bluuebunny/crossref_metadata_2025 huggingface dataset:
A statistical framework for the robust detection of hidden variation in single cell transcriptomes
Authors: Lee Donghyung , Cheng Anthony , Bolisetty Mohan , Ucar Duygu
Published: June 2017

Single cell RNA-sequencing (scRNA-seq) precisely characterize gene expression levels and dissect variation in expression associated with the state (technical or biological) and the type of the cell, which is averaged out in bulk measurements. Multiple and correlated sources contribute to gene expression variation in single cells, which makes their estimation difficult with the existing methods developed for bulk measurements (e.g., surrogate variable analysis (SVA)) that estimate orthogonal transformations of these sources. We developed iteratively adjusted surrogate variable analysis (IA-SVA) that can estimate hidden and correlated sources of variation by identifying a set of genes affected with each hidden factor in an iterative manner. Analysis of scRNA-seq data from human cells showed that IA-SVA could accurately capture hidden variation arising from technical (e.g., stacked doublet cells) or biological sources (e.g., cell type or cell-cycle stage). Furthermore, IA-SVA delivers a set of genes associated with the detected hidden source to be used in downstream data analyses. As a proof of concept, IA-SVA recapitulated known marker genes for islet cell subsets (e.g., alpha, beta), which improved the grouping of subsets into distinct clusters. Taken together, IA-SVA is an effective and novel method to dissect multiple and correlated sources of variation in scRNA-seq data.
High Frequency Actionable Pathogenic Exome Mutations in an Average-Risk Cohort
Authors: Rego Shannon , Dagan-Rosenfeld Orit , Zhou Wenyu , Reza Sailani M. , Limcaoco Patricia , Colbert Elizabeth , Avina Monika , Wheeler Jessica , Craig Colleen , Salins Denis , Röst Hannes L. , Dunn Jessilyn , McLaughlin Tracey , Steinmetz Lars M. , Bernstein Jonathan A. , Snyder Michael P.
Published: June 2017

Whole exome sequencing (WES) is increasingly utilized in both clinical and non-clinical settings, but little is known about the utility of WES in healthy individuals. In order to determine the frequency of both medically actionable and non-actionable but medically relevant exome findings in the general population we assessed the exomes of 70 participants who have been extensively characterized over the past several years as part of a longitudinal integrated multi-omics profiling study at Stanford University. We assessed exomes for rare likely pathogenic and pathogenic variants in genes associated with Mendelian disease in the Online Mendelian Inheritance in Man (OMIM) database. We used American College of Medical Genetics (ACMG) guidelines were used for the classification of rare sequence variants, and additionally we assessed pharmacogenetic variants. Twelve out of 70 (17%) participants had medically actionable findings in Mendelian disease genes, including 6 (9%) with mutations in genes not currently included in the ACMG’s list of 59 actionable genes. This number is higher than that reported in previous studies and suggests added benefit from utilizing expanded gene lists and manual curation to assess actionable findings. A total of 60 participants (89%) had non-actionable findings identified including 57 who were found to be mutation carriers for recessive diseases and 21 who have increased Alzheimer’s disease risk due to heterozyg ous or homozygousAPOEe4 alleles (18 participants had both). These results suggest that exome sequencing may have considerably more utility for health management in the general population than previously thought.
The coalescent for prokaryotes with homologous recombination from external source
Authors: Akita Tetsuya , Takuno Shohei , Innan Hideki
Published: June 2017

The coalescent process for prokaryote species is theoretically considered. Prokaryotes undergo homologous recombination not only with other individuals within the same species (intra-specific recombination) but also with other species (inter-specific recombination). This work particularly focuses the latter because the former has been well incorporated in the framework of the coalescent. We here developed a simulation framework for generating patterns of SNPs (single nucleotide polymorphisms) allowing integration of external DNA out of the focal species, and a simulator namedmsProwas developed. We found that the joint work of intra- and inter-specific recombination creates a complex pattern of SNPs. The direct effect of inter-specific recombination is to increase the amount of polymorphism. Because inter-specific recombination is very rare in general, it creates a regions with an exceptionally high level of polymorphisms. Following an inter-specific recombination event, intra-specific recombination chop the integrated foreign DNA into small pieces, making a complicated pattern of SNPs that looks as if foreign DNAs were integrated multiple times. This work with themsProsimulator would be useful to understand and evaluate the relative contribution of intra- and inter specific recombination to creating complicated patterns of SNPs in prokaryotes.
Moment-to-moment fluctuations in neuronal excitability bias subjective perception rather than decision-making
Authors: Iemi Luca , Busch Niko A
Published: June 2017

Perceiving an external stimulus not only depends on the physical features of the stimulus, but also fundamentally on the current state of neuronal excitability, indexed by the power of ongoing alpha oscillations. Recent studies suggest that heightened excitability does not improve perceptual acuity, but biases observers to report the presence of a stimulus regardless of its physical presence. It is unknown whether this bias is due to changes in observers’ subjective perceptual experience (perceptual bias) or their perception-independent decision-making strategy (decision bias). We tested these alternative interpretations in an EEG experiment in which human participants performed two-interval forced choice (2IFC) detection and discrimination. According to signal detection theory, perceptual bias only affects 2IFC detection, but not discrimination, while interval decision bias should be task-independent. We found that detection was optimal in trials in which excitability before the stimulus-present interval exceeded that before the stimulus-absent interval, consistent with an effect of excitability on perceptual bias. By contrast, discrimination accuracy was unaffected by excitability fluctuations between intervals, ruling out an effect on interval decision bias. We conclude that the current state of neuronal excitability biases the perceptual experience itself, rather than the decision process.
A resource-rational theory of set size effects in visual working memory
Authors: van den Berg Ronald , Ma Wei Ji
Published: June 2017

Encoding precision in visual working memory decreases with the number of encoded items. Here, we propose a normative theory for such set size effects: the brain minimizes a weighted sum of an error-based behavioral cost and a neural encoding cost. We construct a model from this theory and find that it predicts set size effects. Notably, these effects are mediated by probing probability, which aligns with previous empirical findings. The model accounts well for effects of both set size and probing probability on encoding precision in nine delayed-estimation experiments. Moreover, we find support for the prediction that the total amount of invested resource can vary non-monotonically with set size. Finally, we show that it is sometimes optimal to encode only a subset or even none of the relevant items in a task. Our findings raise the possibility that cognitive “limitations” arise from rational cost minimization rather than from constraints.
Impairment of mitochondrial respiratory function as an early biomarker of apoptosis induced by growth factor removal
Authors: Lemieux Hélène , Subarsky Patrick , Doblander Christine , Wurm Martin , Troppmair Jakob , Gnaiger Erich
Published: June 2017

Intracellular signaling pathways not only control cell proliferation and survival, but also regulate the provision of cellular energy and building blocks through mitochondrial and non-mitochondrial metabolism. Wild-type and oncogenic RAF kinases have been shown to prevent apoptosis following the removal of interleukin 3 (IL-3) from mouse pro-myeloid 32D cells by reducing mitochondrial reactive oxygen species production. To study primary effects of RAF on mitochondrial energy metabolism, we applied high-resolution respirometry after short-term IL-3 deprivation (8 h), before 32D cells show detectable signs of cell death. Respiration in intact 32D cells was suppressed as an early event following removal of IL-3, but remained more stable in 32D cells expressing the v-RAF oncogene. In permeabilized 32D cells deprived of IL-3, respiratory capacities of the NADH-pathway, the convergent NADH&succinate-pathway, and Complex IV activity were decreased compared to cells grown in the presence of IL-3, whereas succinate-supported respiration remained unchanged, consistent with control by Complex IV. The apparent Complex IV excess capacity was zero above NADH&succinate-pathway capacity reconstituting tricarboxylic acid cycle function. In comparison, electron flow reached only 60% when supported by succinate alone through Complexes II, III and IV, and was therefore relatively insensitive to Complex IV injuries up to a threshold of 40% inhibition. A slight increase in respiration following addition of cytochromec, a marker of mitochondrial outer membrane leakage, was present after IL-3 depletion, indicating mitochondrial fragility. Our results highlight a novel link between the key mitogenic and survival kinase CRAF and mitochondrial energy homeostasis.
Effects of Human-Animal Interaction on Dog Salivary and Plasma Oxytocin and Vasopressin
Authors: MacLean Evan L. , Gesquiere Laurence R. , Gee Nancy , Levy Kerinne , Lance Martin W. , Sue Carter C.
Published: June 2017

Oxytocin (OT) and Vasopressin (AVP) are neuropeptides with diverse effects on social behavior, cognition and stress responses. Recent studies suggest that OT facilitates and responds to affiliative forms of human-animal interaction (HAI). However, previous studies measuring OT and AVP in dogs have been limited to measures from blood or urine, which present concerns related to the invasiveness of sample collection, the potential for matrix interference in immunoassays, and whether samples can be collected at precise time points to assess event-linked endocrine responses. Previous studies from our laboratory validated salivary measures of OT and AVP in dogs, however, it is currently unknown whether these measures respond dynamically to aspects of HAI. Here, we investigated the effects of affiliative forms of HAI on both plasma and salivary OT and AVP in dogs. We employed a between-subjects design with a group of Labrador retrievers and Labrador retriever X golden retriever crosses (23 females, 15 males). Half of the dogs engaged in 10 minutes of free-form friendly interaction with a human experimenter (HAI condition), and the other half rested quietly in the same environment, without human interaction (control condition). We collected blood and saliva samples before, and immediately following both experimental conditions, and all samples were analyzed using enzyme-linked immunosorbent assays (ELISAs) following previously validated protocols. Dogs participating in HAI exhibited a significant increase in both salivary OT (+39%) and plasma OT (+5.7%) whereas dogs in the control group did not. Salivary AVP showed no change in the HAI group but increased significantly (+33%) in the control group. Plasma AVP decreased significantly following HAI (-13%) but did not change across time in the control condition. Within the dogs exposed to HAI, increases in salivary OT, and decreases in plasma AVP, were predicted by the extent of affiliative behaviour between the dog and human (indexed by scores from a principal components analysis of social behaviours between the dog and human). Collectively our results suggest that measures of salivary OT and AVP provide useful biomarkers in studies of HAI, and afford a flexible and noninvasive toolkit than can be employed in diverse research contexts.
Bridging the dynamics and organization of chromatin domains by mathematical modeling
Authors: Shinkai Soya , Nozaki Tadasu , Maeshima Kazuhiro , Togashi Yuichi
Published: June 2017

The genome is three-dimensionally organized in the cell, and the mammalian genome DNA is partitioned into submegabase-sized chromatin domains. Genome functions are regulated within and across the domains according to their organization, whereas the chromatin itself is highly dynamic. However, the details of such dynamic organization of chromatin domains in living cells remain unclear. To unify chromatin dynamics and organization, we recently demonstrated that structural information of chromatin domains in living human cells can be extracted from analyses of the subdiffusive nucleosome movement using mathematical modeling. Our mathematical analysis suggested that as the chromatin domain becomes smaller and more compact, nucleosome movement becomes increasingly restricted. Here, we show the implication of these results for bridging the gap between chromatin dynamics and organization, and provide physical insight into chromatin domains as efficient units to conduct genome functions in the thermal noisy environment of the cell.

Extra View to

Shinkai S, Nozaki T, Maeshima K, Togashi Y. Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells. PLoS Comput Biol. 2016;12(10):e1005136. doi: 10.1371/journal.pcbi.1005136. PubMed PMID: 27764097; PubMed Central PMCID: PMCPMC5072619.

Funding

This work was supported by Platform Project for Supporting in Drug Discovery and Life Science Research (Platform for Dynamic Approaches to Living System) from MEXT and AMED; KAKENHI under Grant JP16H01408, JP23115007, JP23115005, JP16H04746; CREST grant (JPMJCR15G2) from JST; and Research Fellowship for Young Scientists under Grant JP13J04821, JP16J07205.

Disclosure

No potential conflicts of interest were disclosed.

Acknowledgements

We would like to thank Dr. Takashi Toda for comments regarding the manuscript.
IFNα, a potential biomarker for stress vitiligo risk
Authors: Wu Huali , Wang Ting , Cai Minxuan , Fu Mengsi , Ping Fengfeng , He Ling , An Xiaohong , Shi Zhixiang , Xia Zhenjiang , Shang Jing
Published: June 2017

Neural hypothesis has become an important aspect of vitiligo, yet without corresponding diagnostic indicators. We preliminarily found 32 cases of vitiligo patients with certain aggregation of mental factors. In peripheral blood mononuclear cells (PBMCs) of these patients, transcriptome analyses revealed that the circulation expression of a type I interferon (IFN-I)-dependent genes was induced. Also, serum IFNα was elevated in vitiligo patients with depression. Therefore, our hypothesis is whether IFNα levels predict the occurrence of psychiatric vitiligo. Through the establishment of stress-induced depigmentation model, serum IFNα also showed increase. Intracerebroventricular and subcutaneous IFNα injection can both elicit not only depressive behavior but also vitiligo-like characteristics. Mechanistically, central IFNα induces the release of dorsal root ganglion (DRG) substance P (SP) to inhibit melanogenesis. Peripheral IFNα disturbs cutaneous-neuro-endocrine microenvironment. Type I IFN (IFNα) pathway-related genes in stress vitiligo were significantly discriminating from non-stress vitiligo, while that of type II IFN pathway was not.
Fibroblast Growth Factor Signaling Instructs Ensheathing Glia Wrapping ofDrosophilaOlfactory Glomeruli
Authors: Wu Bing , Li Jiefu , Chou Ya-Hui , Luginbuhl David , Luo Liqun
Published: June 2017

The formation of complex yet highly organized neural circuits requires interactions between neurons and glia. During the assembly of theDrosophilaolfactory circuit, 50 olfactory receptor neuron (ORN) classes and 50 projection neuron (PN) classes form synaptic connections in 50 glomerular compartments in the antennal lobe, each of which represents a discrete olfactory information processing channel. Each compartment is separated from the adjacent compartments by membranous processes from ensheathing glia. Here we show that Thisbe, a fibroblast growth factor (FGF) released from olfactory neurons, particularly local interneurons, instructs ensheathing glia to wrap each glomerulus. The Heartless FGF receptor acts cell-autonomously in ensheathing glia to regulate process extension so as to insulate each neuropil compartment. Overexpressing Thisbe in ORNs or PNs causes over-wrapping of glomeruli to which their axons or dendrites target. Failure to establish the FGF-dependent glia structure disrupts precise ORN axon targeting and discrete glomerular formation.

Significance Statement

This research reports that reciprocal interactions betweenDrosophilaolfactory neurons and ensheathing glia mediate the formation of neuronal compartments—groups of synapses that are packed into discrete structures called glomeruli that carry specific olfactory information. Ensheathing glia respond to a neuronal cue, the fibroblast growth factor (FGF) Thisbe, to pattern the boundaries of the nascent compartments. Neural compartments in turn require such glial barriers to separate themselves from neighboring compartments, so as to ensure the correct organization of the olfactory circuit. These findings highlight the importance of glia in the assembly and maintenance of neural circuits and the functions of FGF signaling in these processes.
Ownership structure and the choice of SEO issue method in the UK
Authors: Andrikopoulos Panagiotis , Sun Ji , Guo Jie
Published: June 2017

Purpose

The purpose of this paper is to analyse the role of ownership characteristics in a firm’s choice of alternative seasoned equity offering (SEO) methods, offer price discounts, and market reactions to such announcements within the UK setting.

Design/methodology/approach

The study examines 697 SEO events of firms traded in the UK during the period 1998 to 2012 using multivariate and binomial logistic regression models. Ordinary least square models are also used to examine how ownership variables affect offer price discounts and stock market performance during the announcement of such corporate events.

Findings

The authors show that placings and open offers (OOs) are the preferred methods for issuing equity by firms with higher managerial ownership. Thus, the evidence strongly supports the prediction of the entrenched management hypothesis. Moreover, the probability of choosing a combination of placings and OOs is also found to be significantly related to issue size, offer discount, leverage, and previous stock performance. The results show that pre-issue market conditions have a significant effect on the choice of issue method with rights offers (ROs) and the combination of placings and OOs primarily utilised by firms for issuing equity during hot market periods.

Originality/value

Unlike prior SEOs’ studies in the UK that predominantly concentrate on the use of ROs and placings, this study examines, for the first time, the link between OOs and the combination of placings and OOs with ownership concentration. The authors also investigate how offer price discounts are related to the firms’ ownership structure, various company micro-characteristics and the wider market conditions.
Bank earnings management and income smoothing using commission and fee income
Authors: Ozili Peterson K.
Published: June 2017

Purpose

The purpose of this paper is to investigate whether European banks use commission and fee income (CF) to smooth reported earnings or to persistently increase reported earnings as an income-increasing earnings management strategy.

Design/methodology/approach

The author tests the income-smoothing hypothesis following the approach of Stubben (2010) and Ahmedet al.(1999).

Findings

The author finds that European banks use CF to smooth reported earnings and this behaviour is pronounced among non-too-big-to-fail (NTBTF) European banks compared to too-big-to-fail (TBTF) European banks. The author also finds a positive and significant correlation between interest income and non-interest income (CF) indicating increased systematic risk due to reduced diversification benefits. The author also finds that the CF of NTBTF banks is procyclical with fluctuating economic conditions but not for TBTF banks. Also, the author finds evidence for income-increasing earnings management in the post-crisis period, for larger European banks and when banks have higherex postinterest income, implying that the propensity to engage in income-increasing earnings management significantly depends on bank size andex postinterest margin considerations. The findings have policy implications.

Originality/value

The author examines alternative financial numbers that banks use to manage earnings. The author focusses on income smoothing via CF among European banks, a context that has not been explored in the literature.
Ageing and the social economy
Authors: Murtagh Brendan
Published: June 2017

Purpose

This purpose of this paper is to concern with the extent to which social economies can be constructed as alternatives to private and state markets and their purported neoliberal tendencies.

Design/methodology/approach

The paper presents a meta-evaluation of an integrated set of projects supported by philanthropic investment to build finance, skills, entrepreneurship, social enterprises and non-monetised trading in the age sector in Northern Ireland.

Findings

The programme had important successes in stimulating social entrepreneurship, improving employability and showing how social enterprises can be incubated and scaled to offer new services for older people. It also improved skills in contract readiness, but this did not translate into new borrowing or trading models, even among larger NGOs.

Research limitations/implications

In that all economies are, to some extent, constructed and socially mediated, there is value in thinking through the components, relationships and projects that might make the ecosystem work more effectively. This should not just offer a counterweight to the market but could explore how an alternative arena for producing and consuming goods and services can be formed, especially among potentially vulnerable age communities.

Originality/value

The albeit, small-scale investment in a range of interrelated projects shows not only the value in experimentation but also the limits in planned attempts to construct social markets. The analysis shows that social economies need to respond to the priorities of older people, grown from community initiatives and better connected to the capabilities and resources of the sector.
The hierarchy of predictability in ecological restoration: are vegetation structure and functional diversity more predictable than community composition?
Authors: Laughlin Daniel C. , Strahan Robert T. , Moore Margaret M. , Fulé Peter Z. , Huffman David W. , Covington W. Wallace
Published: June 2017

Predicting restoration outcomes requires an understanding of the natural variability of ecosystem properties. A hierarchy of predictability has been proposed that ranks measures of restoration success from most‐to‐least predictable in the following order: vegetation structure > taxonomic diversity > functional diversity > taxonomic composition. This hierarchy has not been tested empirically, and the location within the hierarchy of trait‐based measures, such as community‐level trait means and variances, is not well understood.

Our objective was to test the hierarchy of predictability in one of the longest running ecological restoration experiments in the westernUSA. We used linear mixed effects models to analyse changes in herbaceous biomass, species richness, two functional diversity (FD) indices, community‐weighted mean (CWM) traits and taxonomic composition among experimental restoration treatments from 1992 to 2014 in a ponderosa pine‐bunchgrass ecosystem. Restoration treatments included combinations of light or heavy tree thinning and no fire or repeated prescribed fire every 4 years to release the herbaceous understorey from overstorey competition.

Herbaceous biomass and species richness were the two most predictable and least variable measures of success, whereas taxonomic composition exhibited the highest variability among plots through time. Trait‐based measures of FD tended to be more predictable and less variable than CWM trait values in this experiment. Both CWM trait values and FD were less variable among plots than taxonomic composition.

Synthesis and applications. Ecosystem properties that are intrinsically more variable over space and time will often be the least predictable restoration outcomes. Restoration practitioners can expect vegetation structure, species richness and functional diversity to be more predictable and less variable than taxonomic composition, which can exhibit dynamic responses to restoration treatments over time. Monitoring dominant native and invasive species will always be important, but given the functional redundancy that can occur within communities, strict targets based on composition may rarely be met. Trait‐based metrics that integrate taxonomic composition into their calculation are less variable and potentially more meaningful for evaluating ecosystem responses. The hierarchy of predictability should be tested in a range of ecosystems to determine its generality.
Marine mammals and sonar: Dose‐response studies, the risk‐disturbance hypothesis and the role of exposure context
Authors: Harris Catriona M. , Thomas Len , Falcone Erin A. , Hildebrand John , Houser Dorian , Kvadsheim Petter H. , Lam Frans‐Peter A. , Miller Patrick J. O. , Moretti David J. , Read Andrew J. , Slabbekoorn Hans , Southall Brandon L. , Tyack Peter L. , Wartzok Douglas , Janik Vincent M.
Published: June 2017

Marine mammals may be negatively affected by anthropogenic noise. Behavioural response studies (BRS) aim to establish a relationship between noise exposure conditions (dose) from a potential stressor and associated behavioural responses of animals. A recent series of BRS have focused on the effects of naval sonar sounds on cetaceans. Here, we review the current state of understanding of naval sonar impact on marine mammals and highlight knowledge gaps and future research priorities.

Many marine mammal species exhibit responses to naval sonar sounds. However, responses vary between and within individuals and populations, highlighting the importance of exposure context in modulating dose–response relationships.

There is increasing support from both terrestrial and marine systems for the risk‐disturbance hypothesis as an explanation for underlying response processes. This proposes that sonar sounds may be perceived by animals as a threat, evoking a response shaped by the underlying species‐specific risk of predation and anti‐predator strategy. An understanding of responses within both the dose–response and risk‐disturbance frameworks may enhance our ability to predict responsiveness for unstudied species and populations.

Many observed behavioural responses are energetically costly, but the way that these responses may lead to long‐term individual and population‐level impacts is poorly understood.

Synthesis and applications. Behavioural response studies have greatly improved our understanding of the potential effects of naval sonar on marine mammals. Despite data gaps, we believe a dose‐response approach within a risk‐disturbance framework will enhance our ability to predict responsiveness for unstudied species and populations. We advocate for (1) regulatory frameworks to utilize peer‐reviewed research findings when making predictions of impact, (2) regulatory frameworks to account for the inherent uncertainty in predictions of impact and (3) investment in monitoring programmes that are both directed by recent research and offer opportunities for validation of predictions at the individual and population level.
Ecological engineering through fire‐herbivory feedbacks drives the formation of savanna grazing lawns
Authors: Donaldson Jason E. , Archibald Sally , Govender Navashni , Pollard Drew , Luhdo Zoë , Parr Catherine L.
Published: June 2017

Variation in grass height is beneficial to biodiversity conservation in savanna landscapes. Theory predicts that small fires can promote short‐grass areas within savannas. We experimentally assessed the influence of fire season and size on grass height and the resultant response of wild grazer communities and tested three hypotheses: (1) repeated small fires in tall‐grass savannas increase short‐grass grazer densities in the post‐burn environment; (2) increased grazer densities maintain grass height in a short, palatable state and drive feedbacks that exclude fire; and (3) late‐dry season burns concentrate grazers more effectively than early dry season burns.

We repeatedly applied annual treatments (unburned, early‐ and late‐burns) in 0.25‐, 5‐ and 25‐ha plots over a period of 3 years in a tall‐grass savanna system in Kruger National Park, South Africa. Dung counts for grazer density and grass height data were collected along 50‐m transects. Grass height was measured in paired 1‐m2herbivore exclosures on plots before and after applied fires.

Dung data indicate that wildebeest occurred most frequently in grass heights below 5 cm. Their preference for plots regardless of fire size or season increased over time with each repeated burn. Zebra and buffalo favoured burns immediately post‐fire, but buffalo did not actively select for burnt areas over longer time periods.

By the second year of treatment, herbivory maintained 28% and 91% of the grass height below 10 cm in the early‐ and late‐season burns respectively. In contrast, herbivory on the unburned treatments had no effect on grass height.

Synthesis and applications. Fires less than 25 ha in size attracted sufficient grazing herbivores to shorten grass height. Repetition of the fire treatments resulted in the active selection of these areas in the longer term by wildebeest, impala and, to a lesser degree, zebra. Grazing pressure was high enough to initiate positive feedbacks and maintain lawns after only two seasons of burning and, depending on the season of burn, reduced grass height to a level that excluded repeat fires. Our study demonstrated that theory on grazer use of the post‐fire environment can be implemented practically by applying small repeated burns to promote the formation of short‐grass areas within savannas.
Land use history and seed dispersal drive divergent plant community assembly patterns in urban vacant lots
Authors: Johnson Anna L. , Borowy Dorothy , Swan Christopher M.
Published: June 2017

Despite high levels of disturbance and habitat modification, urban ecosystems still host substantial levels of biodiversity. The processes that maintain existing levels of diversity, however, remain understudied. Identifying the links between urban ecological processes and patterns has, therefore, become a fundamental research goal to support urban biodiversity and ecosystem functioning.

We conducted a study to determine how the diversity and composition of urban plant communities is affected by spatially and temporally variable land use legacies. We constructed a chronosequence of vacant lot properties covering a range of 3–22 years since demolition, in an urban neighbourhood in Baltimore, Maryland (USA). Surveys of herbaceous plant species abundance were conducted during the summers of 2012 and 2013 in sections of each vacant lot where the building previously stood (the “building footprint”) and sections of the lot that was previously a backyard or garden (the “remnant garden”).

We found divergent patterns in plant community composition between areas of vacant lots with varying land use histories. This includes significant shifts in the functional composition of biotically vectored seed dispersal strategies, as well as an increase in seed mass and terminal velocity trait values of plant communities in building footprints over time. In addition, we found that plant communities in different sections of the same vacant lot tended to become more functionally dissimilar in seed dispersal strategies over time. In contrast, we found no significant changes in taxonomic diversity over time for any of our measures.

Policy implications. Our study suggests that regional‐scale patterns of seed dispersal interact with diverse land use legacies to structure the plant communities of urban vacant lots. Although it has been suggested that highly altered local environmental conditions and competition from introduced species limit native plant diversity in urban environments, we find seed dispersal to be a more significant driver of urban plant community assembly patterns. Implementing management strategies that focus on habitat connectivity and enhancing species pools via seeding may present an effective strategy for promoting more successful establishment of diverse plant communities in urban environments.
Eco‐engineering urban infrastructure for marine and coastal biodiversity: Which interventions have the greatest ecological benefit?
Authors: Strain Elisabeth M. A. , Olabarria Celia , Mayer‐Pinto Mariana , Cumbo Vivian , Morris Rebecca L. , Bugnot Ana B. , Dafforn Katherine A. , Heery Eliza , Firth Louise B. , Brooks Paul R. , Bishop Melanie J.
Published: June 2017

Along urbanised coastlines, urban infrastructure is increasingly becoming the dominant habitat. These structures are often poor surrogates for natural habitats, and a diversity of eco‐engineering approaches have been trialled to enhance their biodiversity, with varying success.

We undertook a quantitative meta‐analysis and qualitative review of 109 studies to compare the efficacy of common eco‐engineering approaches (e.g. increasing texture, crevices, pits, holes, elevations and habitat‐forming taxa) in enhancing the biodiversity of key functional groups of organisms, across a variety of habitat settings and spatial scales.

All interventions, with one exception, increased the abundance or number of species of one or more of the functional groups considered. Nevertheless, the magnitude of effect varied markedly among groups and habitat settings. In the intertidal, interventions that provided moisture and shade had the greatest effect on the richness of sessile and mobile organisms, while water‐retaining features had the greatest effect on the richness of fish. In contrast, in the subtidal, small‐scale depressions which provide refuge to new recruits from predators and other environmental stressors such as waves, had higher abundances of sessile organisms while elevated structures had higher numbers and abundances of fish. The taxa that responded most positively to eco‐engineering in the intertidal were those whose body size most closely matched the dimensions of the resulting intervention.

Synthesis and applications. The efficacy of eco‐engineering interventions varies among habitat settings and functional groups. This indicates the importance of developing site‐specific approaches that match the target taxa and dominant stressors. Furthermore, because different types of intervention are effective at enhancing different groups of organisms, ideally a range of approaches should be applied simultaneously to maximise niche diversity.
Can weeds enhance profitability? Integrating ecological concepts to address crop‐weed competition and yield quality
Authors: Gibson David J. , Young Bryan G. , Wood Andrew J.
Published: June 2017

Sustainable cropping systems are needed for future food security. One aspect of sustainable cropping is to manage for desirable grain quality of crops including seed size, protein, oil and metabolite composition.

Plant ecology theory on niche relationships and interspecific competition predicts that subordinate species mixtures (i.e. weed species) will affect dominant (i.e. crop) species offspring quality. Beyond individual weed species effects on crop quality, we hypothesise that the integrated effect of weed mixtures will be influenced by taxonomic, functional trait and phylogenetic diversity.

Reviewing Glycine max (soybean)–weed systems, we show a complex relationship between the weed community and G. max seed protein, oil, mean seed mass and physiological markers (relative water content, trigonelline leaf content, fluorescence, foliar Cu, Fe and Zn). Increased levels of weed competition led to increased seed protein, at the expense of seed oil.

Synthesis. We propose that research on interspecific relationships between crops and weeds consider weed species diversity, weed functional traits associated with the Leaf‐Height‐Seed strategy and phylogenetic relationships to identify weed mixtures (either sown or manipulated through herbicide control) best suited to minimise their detrimental effects on yield while maximising crop quality as part of sustainable cropping systems.
Phenological diversity provides opportunities for climate change adaptation in winegrapes
Authors: Wolkovich E. M. , Burge D. O. , Walker M. A. , Nicholas K. A.
Published: June 2017

Climate change poses an unprecedented challenge to agriculture. While growers have always struggled with year‐to‐year variation in climate – early rains or unusually hot summers – climate change provides a major directional shift in mean climate.

Across the globe, growing regions are warming and plants are shifting in both time and space. Current and future shifts pose a major challenge to researchers and growers alike, yet they also highlight a major avenue to adapt crops to climate change – by understanding and exploiting phenological diversity.

Using winegrapes (Vitis vinifera subsp. vinifera) as a case study, we review the phenological diversity present within one crop and its underlying environmental and genetic drivers. In winegrapes, harvest dates are strongly tied to temperature, but this sensitivity varies greatly, with different cultivars (or ‘varieties’) of grapes ripening much more or less for the same amount of warming.

Synthesis. This phenological diversity provides a mechanism to help growers adapt winegrapes to shifting climates – by planting different varieties that will grow well under current and future climate regimes. More generally, understanding phenological diversity – including its environmental vs. genetic components – offers a major avenue to use ecological knowledge to advance adaptation for winegrapes, and many other crops, to climate change.
Kin recognition, multilevel selection and altruism in crop sustainability
Authors: Murphy Guillermo P. , Swanton Clarence J. , Van Acker Rene C. , Dudley Susan A.
Published: June 2017

Intraspecific competition among crop plants is undesirable. Less competitive crops are predicted to increase yield and decrease the need for added resources.

Wild plants demonstrate the ability to recognize kin and potentially help their relatives by reducing their competitive behaviours, a form of altruism. Altruism can also evolve through multilevel selection. Are these processes relevant to sustainable agriculture?

Crops do grow predictably with kin. However, their evolution is more strongly dictated by artificial selection (crop breeding), which incorporates individual and group selection, making multilevel selection more relevant than kin selection in favouring altruism. While current crop breeding protocols attempt to target the reduction of competitive traits, early mass selection may have the opposite effect.

We predict that kin recognition itself is not relevant to crops, because of the consistently high relatedness within crop stands. Nonetheless, crops have shown cultivar and kin recognition. We argue that these responses cannot be assumed to demonstrate altruism, as current breeding practices offer little opportunity for kin selection.

Synthesis. There is the opportunity to favour altruism through artificial breeding. Here we suggest how crop breeding protocols could be changed to favour cooperation by increasing group selection during early breeding.
Benefits of increasing plant diversity in sustainable agroecosystems
Authors: Isbell Forest , Adler Paul R. , Eisenhauer Nico , Fornara Dario , Kimmel Kaitlin , Kremen Claire , Letourneau Deborah K. , Liebman Matt , Polley H. Wayne , Quijas Sandra , Scherer‐Lorenzen Michael
Published: June 2017

Recent studies have revealed many potential benefits of increasing plant diversity in natural ecosystems, as well as in agroecosystems and production forests. Plant diversity potentially provides a partial to complete substitute for many costly agricultural inputs, such as fertilizers, pesticides, imported pollinators and irrigation. Diversification strategies include enhancing crop genetic diversity, mixed plantings, rotating crops, agroforestry and diversifying landscapes surrounding croplands.

Here we briefly review studies considering how increasing plant diversity influences the production of crops, forage, and wood, yield stability, and several regulating and supporting agroecosystem services. We also discuss challenges and recommendations for diversifying agroecosystems.

There is consistently strong evidence that strategically increasing plant diversity increases crop and forage yield, wood production, yield stability, pollinators, weed suppression and pest suppression, whereas effects of diversification on soil nutrients and carbon remain poorly understood.

Synthesis. The benefits of diversifying agroecosystems are expected to be greatest where the aims are to sustainably intensify production while reducing conventional inputs or to optimize both yields and ecosystem services. Over the next few decades, as monoculture yields continue to decelerate or decline for many crops, and as demand for ecosystem services continues to rise, diversification could become an essential tool for sustaining production and ecosystem services in croplands, rangelands and production forests.
Plant ecological solutions to global food security
Authors: Bardgett Richard D. , Gibson David J.
Published: June 2017

As global climate changes and the world population increases, agriculture faces an enormous challenge to increase food production in an equitable and sustainable manner. Principles and concepts derived directly from plant ecological research can help meet this challenge.

This series of 10 mini‐reviews considers some of the key ways that plant ecologists can help inform and contribute to meeting this challenge.

The papers are grouped into three main themes of plant ecology, namely plant community diversity and structure, plant population dynamics and plant interactions, and plant–soil (below‐ground) interactions.

Synthesis. We identify a number of important knowledge gaps in areas where plant ecological research can contribute towards improving yield, nutrition, ecosystem services and environmental resilience of agricultural systems. However, the adoption of plant ecological principles in sustainable agriculture will require practical approaches to their implementation along with improved understanding of social and economic barriers.
Comparison of three methods for measuring height in rehabilitation inpatients and the impact on body mass index classification: An open prospective study
Authors: McDougall Karen E. , Stewart Alison J. , Argiriou Alison M. , Huggins Catherine E. , New Peter W.
Published: June 2017

Aim

To compare standing height, estimated current height and demi‐span estimated height and examine their impact on body mass index (BMI) classification.

Methods

Cross‐sectional data was collected on 104 patients admitted to an adult rehabilitation ward and seen by the dietitian. Patient's standing, estimated current height and demi‐span estimated height were collected and grouped by age: 19–64 and ≥65 years.

Results

The limits of agreement (95% confidence interval) for estimated current height compared with standing height were +9.9 cm and −7.9 cm, in contrast to +8.7 cm and −14.3 cm for demi‐span estimated height. Demi‐span underestimated height when compared with standing height in both age groups, 19–64 years: (mean ± SD) 3.0 ± 6.5 cm (P = 0.001, n = 68) and ≥ 65 year age group 4.0 ± 6.0 cm (P < 0.001, n = 36), resulting in a significantly greater mean BMI (analysis of variance P < 0.001, P = 0.02). In the 19‐64 and ≥65 year age groups, 3% (2/68) and 10% (4/36) of patients, respectively, had a different BMI classification using demi‐span estimated height compared with standing height.

Conclusions

Estimated current height is a simple and practical alternative if standing height is unable to be obtained when performing a nutrition assessment. Demi‐span estimated height should be used with caution when calculating BMI to assess nutritional status, particularly in the elderly.
William Laud and the Parliamentary Politics of 1628–9
Authors: Parry Mark
Published: June 2017

This article seeks to highlight the important part played by Bishop William Laud in the counsels of Charles I in the 1620s, and, in particular, his involvement in the parliamentary sessions of 1628 and 1629. Having demonstrated his usefulness as a parliamentary spokesman for the crown in the parliaments of 1625 and 1626, and having been promoted to the privy council, the parliament of 1628–9 witnessed the height of Laud's parliamentary engagement. His key role as a writer of memoranda and speeches both for the duke of Buckingham and for Charles himself demonstrate the weight accorded to his political views. These views, reflected in his writings, sermons and his contributions to parliamentary debate, embody a dislike of parliamentary bargaining, a firm commitment to uphold the royal prerogative, particularly in matters of taxation, and a determination to resist encroachments upon it by the common lawyers, whether by the confirmation of Magna Carta or in the form of the Petition of Right. The expression of these views in such an emphatic fashion would come back to bite him, in the parliamentary attacks on him in 1629, but above all at his trial in 1644. Nevertheless, his articulation of them suggests that Laud himself was a more considered political thinker, and a more active politician, than he has hitherto been given credit for, and that there were ideas around in influential conciliar circles that do not appear to reflect the ‘anti‐absolutist’ consensus that, it is widely claimed, prevailed within the early Stuart political nation.
Sir Henry Cavendish (1732–1804), Parliamentarian in Two Countries
Authors: Thomas P.D.G.
Published: June 2017

Sir Henry Cavendish, who sat in the Irish parliament from 1766 to 1768 and from 1776 to 1800, and in the Westminster parliament from 1768 to 1774, was a parliamentarian par excellence. His chief claim to fame is as a parliamentary diarist, in both houses of commons, noting down in shorthand some five million words. But this article is on Cavendish as a politician. He was a prolific speaker in both parliaments. But finding himself only a second‐rate debater, he cultivated two fields of expertise: finance, and, above all, parliamentary procedure. Here his knowledge soon became unequalled, and virtually unchallenged by the last two decades of the Irish parliament, where he became notorious as a master of obstruction. His political career was erratic, often in opposition, increasingly in government, a permanent officeholder by the end.