bluuebunny/crossref_metadata_2025 huggingface dataset:
Radioembolization-induced liver disease: a systematic review
Authors: Braat Manon N.G.J.A. , van Erpecum Karel J. , Zonnenberg Bernard A. , van den Bosch Maurice A.J. , Lam Marnix G.E.H.
Published: December 2016

Radioembolization (RE) is a relatively novel treatment modality for primary and secondary hepatic malignancies. Microspheres embedded with a β-emitting radioisotope are injected into the hepatic artery, resulting in microsphere deposition in the tumor arterioles and normal portal triads. Microsphere deposition in nontumorous parenchyma can result in radiation-induced liver injury, with lethal RE-induced liver disease (REILD) at the outer end of the spectrum. The primary aim of this study was to evaluate RE-related hepatotoxicity and present an overview of the currently applied definitions and clinically relevant characteristics of REILD. A systematic literature search on REILD was performed. Studies after the introduction of the term REILD (2008) were screened for definitions of REILD. Hepatotoxicity and applied definitions of REILD were compared. Liver biochemistry test abnormalities occur in up to 100% of patients after RE, mostly self-limiting. The incidence of symptomatic REILD varied between 0 and 31%, although in most reports, the incidence was 0–8%, with a lethal outcome in 0–5%. With the exception of bilirubin, the presentation of hepatotoxicity and REILD was similar for cirrhotic and noncirrhotic patients. No uniform definition of REILD was established in the current literature. Here, we propose a unifying definition and grading system for REILD. RE-related hepatotoxicity is a common phenomenon; symptomatic REILD, however, is rare. Currently, reporting of REILD is highly variable, precluding reliable comparison between studies, identification of risk factors, and treatment developments.
Vitamin D in pediatric gastrointestinal disease
Authors: Ahlawat Rajni , Weinstein Toba , Pettei Michael J.
Published: December 2016

Purpose of review

The purpose of this review is to examine the prevalence of vitamin D deficiency in pediatric gastrointestinal disease, specifically celiac disease and inflammatory bowel disease (IBD); to discuss the role of vitamin D and its deficiency in gastrointestinal disease pathophysiology; and to present current literature regarding diagnosis and treatment of vitamin D deficiency in these pediatric gastrointestinal diseases.

Recent findings

Vitamin D deficiency is common in children with gastrointestinal symptoms and disease processes. In celiac disease, vitamin D status should be routinely assessed at the time of diagnosis and during subsequent follow up if deficient. There is growing evidence to suggest an inverse association between vitamin D and IBD activity; however, the therapeutic role of vitamin D in IBD patients requires further investigation.

Suboptimal vitamin D status commonly occurs in children with gastrointestinal disease. It is advisable to check serum 25-hydroxy vitamin D levels in children with newly diagnosed celiac disease and IBD. In celiac disease, vitamin D status should be assessed during subsequent follow up if deficient. In IBD, 25-hydroxy vitamin D levels should be checked at least yearly. Therapy should be provided to maintain a level of greater than 30 ng/ml but less than 100 ng/ml; however, the ideal vitamin D dosing regimen to treat vitamin D deficiency and to maintain this optimum level remains unknown. The role of vitamin D as a therapeutic agent in IBD is still under investigation.
Does sensory transcutaneous electrical stimulation prevent pneumonia in the acute stage of stroke? A preliminary study
Authors: Hamada Satoshi , Yamaguchi Hirofumi , Hara Hiroyoshi
Published: December 2016

Acute stroke patients with dysphagia are at risk of developing pulmonary infection, which increases the risk of death. Therefore, optimal management of dysphagia is essential; however, available evidence supporting the effectiveness of dysphagia treatments is limited. Surface electrical stimulation (e-stim) has been developed as a new treatment modality for dysphagia. In this study, we investigated the efficacy of surface sensory e-stim therapy in preventing pulmonary infection in 53 acute stroke patients with dysphagia. The risk of pulmonary infection was significantly decreased in the general dysphagia/surface e-stim combination therapy group. We considered that surface e-stim therapy can impact dysphagia treatment in acute stroke patients, particularly in preventing pulmonary infection. Future large and randomized studies are needed to evaluate the effects of surface sensory e-stim therapy on acute stroke patients.
Nursing Students' Intrinsic Motivation and Performance on the Licensure Examination
Authors: Hackney Michele G.
Published: December 2016

Unsuccessful attempts at licensure adversely affect graduates, prelicensure nursing education programs, health care agencies, and ultimately, patient safety. The purpose of this quantitative, correlational study was to investigate the relationship between nursing students' intrinsic motivation and performance on the licensure examination. Nursing students responded to 12 questions related to reasons for learning as indicators of motivation type. Results indicated no statistically significant correlations between variables.
Patient Simulation for Assessment of Layperson Management of Opioid Overdose With Intranasal Naloxone in a Recently Released Prisoner Cohort
Authors: Kobayashi Leo , Green Traci C. , Bowman Sarah E. , Ray Madeline C. , McKenzie Michelle S. , Rich Josiah D.
Published: December 2016

Introduction

Investigators applied simulation to an experimental program that educated, trained, and assessed at-risk, volunteering prisoners on opioid overdose (OD) prevention, recognition, and layperson management with intranasal (IN) naloxone.

Methods

Consenting inmates were assessed for OD-related experience and knowledge then exposed on-site to standardized didactics and educational DVD (without simulation). Subjects were provided with IN naloxone kits at time of release and scheduled for postrelease assessment. At follow-up, the subjects were evaluated for their performance of layperson opioid OD resuscitative skills during video-recorded simulations. Two investigators independently scored each subject's resuscitative actions with a 21-item checklist; post hoc video reviews were separately completed to adjudicate subjects' interactions for overall benefit or harm.

Results

One hundred three prisoners completed the baseline assessment and study intervention and then were prescribed IN naloxone kits. One-month follow-up and simulation data were available for 85 subjects (82.5% of trained recruits) who had been released and resided in the community. Subjects' simulation checklist median score was 12.0 (interquartile range, 11.0–15.0) of 21 total indicated actions. Forty-four participants (51.8%) correctly administered naloxone; 16 additional subjects (18.8%) suboptimally administered naloxone. Nonindicated actions, primarily chest compressions, were observed in 49.4% of simulations. Simulated resuscitative actions by 80 subjects (94.1%) were determined post hoc to be beneficial overall for patients overdosing on opioids.

Conclusions

As part of an opioid OD prevention research program for at-risk inmates, investigators applied simulation to 1-month follow-up assessments of knowledge retention and skills acquisition in postrelease participants. Simulation supplemented traditional research tools for investigation of layperson OD management.
A Taxonomy of Delivery and Documentation Deviations During Delivery of High-Fidelity Simulations
Authors: McIvor William R. , Banerjee Arna , Boulet John R. , Bekhuis Tanja , Tseytlin Eugene , Torsher Laurence , DeMaria Samuel , Rask John P. , Shotwell Matthew S. , Burden Amanda , Cooper Jeffrey B. , Gaba David M. , Levine Adam , Park Christine , Sinz Elizabeth , Steadman Randolph H. , Weinger Matthew B.
Published: December 2016

Introduction

We developed a taxonomy of simulation delivery and documentation deviations noted during a multicenter, high-fidelity simulation trial that was conducted to assess practicing physicians' performance. Eight simulation centers sought to implement standardized scenarios over 2 years. Rules, guidelines, and detailed scenario scripts were established to facilitate reproducible scenario delivery; however, pilot trials revealed deviations from those rubrics. A taxonomy with hierarchically arranged terms that define a lack of standardization of simulation scenario delivery was then created to aid educators and researchers in assessing and describing their ability to reproducibly conduct simulations.

Methods

Thirty-six types of delivery or documentation deviations were identified from the scenario scripts and study rules. Using a Delphi technique and open card sorting, simulation experts formulated a taxonomy of high-fidelity simulation execution and documentation deviations. The taxonomy was iteratively refined and then tested by 2 investigators not involved with its development.

Results

The taxonomy has 2 main classes, simulation center deviation and participant deviation, which are further subdivided into as many as 6 subclasses. Inter-rater classification agreement using the taxonomy was 74% or greater for each of the 7 levels of its hierarchy. Cohen kappa calculations confirmed substantial agreement beyond that expected by chance. All deviations were classified within the taxonomy.

Conclusions

This is a useful taxonomy that standardizes terms for simulation delivery and documentation deviations, facilitates quality assurance in scenario delivery, and enables quantification of the impact of deviations upon simulation-based performance assessment.
Developing a Conversational Virtual Standardized Patient to Enable Students to Practice History-Taking Skills
Authors: Maicher Kellen , Danforth Douglas , Price Alan , Zimmerman Laura , Wilcox Bruce , Liston Beth , Cronau Holly , Belknap Laurie , Ledford Cynthia , Way David , Post Doug , Macerollo Allison , Rizer Milisa
Published: December 2016

Introduction

Although traditional virtual patient simulations are designed to teach and assess clinical reasoning skills, few employ conversational dialogue with the patients. The virtual standardized patients (VSPs) described herein represent standardized patients that students interview using natural language. Students take histories and develop differential diagnoses of the VSPs as much as they would with standardized or actual patients. The student-VSP interactions are recorded, creating a comprehensive record of questions and the order in which they were asked, which can be analyzed to assess information-gathering skills. Students document the encounter in an electronic medical record created for the VSPs.

Methods

The VSP was developed by integrating a dialogue management system (ChatScript) with emotionally responsive 3D characters created in a high-fidelity game engine (Unity). The system was tested with medical students at the Ohio State University College of Medicine. Students are able to take a history of a VSP, develop a differential diagnosis, and document the encounter in the electronic medical record.

Results

Accuracy of the VSP responses ranged from 79% to 86%, depending on the complexity of the case, type of history obtained, and skill of the student. Students were able to accurately develop an appropriate differential diagnosis on the basis of the information provided by the patient during the encounter.

Conclusions

The VSP enables students to practice their history-taking skills before encounters with standardized or actual patients. Future developments will focus on creating an assessment module that will automatically analyze VSP sessions and provide immediate student feedback.
Evaluation of a Simpler Tool to Assess Nontechnical Skills During Simulated Critical Events
Authors: Watkins Scott C. , Roberts David A. , Boulet John R. , McEvoy Matthew D. , Weinger Matthew B.
Published: December 2016

Introduction

Management of critical events requires teams to employ nontechnical skills (NTS), such as teamwork, communication, decision making, and vigilance. We sought to estimate the reliability and provide evidence for the validity of the ratings gathered using a new tool for assessing the NTS of anesthesia providers, the behaviorally anchored rating scale (BARS), and compare its scores with those of an established NTS tool, the Anaesthetists' Nontechnical Skills (ANTS) scale.

Methods

Six previously trained raters (4 novices and 2 experts) reviewed and scored 18 recorded simulated pediatric crisis management scenarios using a modified ANTS and a BARS tool. Pearson correlation coefficients were calculated separately for the novice and expert raters, by scenario, and overall.

Results

The intrarater reliability of the ANTS total score was 0.73 (expert, 0.57; novice, 0.84); for the BARS tool, it was 0.80 (expert, 0.79; novice, 0.81). The average interrater reliability of BARS scores (0.58) was better than ANTS scores (0.37), and the interrater reliabilities of scores from novices (0.69 BARS and 0.52 ANTS) were better than those obtained from experts (0.47 BARS and 0.21 ANTS) for both scoring instruments. The Pearson correlation between the ANTS and BARS total scores was 0.74.

Conclusions

Overall, reliability estimates were better for the BARS scores than the ANTS scores. For both measures, the intrarater and interrater reliability was better for novices compared with domain experts, suggesting that properly trained novices can reliably assess the NTS of anesthesia providers managing a simulated critical event. There was substantial correlation between the 2 scoring instruments, suggesting that the tools measured similar constructs. The BARS tool can be an alternative to the ANTS scale for the formative assessment of NTS of anesthesia providers.
The male handicap: male-biased mortality explains skewed sex ratios in brown trout embryos
Authors: Morán P. , Labbé L. , Garcia de Leaniz C.
Published: December 2016

Juvenile sex ratios are often assumed to be equal for many species with genetic sex determination, but this has rarely been tested in fish embryos due to their small size and absence of sex-specific markers. We artificially crossed three populations of brown trout and used a recently developed genetic marker for sexing the offspring of both pure and hybrid crosses. Sex ratios (SR = proportion of males) varied widely one month after hatching ranging from 0.15 to 0.90 (mean = 0.39 ± 0.03). Families with high survival tended to produce balanced or male-biased sex ratios, but SR was significantly female-biased when survival was low, suggesting that males sustain higher mortality during development. No difference in SR was found between pure and hybrid families, but the existence of sire × dam interactions suggests that genetic incompatibility may play a role in determining sex ratios. Our findings have implications for animal breeding and conservation because skewed sex ratios will tend to reduce effective population size and bias selection estimates.
Multi-casting approach for vascular networks in cellularized hydrogels
Authors: Justin Alexander W. , Brooks Roger A. , Markaki Athina E.
Published: December 2016

Vascularization is essential for living tissue and remains a major challenge in the field of tissue engineering. A lack of a perfusable channel network within a large and densely populated tissue engineered construct leads to necrotic core formation, preventing fabrication of functional tissues and organs. We report a new method for producing a hierarchical, three-dimensional (3D) and perfusable vasculature in a large, cellularized fibrin hydrogel. Bifurcating channels, varying in size from 1 mm to 200–250 µm, are formed using a novel process in which we convert a 3D printed thermoplastic material into a gelatin network template, by way of an intermediate alginate hydrogel. This enables a CAD-based model design, which is highly customizable, reproducible, and which can yield highly complex architectures, to be made into a removable material, which can be used in cellular environments. Our approach yields constructs with a uniform and high density of cells in the bulk, made from bioactive collagen and fibrin hydrogels. Using standard cell staining and immuno-histochemistry techniques, we showed good cell seeding and the presence of tight junctions between channel endothelial cells, and high cell viability and cell spreading in the bulk hydrogel.
NMJ-morph reveals principal components of synaptic morphology influencing structure–function relationships at the neuromuscular junction
Authors: Jones Ross A. , Reich Caitlan D. , Dissanayake Kosala N. , Kristmundsdottir Fanney , Findlater Gordon S. , Ribchester Richard R. , Simmen Martin W. , Gillingwater Thomas H.
Published: December 2016

The ability to form synapses is one of the fundamental properties required by the mammalian nervous system to generate network connectivity. Structural and functional diversity among synaptic populations is a key hallmark of network diversity, and yet we know comparatively little about the morphological principles that govern variability in the size, shape and strength of synapses. Using the mouse neuromuscular junction (NMJ) as an experimentally accessible model synapse, we report on the development of a robust, standardized methodology to facilitate comparative morphometric analysis of synapses (‘NMJ-morph’). We used NMJ-morph to generate baseline morphological reference data for 21 separate pre- and post-synaptic variables from 2160 individual NMJs belonging to nine anatomically distinct populations of synapses, revealing systematic differences in NMJ morphology between defined synaptic populations. Principal components analysis revealed that overall NMJ size and the degree of synaptic fragmentation, alongside pre-synaptic axon diameter, were the most critical parameters in defining synaptic morphology. ‘Average’ synaptic morphology was remarkably conserved between comparable synapses from the left and right sides of the body. Systematic differences in synaptic morphology predicted corresponding differences in synaptic function that were supported by physiological recordings, confirming the robust relationship between synaptic size and strength.
Tumour biomarkers: homeostasis as a novel prognostic indicator
Authors: Falco Michela , Palma Giuseppe , Rea Domenica , De Biase Davide , Scala Stefania , D'Aiuto Massimiliano , Facchini Gaetano , Perdonà Sisto , Barbieri Antonio , Arra Claudio
Published: December 2016

The term ‘personalized medicine’ refers to a medical procedure that consists in the grouping of patients based on their predicted individual response to therapy or risk of disease. In oncologic patients, a ‘tailored’ therapeutic approach may potentially improve their survival and well-being by not only reducing the tumour, but also enhancing therapeutic response and minimizing the adverse effects. Diagnostic tests are often used to select appropriate and optimal therapies that rely both on patient genome and other molecular/cellular analysis. Several studies have shown that lifestyle and environmental factors can influence the epigenome and that epigenetic events may be involved in carcinogenesis. Thus, in addition to traditional biomarkers, epigenetic factors are raising considerable interest, because they could potentially be used as an excellent tool for cancer diagnosis and prognosis. In this review, we summarize the role of conventional cancer genetic biomarkers and their association with epigenomics. Furthermore, we will focus on the so-called ‘homeostatic biomarkers’ that result from the physiological response to cancer, emphasizing the concept that an altered ‘new’ homeostasis influence not only tumour environment, but also the whole organism.
Invasive mutualisms between a plant pathogen and insect vectors in the Middle East and Brazil
Authors: Queiroz Renan Batista , Donkersley Philip , Silva Fábio Nascimento , Al-Mahmmoli Issa Hashil , Al-Sadi Abdullah Mohammed , Carvalho Claudine Márcia , Elliot Simon L.
Published: December 2016

Complex multi-trophic interactions in vectorborne diseases limit our understanding and ability to predict outbreaks. Arthropod-vectored pathogens are especially problematic, with the potential for novel interspecific interactions during invasions. Variations and novelties in plant–arthropod–pathogen triumvirates present significant threats to global food security. We examined aspects of a phytoplasma pathogen of citrus across two continents. ‘CandidatusPhytoplasma aurantifolia’ causes Witches' Broom Disease of Lime (WBDL) and has devastated citrus production in the Middle East. A variant of this phytoplasma currently displays asymptomatic or ‘silent’ infections in Brazil. We first studied vector capacity and fitness impacts of the pathogen on its vectors. The potential for co-occurring weed species to act as pathogen reservoirs was analysed and key transmission periods in the year were also studied. We demonstrate that two invasive hemipteran insects—Diaphorina citriandHishimonus phycitis—can vector the phytoplasma. Feeding on phytoplasma-infected hosts greatly increased reproduction of its invasive vectorD. citriboth in Oman and Brazil; suggesting that increased fitness of invasive insect vectors thereby further increases the pathogen's capacity to spread. Based on our findings, this is a robust system for studying the effects of invasions on vectorborne diseases and highlights concerns about its spread to warmer, drier regions of Brazil.
Clap-and-fling mechanism in a hovering insect-like two-winged flapping-wing micro air vehicle
Authors: Phan Hoang Vu , Au Thi Kim Loan , Park Hoon Cheol
Published: December 2016

This study used numerical and experimental approaches to investigate the role played by the clap-and-fling mechanism in enhancing force generation in hovering insect-like two-winged flapping-wing micro air vehicle (FW-MAV). The flapping mechanism was designed to symmetrically flap wings at a high flapping amplitude of approximately 192°. The clap-and-fling mechanisms were thereby implemented at both dorsal and ventral stroke reversals. A computational fluid dynamic (CFD) model was constructed based on three-dimensional wing kinematics to estimate the force generation, which was validated by the measured forces using a 6-axis load cell. The computed forces proved that the CFD model provided reasonable estimation with differences less than 8%, when compared with the measured forces. The measurement indicated that the clap and flings at both the stroke reversals augmented the average vertical force by 16.2% when compared with the force without the clap-and-fling effect. In the CFD simulation, the clap and flings enhanced the vertical force by 11.5% and horizontal drag force by 18.4%. The observations indicated that both the fling and the clap contributed to the augmented vertical force by 62.6% and 37.4%, respectively, and to the augmented horizontal drag force by 71.7% and 28.3%, respectively. The flow structures suggested that a strong downwash was expelled from the opening gap between the trailing edges during the fling as well as the clap at each stroke reversal. In addition to the fling phases, the influx of air into the low-pressure region between the wings from the leading edges also significantly contributed to augmentation of the vertical force. The study conducted for high Reynolds numbers also confirmed that the effect of the clap and fling was insignificant when the minimum distance between the two wings exceeded 1.2c (c = wing chord). Thus, the clap and flings were successfully implemented in the FW-MAV, and there was a significant improvement in the vertical force.
Multiphase wavetrains, singular wave interactions and the emergence of the Korteweg–de Vries equation
Authors: Ratliff Daniel J. , Bridges Thomas J.
Published: December 2016

Multiphase wavetrains are multiperiodic travelling waves with a set of distinct wavenumbers and distinct frequencies. In conservative systems, such families are associated with the conservation of wave action or other conservation law. At generic points (where the Jacobian of the wave action flux is non-degenerate), modulation of the wavetrain leads to the dispersionless multiphase conservation of wave action. The main result of this paper is that modulation of the multiphase wavetrain, when the Jacobian of the wave action flux vector is singular, morphs the vector-valued conservation law into the scalar Korteweg–de Vries (KdV) equation. The coefficients in the emergent KdV equation have a geometrical interpretation in terms of projection of the vector components of the conservation law. The theory herein is restricted to two phases to simplify presentation, with extensions to any finite dimension discussed in the concluding remarks. Two applications of the theory are presented: a coupled nonlinear Schrödinger equation and two-layer shallow-water hydrodynamics with a free surface. Both have two-phase solutions where criticality and the properties of the emergent KdV equation can be determined analytically.
Understanding the value of plant diversity for ecosystem functioning through niche theory
Authors: Turnbull Lindsay A. , Isbell Forest , Purves Drew W. , Loreau Michel , Hector Andy
Published: December 2016

Biodiversity experiments have generated robust empirical results supporting the hypothesis that ecosystems function better when they contain more species. Given that ecosystems provide services that are valued by humans, this inevitably suggests that the loss of species from natural ecosystems could diminish their value. This raises two important questions. First, will experimental results translate into the real world, where species are being lost at an alarming rate? And second, what are the benefits and pitfalls of such valuation exercises? We argue that the empirical results obtained in experiments are entirely consistent with well-established theories of species coexistence. We then examine the current body of work through the lens of niche theory and highlight where closer links with theory could open up opportunities for future research. We argue that niche theory predicts that diversity–functioning relationships are likely to be stronger (and require more species) in the field than in simplified experimental settings. However, we caution that while many of the biological processes that promote coexistence can also generate diversity–function relationships, there is no simple mapping between the two. This implies that valuation exercises need to proceed with care.
Microbes in the Anthropocene: spillover of agriculturally selected bacteria and their impact on natural ecosystems
Authors: Bell Thomas , Tylianakis Jason M.
Published: December 2016

Soil microbial communities are enormously diverse, with at least millions of species and trillions of genes unknown to science or poorly described. Soil microbial communities are key components of agriculture, for example, in provisioning nitrogen and protecting crops from pathogens, providing overall ecosystem services in excess of $1000bn per year. It is important to know how humans are affecting this hidden diversity. Much is known about the negative consequences of agricultural intensification on higher organisms, but almost nothing is known about how alterations to landscapes affect microbial diversity, distributions and processes. We review what is known about spatial flows of microbes and their response to land-use change, and outline nine hypotheses to advance research of microbiomes across landscapes. We hypothesize that intensified agriculture selects for certain taxa and genes, which then ‘spill over’ into adjacent unmodified areas and generate a halo of genetic differentiation around agricultural fields. Consequently, the spatial configuration and management intensity of different habitats combines with the dispersal ability of individual taxa to determine the extent of spillover, which can impact the functioning of adjacent unmodified habitats. When landscapes are heterogeneous and dispersal rates are high, this will select for large genomes that allow exploitation of multiple habitats, a process that may be accelerated through horizontal gene transfer. Continued expansion of agriculture will increase genotypic similarity, making microbial community functioning increasingly variable in human-dominated landscapes, potentially also impacting the consistent provisioning of ecosystem services. While the resulting economic costs have not been calculated, it is clear that dispersal dynamics of microbes should be taken into consideration to ensure that ecosystem functioning and services are maintained in agri-ecosystem mosaics.
Using avian functional traits to assess the impact of land-cover change on ecosystem processes linked to resilience in tropical forests
Authors: Bregman Tom P. , Lees Alexander C. , MacGregor Hannah E. A. , Darski Bianca , de Moura Nárgila G. , Aleixo Alexandre , Barlow Jos , Tobias Joseph A.
Published: December 2016

Vertebrates perform key roles in ecosystem processes via trophic interactions with plants and insects, but the response of these interactions to environmental change is difficult to quantify in complex systems, such as tropical forests. Here, we use the functional trait structure of Amazonian forest bird assemblages to explore the impacts of land-cover change on two ecosystem processes: seed dispersal and insect predation. We show that trait structure in assemblages of frugivorous and insectivorous birds remained stable after primary forests were subjected to logging and fire events, but that further intensification of human land use substantially reduced the functional diversity and dispersion of traits, and resulted in communities that occupied a different region of trait space. These effects were only partially reversed in regenerating secondary forests. Our findings suggest that local extinctions caused by the loss and degradation of tropical forest are non-random with respect to functional traits, thus disrupting the network of trophic interactions regulating seed dispersal by forest birds and herbivory by insects, with important implications for the structure and resilience of human-modified tropical forests. Furthermore, our results illustrate how quantitative functional traits for specific guilds can provide a range of metrics for estimating the contribution of biodiversity to ecosystem processes, and the response of such processes to land-cover change.
Quantifying species contributions to ecosystem processes: a global assessment of functional trait and phylogenetic metrics across avian seed-dispersal networks
Authors: Pigot Alexander L. , Bregman Tom , Sheard Catherine , Daly Benjamin , Etienne Rampal S. , Tobias Joseph A.
Published: December 2016

Quantifying the role of biodiversity in ecosystems not only requires understanding the links between species and the ecological functions and services they provide, but also how these factors relate to measurable indices, such as functional traits and phylogenetic diversity. However, these relationships remain poorly understood, especially for heterotrophic organisms within complex ecological networks. Here, we assemble data on avian traits across a global sample of mutualistic plant–frugivore networks to critically assess how the functional roles of frugivores are associated with their intrinsic traits, as well as their evolutionary and functional distinctiveness. We find strong evidence for niche complementarity, with phenotypically and phylogenetically distinct birds interacting with more unique sets of plants. However, interaction strengths—the number of plant species dependent on a frugivore—were unrelated to evolutionary or functional distinctiveness, largely because distinct frugivores tend to be locally rare, and thus have fewer connections across the network. Instead, interaction strengths were better predicted by intrinsic traits, including body size, gape width and dietary specialization. Our analysis provides general support for the use of traits in quantifying species ecological functions, but also highlights the need to go beyond simple metrics of functional or phylogenetic diversity to consider the multiple pathways through which traits may determine ecological processes.
Understanding the structure and functioning of polar pelagic ecosystems to predict the impacts of change
Authors: Murphy E. J. , Cavanagh R. D. , Drinkwater K. F. , Grant S. M. , Heymans J. J. , Hofmann E. E. , Hunt G. L. , Johnston N. M.
Published: December 2016

The determinants of the structure, functioning and resilience of pelagic ecosystems across most of the polar regions are not well known. Improved understanding is essential for assessing the value of biodiversity and predicting the effects of change (including in biodiversity) on these ecosystems and the services they maintain. Here we focus on the trophic interactions that underpin ecosystem structure, developing comparative analyses of how polar pelagic food webs vary in relation to the environment. We highlight that there is not a singular, generic Arctic or Antarctic pelagic food web, and, although there are characteristic pathways of energy flow dominated by a small number of species, alternative routes are important for maintaining energy transfer and resilience. These more complex routes cannot, however, provide the same rate of energy flow to highest trophic-level species. Food-web structure may be similar in different regions, but the individual species that dominate mid-trophic levels vary across polar regions. The characteristics (traits) of these species are also different and these differences influence a range of food-web processes. Low functional redundancy at key trophic levels makes these ecosystems particularly sensitive to change. To develop models for projecting responses of polar ecosystems to future environmental change, we propose a conceptual framework that links the life histories of pelagic species and the structure of polar food webs.
The emergence, evolution, and diversification of the miR390-TAS3-ARFpathway in land plants
Authors: Xia Rui , Xu Jing , Meyers Blake C.
Published: December 2016

In plants, miR390 directs the production of tasiRNAs fromTRANS-ACTING SIRNA 3(TAS3) transcripts to regulateAUXIN RESPONSIVE FACTOR(ARF) genes, transcription factors critical for auxin signaling; these tasiRNAs are known as tasiARFs. This pathway is highly conserved, with theTAS3as the only one noncoding gene present almost ubiquitously in land plants. To understand the evolution of this miR390-TAS3-ARFpathway, we characterized homologs of these three genes from thousands of plant species, from bryophytes to angiosperms. Both miR390 andTAS3are present and functional in liverworts, confirming their ancestral role to regulateARFsin land plants. We found the lower-stem region ofMIR390genes, critical for accurate DCL1 (DICER-LIKE 1) processing, is conserved in sequence in seed plants. We propose a model for the transition of functional tasiRNA sequences inTAS3genes occurred at the emergence of vascular plants, in which the two miR390 target sites ofTAS3genes showed distinct pairing patterns in different plant lineages. Based on the cleavability of miR390 target sites and the distance between target site and tasiARF we inferred a potential bidirectional processing mechanism exists for someTAS3genes. We also demonstrated a tight mutual selection between tasiARF and its target genes, and characterized unusual aspects and diversity of regulatory components of this pathway. Taken together, these data illuminate the evolutionary path of themiR390-TAS3-ARFpathway in land plants, and demonstrate the significant variation that occurs in the production of phasiRNAs in plants, even in the functionally important and archetypal miR390-TAS3-ARFregulatory circuit.
Community-level facilitation by macroalgal foundation species peaks at an intermediate level of environmental stress
Authors: Scrosati Ricardo A.
Published: December 2016

This paper examines how community-level facilitation by macroalgal foundation species changes with environmental stress. In rocky intertidal habitats, abiotic stress (mainly due to desiccation and thermal extremes during low tides) increases sharply with elevation because of tide dynamics. A previous study done on the Atlantic coast of Nova Scotia (Canada) showed that, at low elevations, where conditions are benign because low tides are brief, fucoid algal canopies (Ascophyllum nodosumandFucusspp.) do not affect the structure of benthic communities. However, at middle and high elevations, where low tides last longer, fucoid canopies limit abiotic extremes near the substrate and, in that way, increase the richness of benthic communities. Richness was measured as the number of benthic algal (except fucoids) and invertebrate species found in replicate quadrats. Using the published data from that study, the present study compares the intensity of facilitation and its importance (relative to all other sources of variation in richness) between middle and high elevations, which represent intermediate and high stress, respectively. Facilitation intensity was calculated as the percent increase in benthic richness between quadrats with low canopy cover and quadrats with high canopy cover, while the importance of facilitation was calculated as the percentage of observed variation in richness that was explained by canopy cover. Data for a total of 688 quadrats surveyed along 350 km of coastline were used. The analyses revealed that both the intensity and importance of facilitation were greater at middle elevations than at high elevations. As canopies were previously found not to affect benthic communities at low elevations, this study indicates that the facilitation–stress relationship viewed at the community level is unimodal for this marine system. Such a trend was already found for some terrestrial systems involving canopy-forming plants as foundation species. Thus, this unimodal pattern may be ubiquitous in nature and, as further studies refine it, might help to predict community-level facilitation depending on environmental stress.
Experimental evolution reveals favored adaptive routes to cell aggregation in yeast
Authors: Hope Elyse A. , Amorosi Clara J. , Miller Aaron W. , Dang Kolena , Heil Caiti Smukowski , Dunham Maitreya J.
Published: December 2016

Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanismsSaccharomyces cerevisiaeuses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones we identified a transposable element insertion in the promoter region of known flocculation geneFLO1, and in an additional five clones we recovered loss-of-function mutations in transcriptional repressorTUP1, which regulatesFLO1and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving aflo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits.
Expanding the language network: Domain-specific hippocampal recruitment during high-level linguistic processing
Authors: Blank Idan A. , Duff Melissa C. , Brown-Schmidt Sarah , Fedorenko Evelina
Published: December 2016

Language processing requires us to encode linear relations between acoustic forms and map them onto hierarchical relations between meaning units. Such relational binding of linguistic elements might recruit the hippocampus given its engagement by similar operations in other cognitive domains. Historically, hippocampal engagement in online language use has received little attention because patients with hippocampal damage are not aphasic. However, recent studies have found that these patients exhibit language impairments when the demands on flexible relational binding are high, suggesting that the hippocampus does, in fact, contribute to linguistic processing. A fundamental question is thus whether language processing engages domain-general hippocampal mechanisms that are also recruited across other cognitive processes or whether, instead, it relies on certain language-selective areas within the hippocampus. To address this question, we conducted the first systematic analysis of hippocampal engagement during comprehension in healthy adults (n=150 across three experiments) using fMRI. Specifically, we functionally localized putative “language-regions” within the hippocampus using a language comprehension task, and found that these regions (i) were selectively engaged by language but not by six non-linguistic tasks; and (ii) were coupled in their activity with the cortical language network during both “rest” and especially story comprehension, but not with the domain-general “multiple-demand (MD)” network. This functional profile did not generalize to other hippocampal regions that were localized using a non-linguistic, working memory task. These findings suggest that some hippocampal mechanisms that maintain and integrate information during language comprehension are not domain-general but rather belong to the language-specific brain network.

Significance statement

According to popular views, language processing is exclusively supported by neocortical mechanisms. However, recent patient studies suggest that language processing may also require the hippocampus, especially when relations among linguistic elements have to be flexibly integrated and maintained. Here, we address a core question about the place of the hippocampus in the cognitive architecture of language: are certain hippocampal operations language-specific rather than domain-general? By extensively characterizing hippocampal recruitment during language comprehension in healthy adults using fMRI, we show that certain hippocampal subregions exhibit signatures of language specificity in both their response profiles and their patterns of activity synchronization with known functional regions in the neocortex. We thus suggest that the hippocampus is a satellite constituent of the language network.
The adaptive significance of phasic colony cycles in army ants
Authors: Garnier Simon , Kronauer Daniel J. C.
Published: December 2016

Army ants are top arthropod predators in tropical forests around the world. The colonies of many army ant species undergo stereotypical behavioral and reproductive cycles, alternating between brood care and reproductive phases. In the brood care phase, colonies contain a cohort of larvae that are synchronized in their development and have to be fed. In the reproductive phase larvae are absent and oviposition takes place. Despite these colony cycles being a striking feature of army ant biology, their adaptive significance is unclear. Here we use a modelling approach to show that cyclic reproduction is favored under conditions where per capita foraging costs decrease with the number of larvae in a colony ("High Cost of Entry" scenario), while continuous reproduction is favored under conditions where per capita foraging costs increase with the number of larvae ("Resource Exhaustion" scenario). We argue that the former scenario specifically applies to army ants, because large raiding parties are required to overpower prey colonies. However, once raiding is successful it provides abundant food for a large cohort of larvae. The latter scenario, on the other hand, will apply to non-army ants, because in those species local resource depletion will force workers to forage over larger distances to feed large larval cohorts. Our model provides the first quantitative framework for understanding the adaptive value of phasic colony cycles in ants.
Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding
Authors: Andrey Guillaume , Schöpflin Robert , Jerković Ivana , Heinrich Verena , Ibrahim Daniel M. , Paliou Christina , Hochradel Myriam , Timmermann Bernd , Haas Stefan , Vingron Martin , Mundlos Stefan
Published: December 2016

Complex regulatory landscapes control the pleiotropic transcriptional activities of developmental genes. For most genes, the number, location, and dynamics of their associated regulatory elements are unknown. In this work, we characterized the three-dimensional chromatin microarchitecture and regulatory landscape of 446 limb-associated gene loci in mouse using Capture-C, ChIP-seq, and RNA-seq in forelimb, hindlimb at three developmental stages, and midbrain. The fine mapping of chromatin interactions revealed a strong preference for functional genomic regions such as repressed or active domains. By combining chromatin marks and interaction peaks, we annotated more than 1000 putative limb enhancers and their associated genes. Moreover, the analysis of chromatin interactions revealed two regimes of chromatin folding, one producing interactions stable across tissues and stages and another one associated with tissue and/or stage-specific interactions. Whereas stable interactions associate strongly with CTCF/RAD21 binding, the intensity of variable interactions correlates with changes in underlying chromatin modifications, specifically at the viewpoint and at the interaction site. In conclusion, this comprehensive data set provides a resource for the characterization of hundreds of limb-associated regulatory landscapes and a framework to interpret the chromatin folding dynamics observed during embryogenesis.
Numerical and spatial patterning of yeast meiotic DNA breaks by Tel1
Authors: Mohibullah Neeman , Keeney Scott
Published: December 2016

The Spo11-generated double-strand breaks (DSBs) that initiate meiotic recombination are dangerous lesions that can disrupt genome integrity, so meiotic cells regulate their number, timing, and distribution. Mechanisms of this regulation remain poorly understood. Here, we use Spo11-oligonucleotide complexes, a byproduct of DSB formation, to reveal aspects of the contribution of the Saccharomyces cerevisiae DNA damage-responsive kinase Tel1 (ortholog of mammalian ATM). A tel1Δ mutant has globally increased amounts of Spo11-oligonucleotide complexes and altered Spo11-oligonucleotide lengths, consistent with conserved roles for Tel1 in control of DSB number and processing. A kinase-dead tel1 mutation similarly increases Spo11-oligonucleotide levels but mutating known Tel1 phosphotargets on Hop1 and Rec114 does not, implicating Tel1 kinase activity and clarifying roles of Tel1 phosphorylation substrates. Deep sequencing of Spo11 oligonucleotides demonstrates that Tel1 shapes the genome-wide DSB landscape in unexpected ways. Early in meiosis, Tel1 absence causes widespread changes in DSB distributions across large chromosomal domains. Many of these changes are erased as meiosis proceeds, however, illustrating homeostatic behavior of DSB regulatory systems. We further find that effects of Tel1 are distinct but partially overlapping with previously described contributions of the recombination regulator Cst9 (also known as Zip3). Finally, we provide evidence indicating that Tel1-dependent DSB interference influences the population-average DSB landscape but also demonstrate that locally inhibitory effects of an artificial hotspot insertion can be both Tel1-independent and chromosomal context-dependent. Our findings delineate Tel1 roles in regulating number and location of DSBs and illuminate the complex interplay between Tel1 and other pathways for DSB control.