bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strategies for complete plastid genome sequencing
Authors: Twyford Alex D. , Ness Rob W. 
Published: November 2016

AbstractPlastid sequencing is an essential tool in the study of plant evolution. This high‐copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low‐cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation‐sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly. These developments allow for a much more streamlined assembly than via conventional short‐range PCR. Although newer methods make complete plastid sequencing possible for any land plant or green alga, there are still challenges for producing finished plastomes particularly from herbarium material or from structurally divergent plastids such as those of parasitic plants.
OpenMEE: Intuitive, open‐source software for meta‐analysis in ecology and evolutionary biology
Authors: Wallace Byron C. , Lajeunesse Marc J. , Dietz George , Dahabreh Issa J. , Trikalinos Thomas A. , Schmid Christopher H. , Gurevitch Jessica 
Published: November 2016

Summary

Meta‐analysis and meta‐regression are statistical methods for synthesizing and modelling the results of different studies, and are critical research synthesis tools in ecology and evolutionary biology (E&E). However, many E&E researchers carry out meta‐analyses using software that is limited in its statistical functionality and is not easily updatable. It is likely that these software limitations have slowed the uptake of new methods in E&E and limited the scope and quality of inferences from research syntheses.

We developed OpenMEE: Open Meta‐analyst for Ecology and Evolution to address the need for advanced, easy‐to‐use software for meta‐analysis and meta‐regression. OpenMEE has a cross‐platform, easy‐to‐use graphical user interface (GUI) that gives E&E researchers access to the diverse and advanced statistical functionalities offered in R, without requiring knowledge of R programming.

OpenMEE offers a suite of advanced meta‐analysis and meta‐regression methods for synthesizing continuous and categorical data, including meta‐regression with multiple covariates and their interactions, phylogenetic analyses, and simple missing data imputation. OpenMEE also supports data importing and exporting, exploratory data analysis, graphing of data, and summary table generation.

As intuitive, open‐source, free software for advanced methods in meta‐analysis, OpenMEE meets the current and pressing needs of the E&E community for teaching meta‐analysis and conducting high‐quality syntheses. Because OpenMEE's statistical components are written in R, new methods and packages can be rapidly incorporated into the software. To fully realize the potential of OpenMEE, we encourage community development with an aim to advance the capabilities of meta‐analyses in E&E.
An environmental DNA‐based method for monitoring spawning activity: a case study, using the endangered Macquarie perch (Macquaria australasica)
Authors: Bylemans Jonas , Furlan Elise M. , Hardy Christopher M. , McGuffie Prudence , Lintermans Mark , Gleeson Dianne M. 
Published: November 2016

Summary

Determining the timing and location of reproductive events is critical for efficient management of species. However, methods currently used for aquatic species are costly, time intensive, biased and often require destructive or injurious sampling. Hence, developing a non‐invasive sampling method to accurately determine the timing and location of reproduction for aquatic species would be extremely valuable.

We conducted an experimental and field study to determine the influence of spawning, and the mass release of spermatozoa in particular, on environmental DNA (eDNA) concentrations. Using a quantitative PCR approach we monitored changes in nuclear and mitochondrial eDNA concentrations over time.

The data from the experimental study and the field survey supported our hypothesis that spawning events are characterized by higher concentrations of nuclear relative to mitochondrial eDNA. Outside of the reproductive period, we find that nuclear and mitochondrial DNA fragments are equally abundant in environmental water samples.

We have shown that changes in the relative abundance of nuclear and mitochondrial eDNA can be used to monitor spawning activity of the endangered Macquarie perch. Our method is likely to be transferrable to other aquatic species and can be particularly useful to increase our understanding of the spawning biology of cryptic, rare or threatened species as well as design and evaluate environmental management actions and determine species establishment.
Food and consumer behavior: why the details matter
Authors: Just David R. , Gabrielyan Gnel 
Published: November 2016

AbstractA growing body of literature now demonstrates the importance of behavioral factors in individual food consumption. However, whether addressing hunger, nutrition, or obesity, food policies are often created to target changes at the aggregate level. These policies ignore such behavioral tools or effects and their potential heterogeneous effects on consumers. In this article, we review the most important results examining food consumption and behavioral economics and provide a thorough discussion of how such tools are now being added to the lexicon of effective policy tools. In addition, we discuss how traditional policy tools that ignore the individual behavioral effects can miss the mark or even backfire. The implication is clear: a thorough understanding of behavioral economics is necessary to create efficient food policy.
Trends and patterns in the triple burden of malnutrition in India
Authors: Meenakshi J. V. 
Published: November 2016

AbstractThis paper brings together recent evidence on what has come to be referred to as the triple burden of malnutrition—consisting of overnutrition, undernutriton, and micronutrient deficiencies—using various anthropometric, biochemical, and diet quality indicators, and juxtaposing these against changes in relative prices. The evidence points to the rapid emergence of overweight as a public health problem, widespread not only in urban, but also in rural areas; associated noncommunicable diseases are also on the rise. Over time, while most indicators of undernutrition have improved, magnitudes are nonetheless high; a persistent problem is anemia, the prevalence of which remains high and unchanged. As for food, more than quantity, it is its quality that appears to be correlated with malnutrition. Yet improvements in diet quality have not been high, and micronutrient intakes remain low. It has become increasingly difficult for the poor to have a diet rich in vegetables, dairy and meat, as their prices (per unit calorie), relative to cereals, have risen faster than for the rich.
Food security as resilience: reconciling definition and measurement
Authors: Upton Joanna B. , Cissé Jennifer Denno , Barrett Christopher B. 
Published: November 2016

AbstractIn this article, we draw out a set of axioms for food security measurement that follow directly from the internationally agreed 1996 FAO definition. Building on recent work on the theory and measurement of development resilience, we then propose an empirical strategy to measure food security that addresses these measurement axioms better than do prevailing measures. We empirically illustrate this approach using a panel data set from northern Kenya.
A text message away: ICTs as a tool to improve food security
Authors: Nakasone Eduardo , Torero Maximo 
Published: November 2016

AbstractThe growing use of ICTs around the world, particularly cellular phone technology, provides a significant development opportunity. Under certain situations, ICTs can improve rural households’ agricultural production, farm profitability, job opportunities, adoption of healthier practices, and risk management. All these effects have the potential to increase wellbeing and food security in rural areas of developing countries. Several challenges to effectively scaling up the use of ICTs for development remain, however. Taking advantage of the opportunities provided by ICTs depends on increased connectivity of marginalized population groups, the content and usefulness of the information provided through ICTs, and the capacity of households in rural areas to understand and act on the information that they receive. We need innovative ways to bring together the public and private sectors to ensure that the three Cs (connectivity, content, and capacity) are addressed as a whole.
Recent weather fluctuations and agricultural yields: implications for climate change
Authors: D'Agostino Anthony Louis , Schlenker Wolfram 
Published: November 2016

AbstractWe summarize recent statistical analyses that link agricultural yields to weather fluctuations. Similar to other sectors, high temperatures play a crucial role in predicting outcomes. Climate change is predicted to significantly increase high temperatures and thereby reduce yields. How good are such models at predicting future outcomes? We show that a statistical model estimated using historic US data on corn and soybean yields from 1950 to 2011 is very capable of predicting aggregate US yields for the years 2012–2015, where 2012 was much hotter than normal and is expected to become the new normal under climate change. We conclude by discussing recent studies on the implication of predicted yield declines with a special focus on adaptation and commodity prices.
Crohn's disease should be considered in children with inflammatory oral lesions
Authors: Skrzat Anna , Olczak‐Kowalczyk Dorota , Turska‐Szybka Anna 
Published: November 2016

AbstractThis systematic review presents the oral manifestations of paediatric Crohn's disease. Our review of 28 papers published from 2000 to 2015 showed that the prevalence of oral manifestations was 10–80%. Specific symptoms included mucosal tags, swelling of the lips, cheeks and gingiva, and cobblestoning mucosa. Nonspecific symptoms included aphthous‐like ulcers, angular cheilitis, lip fissuring and gingivitis.ConclusionThe oral manifestations of Crohn's disease might precede intestinal inflammation or coincide with it. Crohn's disease should be considered in children with multiple oral manifestations and paediatric dentists, and gastroenterologists should be involved in their coordinated evaluation and follow‐up.
Clinical symptom tool that raises the index of suspicion for eosinophilic oesophagitis in adults and drives earlier biopsy for definitive diagnosis
Authors: von Arnim U. , Röhl F.‐W. , Miehlke S. , Jechorek D. , Reinhold D. , Wex T. , Malfertheiner P. 
Published: November 2016

SummaryBackgroundEosinophilic oesophagitis (EoE) and gastro‐oesophageal reflux disease (GERD) present with overlapping symptomatology and it is challenging to distinguish EoE from GERD clinically before endoscopy.AimTo investigate the prognostic value of a set of clinical symptoms and laboratory values in patients with EoE and GERD.MethodsIn this prospective, single‐centre, observational study, we compared clinical and laboratory data from 202 patients with EoE or GERD (10 relevant characteristics). Those characteristics showing potential significance in a univariate analysis were then included in a multivariate analysis.ResultsThe set of 10 characteristics (10‐marker set) was able to distinguish between EoE and GERD with good reliability (correct assignment, i.e. agreement with subsequent EGD, of 94.4%). Reduction of the set to the six statistically and clinically most relevant markers continued to give good reliability (88.9%), and further stepwise reduction led to four‐marker sets comprising history of atopy, history of food impaction, proton pump inhibitor refractory symptoms and either immunoglobulin E or peripheral eosinophilia, with correct assignment rates of 91.3% and 85.1% respectively.ConclusionsWe have developed a simple and easily applicable clinical/laboratory marker set that helps to distinguish EoE from GERD earlier in the treatment course, thus guiding the endoscopist to perform biopsies from the oesophagus to ensure the diagnosis. The application of the scoring system is expected to diagnose EoE earlier and avoiding delay of adequate treatment.
Simeprevir in combination with sofosbuvir in treatment‐naïve and ‐experienced patients with hepatitis C virus genotype 4 infection: a Phase III, open‐label, single‐arm study (PLUTO)
Authors: Buti M. , Calleja J. L. , Lens S. , Diago M. , Ortega E. , Crespo J. , Planas R. , Romero‐Gómez M. , Rodríguez F. G. , Pascasio J. M. , Fevery B. , Kurland D. , Corbett C. , Kalmeijer R. , Jessner W. 
Published: November 2016

SummaryBackgroundHepatitis C virus (HCV) infection is a leading cause of liver cirrhosis and subsequent hepatocellular carcinoma. HCV genotype 4 is found widely in the Middle East, Egypt and Africa, and has also spread into Europe. There are limited data available regarding the use of direct‐acting antiviral agents in HCV genotype 4‐infected patients with cirrhosis.AimTo evaluate in the phase III, open‐label, single‐arm PLUTO study the efficacy and safety of 12 weeks of simeprevir (HCV NS3/4A protease inhibitor) plus sofosbuvir (HCV nucleotide‐analogue NS5B polymerase inhibitor) in treatment‐naïve and (peg)interferon ± ribavirin‐experienced HCV genotype 4‐infected patients, with or without compensated cirrhosis.MethodsAdult patients with chronic HCV genotype 4 infection received simeprevir 150 mg once‐daily and sofosbuvir 400 mg once‐daily for 12 weeks. The primary efficacy endpoint was sustained virologic response 12 weeks after the end of treatment (SVR12). Safety was also assessed.ResultsForty patients received treatment; the majority were male (73%) and treatment‐experienced (68%). Overall, 7/40 (18%) patients had compensated cirrhosis. All patients achieved SVR12 [100% (Clopper‐Pearson 95% confidence interval: 91–100%)]. Adverse events, all Grade 1 or 2, were reported in 20/40 (50%) patients. No serious adverse events were reported and no patients discontinued study treatment. Grade 3 treatment‐emergent laboratory abnormalities were noted in 2/40 (5%) patients.ConclusionsTreatment with simeprevir plus sofosbuvir for 12 weeks resulted in SVR12 rates of 100% in treatment‐naïve and ‐experienced patients with HCV genotype 4 infection with or without compensated cirrhosis, and was well tolerated. [NCT02250807]
Telemetric tracking of scatterhoarding and seed fate in a Central African forest
Authors: Rosin Cooper , Poulsen John R. 
Published: November 2016

AbstractIn seed predation studies, removal of a seed is only the first step of a dynamic process that may result in dispersal rather than seed death. This process, termed seed fate, has received little attention in African forests, particularly in Central Africa. We experimentally assessed the initial steps of seed fate for two tree species—the large‐seeded Pentaclethra macrophylla and the relatively small‐seeded Gambeya lacourtiana—in northeastern Gabon. Specifically, we evaluated whether seed size and seed consumer identity are important determinants of seed fate. We established experimental stations under conspecific fruiting trees, each comprising three seeds fitted with telemetric thread tags to facilitate their recovery, and a motion‐sensitive camera to identify visiting mammals. In total, animals removed 76 tagged seeds from experimental stations. Small Murid rats and mice primarily removed small Gambeya seeds, whereas large‐bodied rodents and mandrills primarily removed large Pentaclethra seeds. Gambeya seeds were carried shorter distances than Pentaclethra seeds and were less likely to be cached. The two large‐bodied rodents handled seeds differently: Cricetomys emini larderhoarded nearly all (N = 15 of 16) encountered Pentaclethra seeds deep in burrows, while Atherurus africanus cached all (N = 5 of 5) encountered Pentaclethra seeds singly under 1–3 cm of leaf litter and soil, at an average distance of 24.2 m and a maximum distance of 46.3 m from experimental stations. This study supports the hypothesis that seed fate varies based on seed size and seed consumer identity, and represents the first telemetric experimental evidence of larderhoarding and scatterhoarding in the region.
Anaphylaxis to foods in a population of adolescents: incidence, characteristics and associated risks
Authors: Vetander M. , Protudjer J. L. P. , Lilja G. , Kull I. , Hedlin G. , van Hage M. , Östblom E. , Bergström A. , Wickman M. 
Published: November 2016

SummaryBackgroundInformation about severe reactions to foods in adolescence is limited.ObjectiveTo describe reactions to foods, including anaphylaxis, with regard to incidence, characteristics and associated risks, among 16‐year‐olds (adolescents) in a large, population‐based birth cohort.MethodsParent‐reported questionnaire data from ages 2–3 months, and 1, 2 and 16 years were used (N = 3153). Anaphylaxis at age 16 years was defined per NIAID/FAAN criteria. Immunoglobulin E (IgE) antibodies to 14 common food and inhalant allergens were analysed at ages 4 (n = 2283) and 16 years (n = 2510). Among adolescents with food‐related symptoms (FRS) and for whom blood was available (n = 221), 25 additional food allergen extracts or allergen components were analysed. Associations between reactions to foods, and sensitization and allergic multimorbidity were investigated.ResultsIn the 12 months prior to the 16‐year assessment, 8.5% of adolescents had FRS. This included 0.8% (n = 24) adolescents who were classified as having anaphylaxis, yielding an incidence rate of 761/100 000 person‐years. One‐third of adolescents accessed health care during anaphylaxis. Allergic multimorbidity in infancy, as well as sensitization to foods and airborne allergens at age 4 years, was associated with an increased risk for FRS in adolescence. Peanuts and tree nuts were the most common culprit foods for anaphylaxis, and fruits and vegetables for non‐anaphylactic reactions. Adolescents with anaphylaxis were significantly more likely to be sensitized to storage proteins (Ara h 2, Cor a 9, Cor a 14) and to be polysensitized to foods (P < 0.001 vs. non‐anaphylactic reactions).Conclusions and Clinical RelevanceThe incidence of food‐induced anaphylaxis during adolescence in our population‐based birth cohort is higher than previously reported. Adolescents with anaphylaxis differ from adolescents with non‐anaphylactic FRS with regard to culprit foods and sensitization. Adolescents with previous anaphylaxis are likely to be polysensitized to foods, particularly tree nut and peanut storage proteins, and which warrants consideration at follow‐up.
Community healthcare professionals overestimate the risk of fatal anaphylaxis for food allergic children
Authors: Hanna H. J. , Emmanuel J. , Naim S. , Umasunthar T. , Boyle R. J. 
Published: November 2016

SummaryBackgroundFatal food anaphylaxis is rare, but a major concern for people with food allergy and their carers. We evaluated whether community healthcare professionals accurately estimate risk of fatal anaphylaxis for food allergic children, and whether accurate risk estimation is related to competence in recognizing and managing anaphylaxis.MethodsWe enrolled 90 community healthcare professionals in a cross‐sectional survey – 30 primary care nurses, 30 school first aiders, 30 community pharmacists. Participant risk estimates for fatal and non‐fatal anaphylaxis, and all‐cause fatalities, were measured using a risk ladder. Participant anaphylaxis knowledge was assessed by questionnaire, and practical skills using a simulated anaphylaxis scenario.ResultsIn all three groups, participants significantly overestimated the risk of fatal anaphylaxis for food allergic children, by a mean factor of 13.5‐fold (95% CI 5.0, 31.6), but did not overestimate non‐fatal anaphylaxis risk or all‐cause fatality risk. We found no evidence of a relationship between successful adrenaline administration and risk estimation.Conclusions and Clinical RelevanceIn conclusion, we have found evidence that community pharmacists, school first aiders and primary care nurses in the UK systematically overestimate the risk of fatal anaphylaxis for a food allergic child. This overestimation may result in increased patient and carer anxiety. Community practitioners who manage childhood food allergy and anaphylaxis need to be educated about the level of risk for fatal anaphylaxis in such children.
Status and Trends in Global Ecosystem Services and Natural Capital: Assessing Progress Toward Aichi Biodiversity Target 14
Authors: Shepherd Ellen , Milner‐Gulland E.J. , Knight Andrew T. , Ling Matthew A. , Darrah Sarah , van Soesbergen Arnout , Burgess Neil D. 
Published: November 2016

AbstractThe Convention on Biological Diversity uses six indicators to assess progress toward Aichi Biodiversity Target 14 (ecosystem services), leaving many elements of the target untracked. We identify 13 ecosystem services as directly essential for human well‐being, and select a set of 21 datasets as indicators of the state of natural capital underpinning those services, the benefits derived from them, and distribution of access to those benefits. Analysis of these indicators supports previous conclusions that there is no overall progress toward Target 14. Sixty percent of our “benefit” indicators have positive trends, whereas 86% of our “state” indicators show a decline in natural capital. This suggests that well‐being is increasing in the near‐term despite environmental degradation, and that unsustainable use of natural capital may fuel human development. As regulating services such as “soil fertility” continue to decline, however, it seems unlikely that this trend can continue without future negative impacts on humanity.
Nitric oxide synthase during early embryonic development in silkworm Bombyx mori: Gene expression, enzyme activity, and tissue distribution
Authors: Kitta Ryo , Kuwamoto Marina , Yamahama Yumi , Mase Keisuke , Sawada Hiroshi 
Published: November 2016

To elucidate the mechanism for embryonic diapause or the breakdown of diapause in Bombyx mori, we biochemically analyzed nitric oxide synthase (NOS) during the embryogenesis of B. mori. The gene expression and enzyme activity of B. mori NOS (BmNOS) were examined in diapause, non‐diapause, and HCl‐treated diapause eggs. In the case of HCl‐treated diapause eggs, the gene expression and enzyme activity of BmNOS were induced by HCl treatment. However, in the case of diapause and non‐diapause eggs during embryogenesis, changes in the BmNOS activity and gene expressions did not coincide except 48–60 h after oviposition in diapause eggs. The results imply that changes in BmNOS activity during the embryogenesis of diapause and non‐diapause eggs are regulated not only at the level of transcription but also post‐transcription. The distribution and localization of BmNOS were also investigated with an immunohistochemical technique using antibodies against the universal NOS; the localization of BmNOS was observed mainly in the cytoplasm of yolk cells in diapause eggs and HCl‐treated diapause eggs. These data suggest that BmNOS has an important role in the early embryonic development of the B. mori.