bluuebunny/crossref_metadata_2025 huggingface dataset:
An epigenetic biomarker of aging for lifespan and healthspan
Authors: Levine Morgan E. , Lu Ake T. , Quach Austin , Chen Brian H. , Assimes Themistocles L. , Bandinelli Stefania , Hou Lifang , Baccarelli Andrea A. , Stewart James D. , Li Yun , Whitsel Eric A. , Wilson James G , Reiner Alex P , Aviv Abraham , Lohman Kurt , Liu Yongmei , Ferrucci Luigi , Horvath Steve
Published: March 2018

Identifying reliable biomarkers of aging is a major goal in geroscience. While the first generation of epigenetic biomarkers of aging were developed using chronological age as a surrogate for biological age, we hypothesized that incorporation of composite clinical measures of phenotypic age that capture differences in lifespan and healthspan may identify novel CpGs and facilitate the development of a more powerful epigenetic biomarker of aging. Using a innovative two-step process, we develop a new epigenetic biomarker of aging, DNAm PhenoAge, that strongly outperforms previous measures in regards to predictions for a variety of aging outcomes, including all-cause mortality, cancers, healthspan, physical functioning, and Alzheimer’s disease. While this biomarker was developed using data from whole blood, it correlates strongly with age in every tissue and cell tested. Based on an in-depth transcriptional analysis in sorted cells, we find that increased epigenetic, relative to chronological age, is associated increased activation of pro-inflammatory and interferon pathways, and decreased activation of transcriptional/translational machinery, DNA damage response, and mitochondrial signatures. Overall, this single epigenetic biomarker of aging is able to capture risks for an array of diverse outcomes across multiple tissues and cells, and provide insight into important pathways in aging.
DensityPath: a level-set algorithm to visualize and reconstruct cell developmental trajectories for large-scale single-cell RNAseq data
Authors: Chen Ziwei , An Shaokun , Bai Xiangqi , Gong Fuzhou , Ma Liang , Wan Lin
Published: March 2018

Cell fates are determined by transition-states which occur during complex biological pro-cesses such as proliferation and differentiation. The advance in single-cell RNA sequencing (scRNAseq) provides the snapshots of single cell transcriptomes, thus offering an essential opportunity to study such complex biological processes. Here, we introduce a novel algorithm, DensityPath, which visualizes and reconstructs the underlying cell developmental trajectories for large-scale scRNAseq data. DensityPath has three merits. Firstly, by adopting the nonlinear dimension reduction algorithm elastic embedding, DensityPath reveals the intrinsic structures of the data. Secondly, by applying the powerful level set clustering method, DensityPath extracts the separate high density clusters of representative cell states (RCSs) from the single cell multimodal density landscape of gene expression space, enabling it to handle the heterogeneous scRNAseq data elegantly and accurately. Thirdly, DensityPath constructs cell state-transition path by finding the geodesic minimum spanning tree of the RCSs on the surface of the density landscape, making it more computationally efficient and accurate for large-scale dataset. The cell state-transition path constructed by DensityPath has the physical interpretation as the minimum-transition-energy (least-cost) path. We demonstrate that DensityPath is capable of identifying complex cell development trajectories with bifurcating and trifurcating branches on the human preimplantation embryos. We demonstrate that DensityPath is robust and has high accuracy of pseudotime calculation and branch assignment on the real scRNAseq as well as simulated datasets.
Vulnerability of invasive glioma cells to lysosomal membrane instabilization
Authors: Joncour Vadim Le , Hyvönen Maija , Filppu Pauliina , Turunen Pauliina S. , Sihto Harri , Burghardt Isabel , Joensuu Heikki , Tynninen Olli , Jääskeläinen Juha , Weller Michael , Lehti Kaisa , Laakkonen Pirjo
Published: March 2018

Diffusive by nature, glioma challenges clinical care by the impossibility of complete surgical resection of tumor, leaving the radio- and chemoresistant cells responsible for recurrence intact. We identified mammary-derived growth inhibitor (MDGI/FABP3) as invasive glioma biomarker. Here, we show that high MDGI expression associated with poor patient survival and promoted invasive glioma cell growth bothin vitroandin vivo, while MDGI silencing drastically compromised patient-derived tumoroid viability via induction of lysosomal membrane permeabilization (LMP). This alternative cell death pathway provokes release of lysosomal hydrolases into the cytosol leading inevitably to the cell death. Our results show a novel functional role for MDGI in glioma cell invasion, survival, and maintenance of the lysosomal membrane integrity as well as an unsuspected sensitivity of glioma cells to an LMP-inducing drug, anti-histamine clemastine. In a preclinical study, clemastine-treatment significantly prolonged the survival of intracranial glioblastoma-bearing animals due to eradication of invasive glioma cells. This glioma cell vulnerability to LMP-inducing drugs opens new horizons for development of novel treatments and suggest re-positioning of an established drug for new indication.
Epigallocatechin-3-Gallate Improves Facial Dysmorphology Associated with Down Syndrome
Authors: Starbuck John M. , Llambrich Sergi , González Ruben , Albaigès Julia , Sarlé Anna , Wouters Jens , González Alejandro , Sevillano Xavier , Sharpe James , de La Torre Rafael , Dierssen Mara , Velde Greetje Vande , Martínez-Abadías Neus
Published: March 2018

In Down syndrome (DS), the overall genetic imbalance caused by trisomy of chromosome 21 leads to a complex pleiotropic phenotype that involves a recognizable set of facial traits. Several studies have shown the potential of epigallocatechin-3-gallate (EGCG), a green tea flavanol, as a therapeutic tool for alleviating different developmental alterations associated with DS, such as cognitive impairment, skull dysmorphologies, and skeletal deficiencies. Here we provide for the first time experimental and clinical evidence of the potential benefits of EGCG treatment to facial morphology. Our results showed that mouse models treated with low dose of EGCG during pre- and postnatal development improved facial dysmorphology. However, the same treatment at high dose produced disparate facial morphology changes with an extremely wide and abnormal range of variation. Our observational study in humans revealed that EGCG treatment since early in development is associated with intermediate facial phenotypes and significant facial improvement scores. Overall, our findings suggest a potential beneficial effect of ECGC on facial development, which requires further research to pinpoint the optimal dosages of EGCG that reliably improve DS phenotypes. Current evidence warns against the non-prescribed intake of this supplement as a health-promoting measure.
A stress recovery signaling network for enhanced flooding tolerance inArabidopsis thaliana
Authors: Yeung Elaine , Veen Hans van , Vashisht Divya , Sobral Paiva Ana Luiza , Hummel Maureen , Steffens Bianka , Steffen-Heins Anja , Sauter Margret , Vries Michel de , Schuurink Robert , Bazin Jérémie , Bailey-Serres Julia , Voesenek Laurentius A.C.J. , Sasidharan Rashmi
Published: March 2018

Abiotic stresses in plants are often transient and the recovery phase following stress removal is critical. Flooding, a major abiotic stress that negatively impacts plant biodiversity and agriculture, is a sequential stress where tolerance is strongly dependent on viability underwater and during the postflooding period. Here we show that inArabidopsis thalianaaccessions (Bay-0 and Lp2-6), different rates of submergence recovery correlate with submergence tolerance and fecundity. A genome-wide assessment of ribosome-associated transcripts in Bay-0 and Lp2-6 revealed a signaling network regulating recovery processes. Differential recovery between the accessions was related to the activity of three genes:RESPIRATORY BURST OXIDASE HOMOLOG(RBOHD),SENESCENCE-ASSOCIATED GENE113(SAG113) andORESARA1(ORE1/NAC6) which function in a regulatory network involving a reactive oxygen species (ROS) burst upon de-submergence and the hormones abscisic acid and ethylene. This regulatory module controls ROS homeostasis, stomatal aperture and chlorophyll degradation during submergence recovery. This work uncovers a signaling network that regulates recovery processes following flooding to hasten the return to pre-stress homeostasis.

Significance statement

Flooding due to extreme weather events can be highly detrimental to plant development and yield. Speedy recovery following stress removal is an important determinant of tolerance, yet mechanisms regulating this remain largely uncharacterized. We identified a regulatory network inArabidopsis thalianathat controls water loss and senescence to influence recovery from prolonged submergence. Targeted control of the molecular mechanisms facilitating stress recovery identified here can potentially improve performance of crops in flood-prone areas.
Metabolic adjustment enhances food web stability
Authors: Quévreux Pierre , Brose Ulrich
Published: March 2018

Understanding ecosystem stability is one of the greatest challenges of ecology. Over several decades, it has been shown that allometric scaling of biological rates and feeding interactions provide stability to complex food web models. Moreover, introducing adaptive responses of organisms to environmental changes (e.g.like adaptive foraging that enables organisms to adapt their diets depending on resources abundance) improved species per-sistence in food webs. Here, we introduce the concept of metabolic adjustment,i.e.the ability of species to slow down their metabolic rates when facing starvation and to increase it in time of plenty. We study the reactions of such a model to nutrient enrichment and the adjustment speed of metabolic rates. We found that increasing nutrient enrichment leads to a paradox of enrichment (increase in biomasses and oscillation amplitudes and ultimately extinction of species) but metabolic adjustment stabilises the system by dampening the oscillations. Metabolic adjustment also increases the average biomass of the top predator in a tri-trophic food chain. In complex food webs, metabolic adjustment has a stabilising effect as it promotes species survival by creating a large diversity of metabolic rates. However, this stabilising effect is mitigated in enriched ecosystems. Phenotypic plasticity of organisms must be considered in food web models to better understand the response of organisms to their environment. As metabolic rate is central in describing biological rates, we must pay attention to its variations to fully understand the population dynamics of natural communities.
Fusing Mobile Phone Sensing and Brain Imaging to Assess Depression in College Students
Authors: Huckins Jeremy F. , daSilva Alex W. , Wang Rui , Wang Weichen , Hedlund Elin L. , Murphy Eilis I. , Lopez Richard B. , Rogers Courtney , Holtzheimer Paul E. , Kelley William M. , Heatherton Todd F. , Wagner Dylan D. , Haxby James V. , Campbell Andrew T.
Published: March 2018

As smartphone usage has become increasingly prevalent in our society, so have rates of depression, particularly among young adults. Individual differences in smartphone usage patterns have been shown to reflect individual differences in underlying affective processes such as depression (Wang et al., 2018). In the current study, we identified a positive relationship between smartphone screen time (e.g. phone unlock duration) and resting-state functional connectivity (RSFC) between the subgenual cingulate cortex (sgCC), a brain region implicated in depression and antidepressant treatment response, and regions of the ventromedial/orbitofrontal cortex, such that increased phone usage was related to stronger connectivity between these regions. We then used this cluster to constrain subsequent analyses looking at depressive symptoms in the same cohort and observed partial replication in a separate cohort. We believe the data and analyses presented here provide relatively simplistic initial analyses which replicate and provide a first step in combining functional brain activity and smartphone usage patterns to better understand issues related to mental health. Smartphones are a prevalent part of modern life and the usage of mobile sensing data from smartphones promises to be an important tool for mental health diagnostics and neuroscience research.
Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient
Authors: Sorensen Jackson W. , Dunivin Taylor K. , Tobin Tammy C. , Shade Ashley
Published: March 2018

Small bacterial and archaeal genomes provide insights into the minimal requirements for life1and seem to be widespread on the microbial phylogenetic tree2. We know that evolutionary processes, mainly selection and drift, can result in microbial genome reduction3,4. However, we do not know the precise environmental pressures that constrain genome size in free-living microorganisms. A study including isolates5has shown that bacteria with high optimum growth temperatures, including thermophiles, often have small genomes6. It is unclear how well this relationship may extend generally to microorganisms in nature7,8, and in particular to those microbes inhabiting complex and highly variable environments like soil3,6,9. To understand the genomic traits of thermally-adapted microorganisms, here we investigated bacterial and archaeal metagenomes from a 45°C gradient of temperate-to-thermal soils overlying the ongoing Centralia, Pennsylvania (USA) coal seam fire. There was a strong relationship between average genome size and temperature: hot soils had small genomes relative to ambient soils (Pearson’s r = −0.910, p < 0.001). There was also an inverse relationship between soil temperature and cell size (Pearson’s r = −0.65, p = 0.021), providing evidence that cell and genome size in the wild are together constrained by temperature. Notably, hot soils had different community structures than ambient soils, implicating ecological selection for thermo-tolerant cells that had small genomes, rather than contemporary genome streamlining within the local populations. Hot soils notably lacked genes for described two-component regulatory systems and antimicrobial production and resistance. Our work provides field evidence for the inverse relationship between microbial genome size and temperature requirements in a diverse, free-living community over a wide range of temperatures that support microbial life. Our findings demonstrate that ecological selection for thermophiles and thermo-tolerant microorganisms can result in smaller average genome sizesin situ, possibly because they have small genomes reminiscent of a more ancestral state.
Association of tamoxifen resistance and lipid reprogramming in breast cancer
Authors: Hultsch Susanne , Kankainen Matti , Paavolainen Lassi , Kovanen Ruusu-Maaria , Ikonen Elina , Kangaspeska Sara , Pietiäinen Vilja , Kallioniemi Olli
Published: March 2018

Background

Tamoxifen treatment of estrogen receptor (ER)-positive breast cancer reduces mortality by 31%. However, over half of advanced ER-positive breast cancers are intrinsically resistant to tamoxifen and about 40% will acquire the resistance during the treatment.

Methods

In order to explore mechanisms underlying endocrine therapy resistance in breast cancer and to identify new therapeutic opportunities, we created tamoxifen-resistant breast cancer cell lines that represent the luminal A or the luminal B. Gene expression patterns revealed by RNA-sequencing in seven tamoxifen-resistant variants were compared with their isogenic parental cells. We further examined those transcriptomic alterations in a publicly available patient cohort.

Results

We show that tamoxifen resistance cannot simply be explained by altered expression of individual genes, common mechanism across all resistant variants, or the appearance of new fusion genes. Instead, the resistant cell lines shared altered gene expression patterns associated with cell cycle, protein modification and metabolism, especially with the cholesterol pathway. In the tamoxifen-resistant T-47D cell variants we observed a striking increase of neutral lipids in lipid droplets as well as an accumulation of free cholesterol in the lysosomes. Tamoxifen-resistant cells were also less prone to lysosomal membrane permeabilization (LMP) and not vulnerable to compounds targeting the lipid metabolism. However, the cells were sensitive to disulfiram, LCS-1, and dasatinib.

Conclusion

Altogether, our findings highlight a major role of LMP prevention in tamoxifen resistance, and suggest novel drug vulnerabilities associated with this phenotype.
On the regulatory evolution of new genes throughout their life history
Authors: Zhang Jia-yu , Zhou Qi
Published: March 2018

Every gene has a birthplace and an age, i.e., a cis-regulatory environment and an evolution lifespan since its origination, yet how gene’s evolution trajectory is shaped by the two remains unclear. Here we address this basic question by comparing phylogenetically dated new genes of different ages among Drosophila and vertebrate species. For both, we find a clear ‘out of testis’ transition from the testis-specific young genes to the broadly expressed old housekeeping genes. Particularly, many new genes have evolved specific activation at maternal-zygotic transition, or distinctive spatiotemporal embryonic expression patterns from the parental genes. We uncover an age-dependent gain/loss of active/repressive histone modifications and cis-regulatory elements, with variations between species and between somatic/germline tissues, which together underpin the stepwise acquisition of novel and important function by new genes. These results illuminate the general evolution trajectory and the underlying regulatory mechanisms of genes throughout their life history.
Escherichia coliLrp regulates one-third of the genome via direct, cooperative, and indirect routes
Authors: Kroner Grace M. , Wolfe Michael B. , Freddolino Peter L.
Published: March 2018

The global regulator Lrp plays a crucial role in regulating metabolism, virulence and motility in response to environmental conditions. Lrp has previously been shown to activate or repress approximately 10% of genes inEscherichia coli. However, the full spectrum of targets, and how Lrp acts to regulate them, has stymied earlier study. We have combined matched ChIP-seq and RNA sequencing under nine physiological conditions to map the binding and regulatory activity of Lrp as it directs responses to nutrient abundance. In addition to identifying hundreds of novel Lrp targets, we observe two new global trends: first, that Lrp will often bind to promoters in a poised position under conditions when it has no regulatory activity, and second, that nutrient levels induce a global shift in the equilibrium between non-specific and sequence-specific DNA binding. The overall regulatory behavior of Lrp, which as we now show regulates 35% ofE. coligenes directly or indirectly under at least one condition, thus arises from the interaction between changes in Lrp binding specificity and cooperative action with other regulators.
A comparison of single-cell trajectory inference methods: towards more accurate and robust tools
Authors: Saelens Wouter , Cannoodt Robrecht , Todorov Helena , Saeys Yvan
Published: March 2018

Using single-cell-omics data, it is now possible to computationally order cells along trajectories, allowing the unbiased study of cellular dynamic processes. Since 2014, more than 50 trajectory inference methods have been developed, each with its own set of methodological characteristics. As a result, choosing a method to infer trajectories is often challenging, since a comprehensive assessment of the performance and robustness of each method is still lacking. In order to facilitate the comparison of the results of these methods to each other and to a gold standard, we developed a global framework to benchmark trajectory inference tools. Using this framework, we compared the trajectories from a total of 29 trajectory inference methods, on a large collection of real and synthetic datasets. We evaluate methods using several metrics, including accuracy of the inferred ordering, correctness of the network topology, code quality and user friendliness. We found that some methods, including Slingshot, TSCAN and Monocle DDRTree, clearly outperform other methods, although their performance depended on the type of trajectory present in the data. Based on our benchmarking results, we therefore developed a set of guidelines for method users. However, our analysis also indicated that there is still a lot of room for improvement, especially for methods detecting complex trajectory topologies. Our evaluation pipeline can therefore be used to spearhead the development of new scalable and more accurate methods, and is available at github.com/dynverse/dynverse.

To our knowledge, this is the first comprehensive assessment of trajectory inference methods. For now, we exclusively evaluated the methods on their default parameters, but plan to add a detailed parameter tuning procedure in the future. We gladly welcome any discussion and feedback on key decisions made as part of this study, including the metrics used in the benchmark, the quality control checklist, and the implementation of the method wrappers. These discussions can be held at github.com/dynverse/dynverse/issues.
Perturbation of ubiquitin homeostasis promotes macrophage oxidative defenses
Authors: Charbonneau Marie-Eve , Passalacqua Karla D. , Hagen Susan E. , Showalter Hollis D. , Wobus Christiane E. , O’Riordan Mary X.D.
Published: March 2018

Innate immune responses rely on specific pattern recognition receptors that induce downstream signaling cascades and promote inflammatory responses. Emerging evidence suggests that cells may also recognize alterations in cellular processes induced by infection. Protein ubiquitination is a post-translational modification essential for maintaining cellular homeostasis, and infection can cause global alterations in the host ubiquitin proteome. Here we used a chemical biology approach to perturb the cellular ubiquitin proteome as a simplified model to study the direct effect of ubiquitin homeostasis on macrophage responses. We show that perturbation of ubiquitin homeostasis results in a rapid and transient burst of reactive oxygen species (ROS) that promotes macrophage anti-infective capacity. ROS production was dependent on the activity of the phagocyte NADPH oxidase NOX2 and was associated with an increase in intracellular calcium. Our findings suggest that major changes in the host ubiquitin landscape may be a potent signal to rapidly deploy innate immune defenses.
Reconstructing imagined letters from early visual cortex reveals tight topographic correspondence between visual mental imagery and perception
Authors: Senden Mario , Emmerling Thomas , Hoof Rick van , Frost Martin , Goebel Rainer
Published: March 2018

Visual mental imagery is the quasi-perceptual experience of “seeing in the mind’s eye”. While a tight correspondence between imagery and perception in terms of subjective experience is well established, their correspondence in terms of neural representations remains insufficiently understood. In the present study, we exploit the high spatial resolution of functional magnetic resonance imaging (fMRI) at 7T, the retinotopic organization of early visual cortex, and machine learning techniques to investigate whether visual imagery of letter shapes preserves the topographic organization of perceived shapes. Sub-millimeter resolution fMRI images were obtained from early visual cortex in six subjects performing visual imagery of four different letter shapes. Predictions of imagery voxel activation patterns based on a population receptive field encoding model and physical letter stimuli provided first evidence in favor of detailed topographic organization. Subsequent visual field reconstructions of imagery data based on the inversion of the encoding model further showed that visual imagery preserves the geometric profile of letter shapes. These results open new avenues for decoding as we show that a denoising autoencoder can be used to pretrain a classifier purely based on perceptual data before fine-tuning it on imagery data. Finally, we show that the autoencoder can project imagery-related voxel activations onto their perceptual counterpart allowing for visually recognizable reconstructions even at the single-trial level. The latter may eventually be utilized for the development of content-based BCI letter-speller systems.
Spontaneous resolution and crystal structure of (2S)-2-(3-nitrophenyl)-3-phenyl-2,3,5,6-tetrahydro-4H-1,3-thiazin-4-one; crystal structure of rac-2-(4-nitrophenyl)-3-phenyl-2,3,5,6-tetrahydro-4H-1,3-thiazin-4-one
Authors: Yennawar Hemant P. , Bradley Heather G. , Perhonitch Kristen C. , Reppert Haley E. , Silverberg Lee J.
Published: March 2018

The crystal structures of isomeric rac-2-(4-nitrophenyl)-3-phenyl-2,3,5,6-tetrahydro-4H-1,3-thiazin-4-one (C16H14N2O3S) (1) and (2S)-2-(3-nitrophenyl)-3-phenyl-2,3,5,6-tetrahydro-4H-1,3-thiazin-4-one (C16H14N2O3S) (2) are reported here. While 1 crystallizes in a centrosymmetric space group, the crystal of 2 chosen for data collection has molecules only with (2S) chirality. This is the result of spontaneous resolution during crystallization, as the synthesis produces a racemic mixture. A crystal with (2R) molecules was also found in the same crystallization vial (structure factors available). The six-membered thiazine ring in both 1 and 2 displays an envelope conformation with the S atom forming the flap. The aryl rings in both structures adopt an approximate V shape with angles between their planes of 46.97 (14)° in 1 and 58.37 (10)° in 2. In both structures, the molecules form layers in the ab plane. Within such a layer in 1, one of the O atoms of the nitrophenyl group accepts a C—H...O hydrogen bond from the CH group at position 5 of the thiazine ring of a molecule of opposite chirality, forming chains along the a-axis direction. Each of the thiazine rings also participate in C—H...O bonds with the same carbon atom as above, resulting in chains along the b-axis direction, albeit of monochiral type. Adjacent layers are consolidated along the c-axis direction by pairs of parallel hydrogen bonds (C—H...O type) between the nitrophenyl groups of enantiomers. In 2, the two C—H...O hydrogen bonds contribute to chain formation along the b-axis direction. Weak edge-to-face interactions between the aryl groups of neighbouring molecules in 1, and C—H...π interactions between a thiazine ring CH group and a phenyl group of a neighboring molecule in 2 are also observed.
Conversion of degraded agricultural landscapes to a smallholder agroforestry system and carbon sequestration in drylands
Authors: Chiemela Stella Nwawulu , Noulèkoun Florent , Chiemela Chinedum Jachinma , Zenebe Amanuel , Abadi Nigussie , Birhane Emiru
Published: March 2018

Purpose

This paper aims at providing the evidence about how carbon sequestration in terrestrial ecosystems could contribute to the decrease of atmospheric CO2 rates through the adoption of appropriate cropping systems such as agroforestry.

Design/methodology/approach

Stratified randomly selected plots were used to collect data on tree diameter at breast height (DBH). Composite soil samples were collected from three soil depths for soil carbon analysis. Above ground biomass estimation was made using an allometric equation. The spectral signature of each plot was extracted to study the statistical relationship between carbon stock and selected vegetation indices.

Findings

There was a significant difference in vegetation and soil carbon stocks among the different land use/land cover types (P < 0.05). The potential carbon stock was highest in the vegetation found in sparsely cultivated land (13.13 ± 1.84 tons ha−1) and in soil in bushland (19.21 ± 3.79 tons ha−1). Carbon sequestration potential of the study area significantly increased (+127174.5 tons CO2e) as a result of conversion of intensively cultivated agricultural lands to agroforestry systems. The amount of sequestered carbon was found to be dependent on species diversity, tree density and tree size. The vegetation indices had a better correlation with soil and total carbon.

Originality/value

The paper has addressed an important aspect in curbing greenhouse gases in integrated land systems. The paper brings a new empirical insight of carbon sequestration potentials of agroforestry systems with a focus on drylands.
The resilient retail entrepreneur: dynamic capabilities for facing natural disasters
Authors: Martinelli Elisa , Tagliazucchi Giulia , Marchi Gianluca
Published: March 2018

Purpose

The purpose of this paper is to investigate the formative dimensions of organizational resilience – namely dynamic capabilities (DCs) and social capital – displayed by retail entrepreneurs in the face of natural disasters (i.e. the 2012 Emilia earthquake). The paper evaluates social capital and the various types of DCs that support small entrepreneurs’ resilience during three temporal units of analysis: before the earthquake, during the emergency period, and during the recovery process.

Design/methodology/approach

The study was performed by applying a qualitative approach based on two focus groups and a double set of semi-structured interviews administered to a sample of eight small retail entrepreneurs hit by the 2012 Emilia earthquake. Content analysis was then applied.

Findings

The findings show that DCs and social capital are instrumental to enhancing organizational resilience; moreover the contribution of each category of DCs (reconfiguration, leveraging, sensing and interpreting, learning and knowledge integration) and social capital to entrepreneurs’ resilience changes according to the temporal phase of the natural disaster under analysis.

Research limitations/implications

This study will provide small retailer entrepreneurs and public authorities with useful insights on how DCs and social capital can practically support recovery paths at different times in the occurrence of a natural disaster.

Originality/value

This study contributes to the scientific debate on organizational resilience in disaster management, studying it through the lens of DCs and social capital, and analyzing the role of different types of DCs in developing entrepreneurs’ resilience during the various periods of a natural disaster. Moreover, it contributes by applying the concepts of resilience and DCs to a poorly investigated entrepreneurial context such as the retail one.
Prey adaptive behaviour under predation risk modify stoichiometry predictions of predator‐induced stress paradigms
Authors: Guariento Rafael Dettogni , Luttbeg Barney , Carneiro Luciana Silva , Caliman Adriano
Published: March 2018

Prey responses to predation risk can affect multiple phenotypic traits that have significant implications for population‐to‐ecosystem‐level properties. The general stress paradigm (hereafterGSP) proposes integrating the principles of ecological stoichiometry and prey physiological plasticity in response to predation risk to provide an explicit mechanistic framework to evaluate the direct influence of predation risk on ecosystem functioning.

However, theoretical attempts evaluating theGSPhave focused on only one component of phenotypic plasticity, neglecting the fact that multiple phenotypic responses can affect nutrient demand and consumption, and therefore, the overall animal effect on nutrient cycling rates and stoichiometry.

In this study, we used a dynamic state variable model to examine how variation in predation and starvation risk on a landscape of patch types that vary in food quality affects the behavioural and physiological phenotypic responses of prey and the linked nutrient and carbon recycling.

We found that the stress imposed by predation risk promotes prey carbon limitation, which leads to increased nutrient release and carbon uptake due to a stoichiometric mismatch between an animal's demand and food stoichiometry. Such effects can be altered by prey shifting spatially to carbon‐ or nutrient‐rich patches. However, the abilities of prey to cope with new physiological demands can be affected by absolute stress level or the predation risk distribution on a spatially implicit landscape of stoichiometric‐divergent patch type availability. Overall, starvation risk can act as a selective force favouring individuals that maximize their growth, thus reducing their nutrient release, but increasing their exposure to predation risk.

Our results provide an important connection between predator‐induced stress ecology and ecosystem functioning, linking organism nutrition and ecological stoichiometry to fitness outcomes, thus improving our understanding of how non‐consumptive predator effects can scale up to ecosystems.

Aplain language summaryis available for this article.
Response of bluebunch wheatgrass to invasion: Differences in competitive ability among invader‐experienced and invader‐naïve populations
Authors: Gibson Alexis , Nelson Cara R. , Atwater Daniel Z.
Published: March 2018

Invasive species may alter selective pressures on native plant populations. Although there is some evidence that competition with invasive plants may lead to differences in competitive ability between populations that have experienced invasion and those that have not, previous results have varied among species but also among populations of the same species.

We conducted a glasshouse experiment to determine whether there was variation in traits or in ability to tolerate or suppress an invasive species among populations of a common native grass that had different histories of exposure to competition from an invasive species. Specifically, we grew seeds of a native grass (Pseudoroegneria spicata) collected from 14 wild populations (six from invaded populations and eight from uninvaded populations) and a cultivar (Anatone) alone or in competition with the invasive aster (Centaurea stoebe) and measured traits of both species during and at the end of a 100‐day growing period.

Pseudoroegneria spicata seedlings from invader‐experienced populations had more leaves than invader‐naïve populations, and juvenile plants from experienced populations were less affected by competition with C. stoebe than were plants from naïve populations.

There were significant differences in traits among populations at the seedling and juvenile life stages, and at both life stages variation among populations was greater than variation among experience types.

The most predictive traits of P. spicata tolerance to competition were number of leaves (seedling and juvenile stage) and total and root biomass (juvenile only). No traits significantly predicted suppression of C. stoebe.

There was not a significant relationship between a population's suppression of C. stoebe and its tolerance of competition.

Our results suggest that, in P. spicata, invasion selects for larger plants and traits that can influence tolerance of competition. If land managers are interested in identifying highly competitive seed sources for revegetation in invaded areas, both population and invader experience type should be considered. As tolerance and suppression do not appear to be related in P. spicata, seed source selection should be driven by the element of competitive ability (either tolerance or suppression) that is most important to project goals.

A plain language summary is available for this article.
Observed Changes in Climate and Streamflow in the Upper Rio Grande Basin
Authors: Chavarria Shaleene B. , Gutzler David S.
Published: March 2018

Observed streamflow and climate data are used to test the hypothesis that climate change is already affecting Rio Grande streamflow volume derived from snowmelt runoff in ways consistent with model‐based projections of 21st‐Century streamflow. Annual and monthly changes in streamflow volume and surface climate variables on the Upper Rio Grande, near its headwaters in southern Colorado, are assessed for water years 1958–2015. Results indicate winter and spring season temperatures in the basin have increased significantly, April 1 snow water equivalent (SWE) has decreased by approximately 25%, and streamflow has declined slightly in the April–July snowmelt runoff season. Small increases in precipitation have reduced the impact of declining snowpack on trends in streamflow. Changes in the snowpack–runoff relationship are noticeable in hydrographs of mean monthly streamflow, but are most apparent in the changing ratios of precipitation (rain + snow, and SWE) to streamflow and in the declining fraction of runoff attributable to snowpack or winter precipitation. The observed changes provide observational confirmation for model projections of decreasing runoff attributable to snowpack, and demonstrate the decreasing utility of snowpack for predicting subsequent streamflow on a seasonal basis in the Upper Rio Grande Basin.
NHR‐49/HNF4 integrates regulation of fatty acid metabolism with a protective transcriptional response to oxidative stress and fasting
Authors: Goh Grace Y. S. , Winter Johnathan J. , Bhanshali Forum , Doering Kelsie R. S. , Lai Regina , Lee Kayoung , Veal Elizabeth A. , Taubert Stefan
Published: March 2018

Endogenous and exogenous stresses elicit transcriptional responses that limit damage and promote cell/organismal survival. Like its mammalian counterparts, hepatocyte nuclear factor 4 (HNF4) and peroxisome proliferator‐activated receptor α (PPARα), Caenorhabditis elegans NHR‐49 is a well‐established regulator of lipid metabolism. Here, we reveal that NHR‐49 is essential to activate a transcriptional response common to organic peroxide and fasting, which includes the pro‐longevity gene fmo‐2/flavin‐containing monooxygenase. These NHR‐49‐dependent, stress‐responsive genes are also upregulated in long‐lived glp‐1/notch receptor mutants, with two of them making critical contributions to the oxidative stress resistance of wild‐type and long‐lived glp‐1 mutants worms. Similar to its role in lipid metabolism, NHR‐49 requires the mediator subunit mdt‐15 to promote stress‐induced gene expression. However, NHR‐49 acts independently from the transcription factor hlh‐30/TFEB that also promotes fmo‐2 expression. We show that activation of the p38 MAPK, PMK‐1, which is important for adaptation to a variety of stresses, is also important for peroxide‐induced expression of a subset of NHR‐49‐dependent genes that includes fmo‐2. However, organic peroxide increases NHR‐49 protein levels, by a posttranscriptional mechanism that does not require PMK‐1 activation. Together, these findings establish a new role for the HNF4/PPARα‐related NHR‐49 as a stress‐activated regulator of cytoprotective gene expression.
Periodontal disease severity is associated with micronutrient intake
Authors: Luo P‐P , Xu H‐S , Chen Y‐W , Wu S‐P
Published: March 2018

Background

This study aimed to examine if specific micronutrients were associated with periodontal disease using data from the US National Health and Nutrition Examination Survey (NHANES) from 2011 to 2014.

Methods

Participants who were aged 30 years or more and received complete periodontal examinations were included. Regression analyses were performed to determine associations of variables of interest with periodontal disease.

Results

Data of 6415 NHANES participants were included in the analysis. Multivariable analysis revealed that less intake of vitamin A (adjusted odds ratio (aOR) = 1.784), vitamin B1 (aOR = 1.334), vitamin C (aOR = 1.401), vitamin E (aOR = 1.576), iron (aOR = 1.234), folate (aOR = 1.254) and phosphorus (aOR = 1.280) was associated with increased severity of periodontal disease. Compared with the highest level of vitamin D intake, the second highest level of vitamin D intake was associated with lower severity of periodontal disease (aOR = 0.727).

Conclusions

Insufficient intake of vitamin A, B1, C and E, iron, folate and phosphorus was significantly associated with severity of periodontal disease. Results of the present study suggest that the above micronutrients may be increased in the diet or taken as dietary supplements in order to reduce severity of periodontal disease.
A note on the robustness of PBIBD(2)s against breakdown in the event of observation loss
Authors: Godolphin Janet D.
Published: March 2018

Robustness against design breakdown following observation loss is investigated for Partially Balanced Incomplete Block Designs with two associate classes (PBIBD(2)s). New results are obtained which add to the body of knowledge on PBIBD(2)s. In particular, using an approach based on theE‐value of a design, all PBIBD(2)s with triangular and Latin square association schemes are established as having optimal block breakdown number. Furthermore, for group divisible designs not covered by existing results in the literature, a sufficient condition for optimal block breakdown number establishes that all members of some design sub‐classes have this property.
Synchronized Pulsatile Flow With Low Systolic Output From Veno‐Arterial Extracorporeal Membrane Oxygenation Improves Myocardial Recovery After Experimental Cardiac Arrest in Pigs
Authors: Voicu Sebastian , Sideris Georgios , Dillinger Jean‐Guillaume , Yannopoulos Demetris , Deye Nicolas , Kang Chantal , Bonneau Michel , Bartos Jason , Kedra Antoni , Bailliart Sophie , Pasteur‐Rousseau Adrien , Amah Guy , Bonnin Philippe , Callebert Jacques , Henry Patrick , Megarbane Bruno
Published: March 2018

Circulatory failure following cardiac arrest (CA) requires catecholamine support and occasionally veno‐arterial extracorporeal membrane oxygenation (vaECMO). VaECMO‐generated blood flow is continuous and retrograde, increasing ventricular stroke work. Our aim was to assess the benefit of a device generating a pulsatile vaECMO flow synchronized with the heart rhythm lowering systolic vaECMO output on the left ventricular ejection fraction (LVEF) and pulmonary capillary pressure (Pcap) after CA. This experimental randomized study in pigs compared standard nonpulsatile vaECMO (control) with pulsatile synchronized vaECMO (study) group using a pulsatility‐generating device. After sedation and intubation, ventricular fibrillation was induced by pacing. After 10‐min ventricular fibrillation, cardiopulmonary resuscitation was performed for 20 min then vaECMO, defibrillation and 0.15 µg/kg/min intravenous epinephrine infusion were initiated. Hemodynamics, Pcap, LVEF by echocardiography and angiography were measured at baseline and every 30 min after the vaECMO start until vaECMO and epinephrine were stopped (at 120 min), and 30 min later. Baseline hemodynamics did not differ between groups; 120 min after vaECMO initiation, LVEF by echocardiography and angiography was significantly higher in the study than control group 55 ± 19% versus 34 ± 13% (P = 0.042), 50 ± 16% versus 33 ± 12% (P = 0.043), respectively. Pcap decreased from baseline by 4.2 ± 8.6 mm Hg in the study group but increased by 5.6 ± 5.9 mm Hg in the control group (P = 0.043). Thirty minutes later, LVEF remained higher in the study group 44 ± 7% versus 26 ± 11% (P = 0.008) while Pcap did not differ. A synchronized pulsatile device decreasing systolic output from vaECMO improved LVEF and Pcap in a pig model of CA and resuscitation.
Selective Cerebro‐Myocardial Perfusion in Complex Neonatal Aortic Arch Pathology: Midterm Results
Authors: Hoxha Stiljan , Abbasciano Riccardo Giuseppe , Sandrini Camilla , Rossetti Lucia , Menon Tiziano , Barozzi Luca , Linardi Daniele , Rungatscher Alessio , Faggian Giuseppe , Luciani Giovanni Battista
Published: March 2018

Aortic arch repair in newborns and infants has traditionally been accomplished using a period of deep hypothermic circulatory arrest. To reduce neurologic and cardiac dysfunction related to circulatory arrest and myocardial ischemia during complex aortic arch surgery, an alternative and novel strategy for cerebro‐myocardial protection was recently developed, where regional low‐flow perfusion is combined with controlled and independent coronary perfusion. The aim of the present retrospective study was to assess short‐term and mid‐term results of selective and independent cerebro‐myocardial perfusion in neonatal aortic arch surgery. From April 2008 to August 2015, 28 consecutive neonates underwent aortic arch surgery under cerebro‐myocardial perfusion. There were 17 male and 11 female, with median age of 15 days (3–30 days) and median body weight of 3 kg (1.6–4.2 kg), 9 (32%) of whom with low body weight (<2.5 kg). The spectrum of pathologies treated was heterogeneous and included 13 neonates having single‐stage biventricular repair (46%), 7 staged biventricular repair (25%), and 8 single‐ventricle repair (29%). All operations were performed under moderate hypothermia and with a “beating heart and brain.” Average cardiopulmonary bypass time was 131 ± 64 min (42–310 min). A period of cardiac arrest to complete intra‐cardiac repair was required in nine patients (32%), and circulatory arrest in 1 to repair total anomalous pulmonary venous connection. Average time of splanchnic ischemia during cerebro‐myocardial perfusion was 30 ± 11 min (15–69 min). Renal dysfunction, requiring a period of peritoneal dialysis was observed in 10 (36%) patients, while liver dysfunction was noted only in 3 (11%). There were three (11%) early and two late deaths during a median follow‐up of 2.9 years (range 6 months–7.7 years), with an actuarial survival of 82% at 7 years. At latest follow‐up, no patient showed signs of cardiac or neurologic dysfunction. The present experience shows that a strategy of selective and independent cerebro‐myocardial perfusion is safe, versatile, and feasible in high‐risk neonates with complex congenital arch pathology. Encouraging outcomes were noted in terms of cardiac and neurological function, with limited end‐organ morbidity.
THE SCOPE FOR NON‐PROFIT OBJECTIVES IN A MIXED OLIGOPOLY UNDER INTERNATIONAL COMPETITION
Authors: WILLNER Johan , GRÖNBLOM Sonja , KAINU Annina , FLINK Johan
Published: March 2018

We ask how the scope for non‐profit objectives in a state‐owned enterprise (SOE) in a mixed oligopoly changes because of competition from firms in another country. There is no change if costs and demand are given, unless the trade partner is a low‐cost country. However, the scope for non‐profit objectives is limited by the country's relative size if wages are market‐clearing and if workers and firms are stationary, because of reduced competitiveness caused by higher real wage rates. The total surplus is then not affected by the actions of the SOE. International trade does not otherwise reduce the scope for its non‐profit objectives if workers and firms are mobile, but productivity differences might require restrictions in order to avoid a complete relocation of the workforce in either country.
Are China's unit labour costs still competitive? A comparison with ASEAN countries
Authors: Cui Yuming , Lu Changrong
Published: March 2018

The rapidly rising wages and renminbi (RMB) revaluation have attracted lively debate about whether China can continue its rapid economic growth by relying on labour‐intensive goods exports. By comparing the competitiveness in labour costs between China and ASEAN countries, with a particular emphasis on unit labour costs, we find that China has lost its competitiveness in labour costs relative to ASEAN countries. However, our results show that some regions in China, such as the northeast and northwest, still have an advantage relative to ASEAN countries. Thus, China can duplicate Akamatsu's Flying Geese Paradigm by transferring labour‐intensive manufacturing industry from its coastal areas to non‐coastal areas.