‐dimensional time domain electromagnetic forward modelling and inversion allows to revisit these procedures. In a Time domain electromagnetic‐induced polarisation survey, a high sampling rate allows early time channels of the electromagnetic data to be recorded. The recovery of chargeability then follows a three‐step workflow: (i) invert early time channel time domain electromagnetic data to recover the three‐dimensional conductivity; (ii) use that conductivity to compute the time domain electromagnetic response at later time channels and subtract this fundamental response from the observations to extract the induced polarisation responses, and (iii) invert the induced polarisation responses to recover a three‐dimensional chargeability. This workflow effectively removes electromagnetic induction effects in the observations and produces better chargeability and conductivity models compared with conventional approaches. In a synthetic example involving a gradient array, we show that the conductivity structure obtained from the early time channel data, which are usually discarded, is superior to that obtained from the steady state direct current voltages. This adds a further reason to collect these electromagnetic data.
Integrating decision triggers into conservation management practice
Authors: de Bie Kelly , Addison Prue F. E. , Cook Carly N. 
Published: November 2017

Abstract

Decision triggers show great potential for facilitating timely management action, promoting evidence‐based management and preventing undesirable changes to the status of species, ecosystems and threats. Integration of decision triggers into day‐to‐day management practice has been slow, constrained by insufficient resources and limited in‐house expertise. Arguably, the greatest impediment is the lack of an overarching process with robust and accessible methods for developing and implementing decision triggers in a manner that fits within an organization's established processes and skill sets.

We identify the steps necessary for setting decision triggers and highlight how these steps align with commonly used conservation planning and management frameworks, for ease of adoption.

We emphasize that decision triggers do not require a known ecological threshold, and can be applied to data‐rich and data‐poor contexts, with single or multiple management objectives.

Synthesis and applications. This work highlights the necessary steps involved, and importantly, the suite of methods that can be used to set decision triggers, with the aim of supporting practitioners in the development of robust and defensible decision triggers.
Sunken Cities: Climate Change, Urban Futures and the Imagination of Submergence
Authors: Dobraszczyk Paul 
Published: November 2017

AbstractClimate change presents multiple challenges to cities—not only in terms of the resilience and sustainability of the urban fabric, but also in relation to how urban inhabitants imagine they might adapt to a future transformed environment. This article explores imaginative modes of thinking in relation to future cities and climate change, focusing on representations of urban drowning or submergence. It considers, in turn, climate‐change fictions—from J.G. Ballard's 1962 novelThe Drowned Worldto Paulo Bacigalupi'sThe Drowned Cities, published in 2012; visual representations from Gustave Doré'sThe New Zealanderin 1872 to Alexis Rockman's 2004Manifest Destiny; and architectural conjecture, from Wolf Hilbertz's Autopia Ampere project from 1970 onwards to CRAB Studio's Soak City in 2009. The article draws out how these imaginaries intersect with theoretical understandings of science fiction and ecology, contending that an emphasis onmultipleimaginaries of climate change is critical to expanding the narrow range of possibilities that currently characterize the literature on cities and climate change. Imaginative texts, images and designs mutually inform each other to encourage holistic ways of approaching how we think about the prospect of urban submergence and to incubate radical responses to it.
Comparison of four methods of endotracheal tube passage in simulated airways: There is room for improved techniques
Authors: Kingma Kirsten , Hofmeyr Ross , Zeng Irene Suilan , Coomarasamy Christin , Brainard Andrew 
Published: November 2017

AbstractObjectiveEndotracheal intubation requires laryngoscopy followed by passage of the endotracheal tube (ETT). Tube passage can be difficult, but there is little evidence to support which adjunct for tube passage is most effective.MethodsThe four tube passage adjuncts tested were the naked ETT, stylet ETT, railroaded bougie and preloaded bougie. Participants completed pre‐ and post‐test surveys identifying demographics, experience and method preference. After instruction, participants completed eight intubations on manikins with ‘easy’ and ‘difficult’ airways.ResultsOne hundred and seventeen practitioners who were experienced emergency medicine physicians, anaesthesiologists and out‐of‐hospital providers completed 936 total ETT attempts. For the ‘difficult’ airway, the percentage first pass success (95% confidence interval [CI]) for the naked ETT was 30.8% (23.1–39.7%). This was significantly lower than the stylet ETT (95.7% [86.6–100%]), the railroaded bougie (75.2% [63.8–86.6%]), or the preloaded bougie (89.7% [79.7–99.7%]). On difficult airways, the median (interquartile range [IQR]) time‐to‐intubation was fastest in the stylet ETT (25.0 s [20.9–32.2 s]) with the railroaded bougie being the slowest (43.2 s [36.5–56.2 s]). Seventy‐nine per cent of participants stated that they would change their practice based on participating in this study. Participants increased their preference for the preloaded bougie from 30.6% to 69.4%.ConclusionThe data show that tube passage with a stylet ETT or a preloaded bougie is superior in terms of higher first pass success, faster time‐to‐intubation and higher post‐test preference. The naked ETT is clearly inferior to other methods. This research supports the recommendation to use a stylet ETT or bougie for every predicted difficult intubation.
Trauma case review: A quality and safety feature of the Victorian State Trauma System
Authors: Pinto Carolyn , Cameron Peter A , Gabbe Belinda , McLellan Susan , Walker Tony 
Published: November 2017

AbstractThe aim of the present study was to describe the trauma case review process and its role in a regionalised trauma system. Victoria has a population of 5.9 million people, accounting for 26% of Australia's population. Victoria has been serviced by an inclusive, organised trauma system since 2000 comprising 138 health services with trauma designations and three major trauma services. Pre‐ and interhospital guidelines prescribe the timely transport of patients to the appropriate level of trauma service. A review of the role and contribution of 10 years of operation of the trauma case review group (CRG) was undertaken to describe the aims, processes and governance surrounding the implementation of an individual case review for specified major trauma patients. Specified patients were those identified by the Victorian State Trauma Registry as being managed outside of established Victorian State Trauma System prehospital and interhospital guidelines. A state‐wide trauma case review process was implemented across the trauma system using data‐informed detection flags and screening criteria. Using data from the Victorian State Trauma Registry, detection flags were correlated with patients at risk of a poorer outcome, thereby ensuring that all patients managed outside of the requirements of established trauma triage and transfer guidelines were subject to review. The CRG provides an individual review process as a technique for assessing and monitoring major trauma patient care and compliance with trauma system triage and transfer guidelines. The process has been effective as a quality and safety strategy by improving clinician knowledge of major trauma triage and transfer guidelines and facilitating improved compliance, particularly with interhospital transfers. Strong compliance has been achieved from health services with the requirement to internally review and respond to CRG concerns regarding ‘high‐risk’ trauma cases. Anecdotal feedback from health services regarding participation in the CRG process has been positive. The trauma case review process is an embedded feature of the Victorian State Trauma System that aims to improve compliance with major trauma guidelines by reviewing major trauma cases that have been managed outside of established triage and transfer guidelines. All trauma‐designated Victorian health services, Ambulance Victoria and Victorian adult and paediatric patient retrieval services might receive trauma cases for review. The process is also an integral component of trauma system clinical governance, which enables the identification of system‐level issues for escalation to the State Trauma Committee and the Victorian Department of Health and Human Services.
A comparison of honeybee (Apis mellifera) queen, worker and drone larvae by RNA‐Seq
Authors: He Xu‐Jiang , Jiang Wu‐Jun , Zhou Mi , Barron Andrew B. , Zeng Zhi‐Jiang 
Published: November 2017

AbstractHoneybees (Apis mellifera) have haplodiploid sex determination: males develop from unfertilized eggs and females develop from fertilized ones. The differences in larval food also determine the development of females. Here we compared the total somatic gene expression profiles of 2‐day and 4‐day‐old drone, queen and worker larvae by RNA‐Seq. The results from a co‐expression network analysis on all expressed genes showed that 2‐day‐old drone and worker larvae were closer in gene expression profiles than 2‐day‐old queen larvae. This indicated that for young larvae (2‐day‐old) environmental factors such as larval diet have a greater effect on gene expression profiles than ploidy or sex determination. Drones had the most distinct gene expression profiles at the 4‐day larval stage, suggesting that haploidy, or sex dramatically affects the gene expression of honeybee larvae. Drone larvae showed fewer differences in gene expression profiles at the 2‐day and 4‐day time points than the worker and queen larval comparisons (598 against 1190 and 1181), suggesting a different pattern of gene expression regulation during the larval development of haploid males compared to diploid females. This study indicates that early in development the queen caste has the most distinct gene expression profile, perhaps reflecting the very rapid growth and morphological specialization of this caste compared to workers and drones. Later in development the haploid male drones have the most distinct gene expression profile, perhaps reflecting the influence of ploidy or sex determination on gene expression.
Effect of In Vitro Digestion on the Total Antioxidant Capacity and Phenolic Content of 3 Species of Oregano (Hedeoma patens, Lippia graveolens, Lippia palmeri)
Authors: Gutiérrez‐Grijalva Erick Paul , Angulo‐Escalante Miguel Angel , León‐Félix Josefina , Heredia J. Basilio 
Published: November 2017

AbstractOregano phenolic compounds have been studied for their anti‐inflammatory properties. Nonetheless, after ingestion, the gastrointestinal environment can affect their antioxidant stability and thus their bioactive properties. To evaluate the effect of in vitro gastrointestinal (GI) digestion on the phenolic compounds of 3 species of oregano (Hedeoma patens, Lippia graveolens, and Lippia palmeri), the total reducing capacity, total flavonoid content, and antioxidant capacity were evaluated before and after in vitro GI digestion. In addition, the phenolic compounds of the 3 oregano species were identified and quantified by UPLC‐PDA before and after in vitro GI digestion. It was shown that the reducing capacity, flavonoid content and antioxidant capacity were affected by the GI digestion process. Moreover, the phenolic compounds identified were apigenin‐7‐glucoside, scutellarein, luteolin, luteolin‐7‐glucoside, phloridzin and chlorogenic acid, and their levels were affected by the in vitro GI process. Our results showed that the phenolic compounds from these 3 species of oregano are affected by the in vitro digestion process, and this effect is largely attributable to pH changes. These changes can modify the bioavailability and further anti‐inflammatory activity of oregano phenolics, and thus, further research is needed.Practical ApplicationOregano is a rich source of polyphenols that have shown bioactive properties like anti‐inflammatory potential. However, little is known of the gastrointestinal fate of oregano polyphenols which is imperative to fully understand its bioaccessibility. Our results are important to develop new administration strategies which could help protect the antioxidant and anti‐inflammatory potential and bioaccessibility of such compounds.
Cyclophilin A promotes non‐small cell lung cancer metastasis via p38 MAPK
Authors: Guo Yinan , Jiang Mei , Zhao Xiaoting , Gu Meng , Wang Ziyu , Xu Shaofa , Yue Wentao 
Published: November 2017

BackgroundCyclophilin A (CypA) is associated with metastasis in diverse cancers; however, its role in lung cancer metastasis and the underlying mechanisms remain poorly understood. Our study investigated the effect of CypA on non‐small cell lung cancer (NSCLC) metastasis in vitro and in vivo to determine its mechanisms.MethodsIn this study, A549 and H1299 cell lines with downregulated and overexpressed CypA, respectively, were constructed by lentivirus transfection of NSCLC cells. in vitro experiments, including wound healing and transwell assays and Western blotting, showed that CypA promoted cancer cell migration and epithelial‐mesenchymal transition in NSCLC. Lung metastasis mouse models were used for the first time to confirm that CypA promoted NSCLC metastasis in vivo. The p38 inhibitor SB203580 was used to show that p38 MAPK is involved in CypA‐mediated NSCLC metastasis.ResultsWound healing and transwell assays showed that the migration of both A549 and H1299 cells decreased in the CypA downregulated group and increased in the CypA overexpressed group. CypA also positively promoted the expression of epithelial‐mesenchymal transition‐relevant proteins. Results of mouse models confirmed that the tumor metastasis rate was much higher in the CypA overexpressed than in the CypA downregulated group. In addition, SB203580 inhibited NSCLC cell migration significantly in the CypA overexpressed group, while the difference in the CypA downregulated group was not significant.ConclusionsIn conclusion, this study demonstrated that CypA promotes NSCLC cancer metastasis via p38 MAPK.