bluuebunny/crossref_metadata_2025 huggingface dataset:
A Review on the New and Old Anticoagulants
Authors: Myers Kayla , Lyden Abbie
Published: January 2019

Anticoagulants serve as the primary strategy for the prevention and treatment of both arterial and venous thromboembolism. Anticoagulants disrupt coagulation by interfering at various points in the coagulation cascade. This class of medications does not lyse clots that already exist; rather, it prevents thrombus formation and prevents or slows the extension of an existing clot. For decades, the standard therapy for patients requiring oral anticoagulation was warfarin. However, due to some of the shortcomings of warfarin, including the need for continuous routine monitoring, longtime onset and offset of anticoagulation effect, major food and drug interactions, and high incidence of bleeding, newer agents, termed direct oral anticoagulants, or DOACs were developed. This article will provide a review of clinically important information regarding the most commonly used anticoagulants and their reversal agents.
Synchronization of sensory gamma oscillations promotes multisensory communication
Authors: Misselhorn Jonas , Schwab Bettina C. , Schneider Till R. , Engel Andreas K.
Published: January 2019

Rhythmic neuronal activity in the gamma range is a signature of active cortical processing and its synchronization across distant sites has been proposed as a fundamental mechanism of network communication. While this has been shown within sensory modalities, we tested whether crosstalk between the senses relies on similar mechanisms. In two consecutive experiments, we used a task in which human participants (male and female) matched amplitude changes of concurrent visual, auditory and tactile stimuli. In this task, matching of congruent stimuli was associated with a behavioral benefit compared to matching of incongruent stimuli. In the first experiment, we used source-level analysis of high-density electroencephalography (EEG) and observed that cross-modal matching of congruent inputs was associated with relatively weaker coherence between gamma oscillations in early sensory regions. Next, we used bifocal high-definition transcranial alternating current stimulation (hd-tACS) to manipulate the strength of coupling between sensory cortices. Here, we used a lateralized version of the task in which hd-tACS was applied either ipsilateral or contralateral to the hemisphere receiving sensory stimuli. Ipsilateral gamma, but not alpha stimulation slowed responses to congruent trials whereas responding to incongruent trials was not changed by tACS. We speculate that fast responding to congruent stimuli involves decoupling of sensory gamma oscillations, which was prevented by tACS. These results indicate that synchronization of gamma oscillations promotes direct communication between sensory modalities. The framework of coupled gamma oscillations underlying cortical communication might thus be generalizable from processing within sensory streams to interactions between sensory networks.

Significance statement

Cortical gamma oscillations structure segregated neural activity and were suggested to represent a fundamental mechanism of network communication. While there is ample evidence for the role of long-range gamma synchronization in unisensory processing, its significance in multisensory networks is still unclear. We show that direct interactions between sensory cortices rely on synchronization of gamma band activity. To that end, we carried out two consecutive experiments using state-of-the-art high-density electroencephalography (EEG) and high-definition transcranial alternating current stimulation (hd-tACS). By complementing an observational with an interventional method, we provide novel evidence for the role of synchronized gamma oscillations in multisensory communication.
DisCVR: Rapid viral diagnosis from high-throughput sequencing data
Authors: Maabar Maha , Davison Andrew J. , Palmarini Massimo , Hughes Joseph
Published: January 2019

High-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample k-mers (22 nucleotide sequences) to k-mers from taxonomically labelled viral genomes. DisCVR was validated using published HTS data for 89 clinical samples from adults with upper respiratory tract infections. These samples had been tested for viruses metagenomically and also by real-time polymerase chain reaction assay, which is the standard diagnostic method. DisCVR detected human viruses with high sensitivity (79%) and specificity (100%), and was able to detect mixed infections. Moreover, it produced results comparable to those in a published metagenomic analysis of 177 blood samples from patients in Nigeria. DisCVR has been designed as a user-friendly tool for detecting human viruses from HTS data using computers with limited RAM and processing power, and includes a graphical user interface to help users interpret and validate the output. It is written in Java and is publicly available from http://bioinformatics.cvr.ac.uk/discvr.php.

Issue Section

Resources
Mice adaptively generate choice variability in a deterministic task
Authors: Belkaid Marwen , Bousseyrol Elise , Cuttoli Romain Durand-de , Dongelmans Malou , Duranté Etienne K. , Yahia Tarek Ahmed , Didienne Steve , Hanesse Bernadette , Come Maxime , Mourot Alex , Naudé Jérémie , Sigaud Olivier , Faure Philippe
Published: January 2019

Can our choices just be driven by chance? To investigate this question, we designed a deterministic setting in which mice reinforce non-repetitive choice sequences, and modeled it using reinforcement learning. Mice progressively increased their choice variability using a memory-free, pseudo-random selection, rather than by learning complex sequences. Our results demonstrate that a decision-making process can self-generate variability and randomness even when the rules governing reward delivery are not stochastic.
Mechanical feedback enables catch bonds to selectively stabilize scanning microvilli at T-cell surfaces
Authors: Pullen Robert H. , Abel Steven M.
Published: January 2019

T cells use microvilli to search the surfaces of antigen-presenting cells for antigenic ligands. The active motion of scanning microvilli provides a force-generating mechanism that is intriguing in light of single-molecule experiments showing that applied forces on stimulatory receptor-ligand bonds increase their lifetimes (catch-bond behavior). In this work, we introduce a theoretical framework to explore the motion of a microvillus tip above an antigen-presenting surface when receptors on the tip stochastically bind to ligands on the surface and dissociate from them in a force-dependent manner. Forces on receptor-ligand bonds impact the motion of the microvillus, leading to feedback between binding and microvillar motion. We use computer simulations to show that the average microvillus velocity varies in a ligand-dependent manner, that catch bonds generate responses in which some microvilli almost completely stop while others move with a broad distribution of velocities, and that the frequency of stopping depends on the concentration of stimulatory ligands. Typically, a small number of catch bonds initially immobilize the microvillus, after which additional bonds accumulate and increase the cumulative receptor-engagement time. Our results demonstrate that catch bonds can selectively slow and stabilize scanning microvilli, suggesting a physical mechanism that may contribute to antigen discrimination by T cells.
High-throughput phenotyping with deep learning gives insight into the genetic architecture of flowering time in wheat
Authors: Wang Xu , Xuan Hong , Evers Byron , Shrestha Sandesh , Pless Robert , Poland Jesse
Published: January 2019

Background

Precise measurement of plant traits with precision and speed on large populations has emerged as a critical bottleneck in connecting genotype to phenotype in genetics and breeding. This bottleneck limits advancements in understanding plant genomes and the development of improved, high-yielding crop varieties.

Results

Here we demonstrate the application of deep learning on proximal imaging from a mobile field vehicle to directly score plant morphology and developmental stages in wheat under field conditions. We developed and trained a convolutional neural network with image datasets labeled from expert visual scores and used this ‘breeder-trained’ network to directly score wheat morphology and developmental stages. For both morphological (awned) and phenological (flowering time) traits, we demonstrate high heritability and extremely high accuracy against the ‘ground-truth’ values from visual scoring. Using the traits scored by the network, we tested genotype-to-phenotype association using the deep learning phenotypes and uncovered novel epistatic interactions for flowering time. Enabled by the time-series high-throughput phenotyping, we describe a new phenotype as the rate of flowering and show heritable genetic control.

Conclusions

We demonstrated a field-based high-throughput phenotyping approach using deep learning that can directly score morphological and developmental phenotypes in genetic populations. Most powerfully, the deep learning approach presented here gives a conceptual advancement in high-throughput plant phenotyping as it can potentially score any trait in any plant species through leveraging expert knowledge from breeders, geneticist, pathologists and physiologists.
Cryo-EM structures reveal a conformational change of SOPA1 during mitochondrial inner membrane fusion
Authors: Zhang Danyang , Zhang Yan , Ma Jun , Niu Tongxin , Chen Wenbo , Pang Xiaoyun , Zhai Yujia , Sun Fei
Published: January 2019

Mammalian mitochondrial inner membrane fusion is mediated by OPA1(optic atrophy 1). Under physiological condition, OPA1 undergoes proteolytic processing to form a membrane-anchored long isoform (LOPA1) and a soluble short isoform (SOPA1). A combination of LOPA1 and SOPA1 are required for membrane fusion, however, the relevant mechanism is not well understood. In this study, we investigate the cryo-EM structures of SOPA1 coated liposome tube at nucleotide-free and GTPγS bound states. SOPA1 exhibits a general structure of dynamin family and can assemble onto membrane in a helical array with a building block of dimer and thus induce membrane tubulation. A predicted amphipathic helix is discovered to mediate the tubulation activity of SOPA1. The binding of GTPγS causes a conformational rotation between GTPase domain and stalk region, and then induces a rearrangement of the helical array and an expansion of the tube, which is opposite to the behavior of other dynamin proteins, suggesting a unique role of SOPA1 in the fusion of mitochondrial inner membrane.
Sex differences in brain correlates of STEM anxiety
Authors: Gonzalez Ariel A. , Bottenhorn Katherine L. , Bartley Jessica E. , Hayes Timothy , Riedel Michael C. , Salo Taylor , Bravo Elsa I. , Odean Rosalie , Nazareth Alina , Laird Robert W. , Sutherland Matthew T. , Brewe Eric , Pruden Shannon M. , Laird Angela R.
Published: January 2019

Anxiety is known to dysregulate the salience, default mode, and central executive networks of the human brain, yet this phenomenon has not been fully explored across the STEM learning experience, where anxiety can impact negatively academic performance. Here, we evaluated anxiety and large-scale brain connectivity in 101 undergraduate physics students. We found sex differences in STEM-related but not clinical anxiety, with longitudinal increases in science anxiety observed for both female and male students. Sex-specific impacts of STEM anxiety on brain connectivity emerged, with male students exhibiting distinct inter-network connectivity for STEM and clinical anxiety and female students demonstrating no significant within-sex correlations. Anxiety was negatively correlated with academic performance in sex-specific ways at both pre-and post-instruction. Moreover, math anxiety in male students mediated the relation between default mode-salience connectivity and course grade. Together, these results reveal complex sex differences in the neural mechanisms driving how anxiety impacts STEM learning.
Genome-scale model of Rhodotorula toruloides metabolism
Authors: Tiukova Ievgeniia A , Prigent Sylvain , Nielsen Jens , Sandgren Mats , Kerkhoven Eduard J
Published: January 2019

The basidiomycete red yeast Rhodotorula toruloides is a promising platform organism for production of biooils. We present rhto-GEM, the first genome-scale model of R. toruloides metabolism, that was largely reconstructed using RAVEN toolbox. The model includes 4869 genes, 897 reactions, and 3334 metabolites. Lipid metabolism was described using the SLIMEr formalism, which allows direct integration of lipid class and acyl chain experimental distribution data. The simulation results confirmed that the R. toruloides model provides valid growth predictions on glucose, xylose and glycerol, while prediction of genetic engineering targets to increase production of linolenic acid and triacylglycerols highlighted genes that have previously been successfully used to increase lipid production. This renders rtho-GEM useful for future studies to improve the production of other industrially important oleochemicals including both value-added fatty acids and carotenoids, while it will also be valuable tool for system-wide omics-data analysis in R. toruloides. Expanding the portfolio of GEMs for lipid accumulating fungi contributes to both understanding of metabolic mechanisms of the oleaginous phenotype but also uncover particularities of lipid production machinery in R. toruloides.
Neural pattern similarity differentially affects memory performance of younger and older adults: Age differences in neural similarity and memory
Authors: Sommer Verena R. , Fandakova Yana , Grandy Thomas H. , Shing Yee Lee , Werkle-Bergner Markus , Sander Myriam C.
Published: January 2019

Age-related memory decline is associated with changes in neural functioning but little is known about how aging affects the quality of information representation in the brain. Whereas a long-standing hypothesis of the aging literature links cognitive impairments to less distinct neural representations in old age, memory studies have shown that high similarity between activity patterns benefits memory performance for the respective stimuli. Here, we addressed this apparent conflict by investigating between-item representational similarity in 50 younger (19–27 years old) and 63 older (63–75 years old) human adults (male and female) who studied scene-word associations using a mnemonic imagery strategy while electroencephalography was recorded. We compared the similarity of spatiotemporal frequency patterns elicited during encoding of items with different subsequent memory fate. Compared to younger adults, older adults’ memory representations were more similar to each other but items that elicited the most similar activity patterns early in the encoding trial were those that were best remembered by older adults. In contrast, young adults’ memory performance benefited from decreased similarity between earlier and later periods in the encoding trials, which might reflect their better success in forming unique memorable mental images of the joint picture–word pair. Our results advance the understanding of the representational properties that give rise to memory quality as well as how these properties change in the course of aging.

Significance statement

Declining memory abilities are one of the most evident limitations for humans when growing older. Despite recent advances of our understanding of how the brain represents and stores information in distributed activation patterns, little is known about how the quality of information representation changes during aging and thus affects memory performance. We investigated how the similarity between neural representations relates to subsequent memory quality in younger and older adults. We present novel evidence that the interaction of pattern similarity and memory performance differs between age groups: Older adults benefited from increased similarity during early encoding whereas young adults benefited from decreased similarity between early and later encoding. These results provide insights into the nature of memory and age-related memory deficits.
DNA-foraging bacteria in the seafloor
Authors: Wasmund Kenneth , Pelikan Claus , Watzka Margarete , Richter Andreas , Noel Amy , Hubert Casey R.J. , Rattei Thomas , Hofmann Thilo , Herbold Craig W. , Loy Alexander
Published: January 2019

Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus as well as nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of key DNA-foraging microorganisms in marine sediments are completely unknown. Here we combined microcosm experiments, stable isotope probing and genome-centric metagenomics to study microbial catabolism of DNA and its sub-components in anoxic marine sediments.13C-DNA added to sediment microcosms was degraded within ten days and mineralised to13CO2. Stable isotope probing showed that diverseCandidatusIzemoplasma,Lutibacter, Shewanella, FusibacteraceaeandNitrincolaceaeincorporated DNA-derived13C-carbon. Genomes representative of the13C-labelled taxa were recovered and all encoded enzymatic repertoires for catabolism of DNA. Comparative genomics indicated that DNA can be digested by diverse members of the orderCandidatusIzemoplasmatales (formerTenericutes), which appear to be specialised DNA-degraders that encode multiple extracellular nucleases.Fusibacteraceaelacked genes for extracellular nucleases but utilised various individual purine- and pyrimidine-based molecules, suggesting they ‘cheated’ on liberated sub-components of DNA. Close relatives of the DNA-degrading taxa are globally distributed in marine sediments, suggesting that these poorly understood taxa contribute widely to the key ecosystem function of degrading and recycling DNA in the seabed.
An MRI Atrophy Biomarker Predicts Global Prognosis in Early De Novo Parkinson’s Disease
Authors: Zeighami Yashar , Fereshtehnejad Seyed-Mohammad , Dadar Mahsa , Collins D. Louis , Postuma Ronald B. , Dagher Alain
Published: January 2019

Background

Commonly used neuroimaging biomarkers in Parkinson’s disease (PD) are useful for diagnosis but poor at predicting outcomes. We explored whether an atrophy pattern from whole-brain structural MRI, measured in the drug-naïve early stage, could predict PD prognosis.

Methods

362 de novo PD patients with T1-weighted MRI (n=222 for the main analysis, 140 for the validation analysis) were recruited from the Parkinson’s Progression Markers Initiative (PPMI). We investigated a previously identified PD-specific network atrophy pattern as a potential biomarker of disease severity and prognosis. Progression trajectories of motor function (MDS-UPDRS-part III), cognition (Montreal Cognitive Assessment (MoCA)), and a global composite outcome measure were compared between atrophy tertiles using mixed effect models. The prognostic value of the MRI atrophy measure was compared with 123I ioflupane single photon emission computed tomography, the postural-instability-gait-disturbance score, and cerebrospinal fluid markers.

Findings

After 4.5 years follow-up, PD-specific atrophy network score at baseline significantly predicted change in UPDRS-part III (r=-0.197, p=0.003), MoCA (r=0.253, p=0.0002) and global composite outcome (r=-0.249, p=0.0002). Compared with the 3rd tertile (i.e. least atrophy), the tertile with the highest baseline atrophy (i.e. the 1st tertile) had a 3-point annual faster progression in UPDRS-part III (p=0.012), faster worsening of posture-instability gait scores (+0.21 further annual increase, p<0.0001), faster decline in MoCA (−0.74 further annual decline in MoCA, p=0.0372) and a +0.38 (p=0.0029) faster annual increase in the global composite z-score. All findings were replicated in a validation analysis using 1.5T MRI. By comparison, the other biomarkers were limited in their ability to predict prognosis either in the main or validation analysis.

Interpretation

A PD-specific network atrophy pattern predicts progression of motor, cognitive, and global outcome in PD, and is a stronger predictor of prognosis than any of the other tested biomarkers. Therefore, it has considerable potential as a prognostic biomarker for clinical trials of early PD.
A Silk-Expressed Pectin Methylesterase Confers Cross-Incompatibility Between Wild and Domesticated Strains of Zea mays
Authors: Lu Yongxian , Hokin Samuel A. , Kermicle Jerry L. , Evans Mathew M. S.
Published: January 2019

Despite being members of the same species, some strains of wild teosinte maintain themselves as a distinct breeding population by blocking fertilization by pollen from neighboring maize plants. These teosinte strains may be in the process of evolving into a separate species, since reproductive barriers that block gene flow are critical components in speciation. This trait is conferred by the Teosinte crossing barrier1-s (Tcb1-s) haplotype, making Tcb1 a speciation gene candidate. Tcb1-s contains a female gene that blocks non-self-type pollen and a male function that enables self-type pollen to overcome that block. The Tcb1-female gene encodes a Pectin Methylesterase, implying that modification of the pollen cell wall by the pistil is a key mechanism by which these teosinte females reject foreign (but closely related) pollen.

One sentence summary

The Tcb1-female gene encodes a Pectin Methylesterase that in teosinte silks prevents fertilization by maize pollen.
Prion-like spreading of Alzheimer’s disease within the brain’s connectome
Authors: Fornari Sveva , Schäfer Amelie , Jucker Mathias , Goriely Alain , Kuhl Ellen
Published: January 2019

The prion hypothesis states that misfolded proteins can act as infectious agents that trigger the misfolding and aggregation of healthy proteins to transmit a variety of neurodegenerative diseases. Increasing evidence suggests that pathogenic proteins in Alzheimer’s disease adapt prion-like mechanisms and spread across the brain along an anatomically connected network. Local kinetics models of protein misfolding and global network models of protein diffusion provide valuable insight into the dynamics of prion-like diseases. Yet, to date, these models have not been combined to simulate how pathological proteins multiply and spread across the human brain. Here we model the prion-like spreading of Alzheimer’s disease by combining misfolding kinetics and network diffusion through a connectivity-weighted Laplacian graph created from 418 brains of the Human Connectome Project. The nodes of the graph represent anatomic regions of interest and the edges represent their con-nectivity, weighted by the mean fiber number divided by the mean fiber length. We show that our brain network model correctly predicts the neuropathological pattern of Alzheimer’s disease and captures the key characteristic features of whole brain models at a fraction of their computational cost. To illustrate the potential of brain network modeling in neurodegeneration, we simulate biomarker curves, infection times, and two promising therapeutic strategies to delay the onset of neurodegeneration: reduced production and increased clearance of misfolded protein.
Selection for antibiotic resistance is reduced when embedded in a natural microbial community
Authors: Klümper Uli , Recker Mario , Zhang Lihong , Yin Xiaole , Zhang Tong , Buckling Angus , Gaze William
Published: January 2019

Antibiotic resistance has emerged as one of the most pressing, global threats to public health. In single-species experiments selection for antibiotic resistance occurs at very low antibiotic concentrations. However, it is unclear how far these findings can be extrapolated to natural environments, where species are embedded within complex communities. We competed isogenic strains of Escherichia coli, differing exclusively in a single chromosomal resistance determinant, in the presence and absence of a pig fecal microbial community across a gradient of antibiotic concentration for two relevant antibiotics: gentamicin and kanamycin. We show that the minimal selective concentration was increased by more than one order of magnitude for both antibiotics when embedded in the community. We identified two general mechanisms were responsible for the increase in minimal selective concentration: an increase in the cost of resistance and a protective effect of the community for the susceptible phenotype. These findings have implications for our understanding of the evolution and selection of antibiotic resistance, and can inform future risk assessment efforts on antibiotic concentrations.
Intracortical neural activity distal to seizure-onset-areas predicts human focal seizures
Authors: Proix Timothée , Aghagolzadeh Mehdi , Madsen Joseph R , Cosgrove Rees , Eskandar Emad , Hochberg Leigh R. , Cash Sydney S. , Truccolo Wilson
Published: January 2019

The apparent unpredictability of epileptic seizures has a major impact in the quality of life of people with pharmacologically resistant seizures. Here, we present initial results and a proof-of-concept of how focal seizures can be predicted early in advance based on intracortical signals recorded from small neocortical patches away from identified seizure onset areas. We show that machine learning algorithms can discriminate between interictal and preictal periods based on multiunit activity (i.e. thresholded action potential counts) and multi-frequency band local field potentials recorded via 4 X 4 mm2microelectrode arrays. Microelectrode arrays were implanted in 5 patients undergoing neuromonitoring for resective surgery. Post-implant analysis revealed arrays were outside the seizure onset areas. Preictal periods were defined as the 1-hour period leading to a seizure. A 5-minute gap between the preictal period and the putative seizure onset was enforced to account for potential errors in the determination of actual seizure onset times. We used extreme gradient boosting and long short-term memory networks for prediction. Prediction accuracy based on the area under the receiver operating characteristic curves reached 90% for at least one feature type in each patient. Importantly, successful prediction could be achieved based exclusively on multiunit activity. This result indicates that preictal activity in the recorded neocortical patches involved not only subthreshold postsynaptic potentials, perhaps driven by the distal seizure onset areas, but also neuronal spiking in distal recurrent neocortical networks. Beyond the commonly identified seizure onset areas, our findings point to the engagement of large-scale neuronal networks in the neural dynamics building up toward a seizure. Our initial results obtained on currently available human intracortical recordings warrant new studies on larger datasets, and open new perspectives for seizure prediction and control by emphasizing the contribution of multiscale neural signals in large-scale neuronal networks.
Long-term fish assemblages of the Ohio River: altered trophic and life history strategies with hydrologic alterations and landuse modifications
Authors: Pyron Mark , Mims Meryl C. , Minder Mario M. , Shields Robert C. , Chodkowski Nicole , Artz Caleb C.
Published: January 2019

Long-term monitoring of species assemblages provides a unique opportunity to test hypotheses regarding environmentally-induced directional trajectories of freshwater species assemblages. We used 57 years of lockchamber fish rotenone and boat electrofishing survey data (1957-2014) collected by the Ohio River Valley Water Sanitation Commission (ORSANCO) to test for directional trajectories in taxonomy, trophic classifications, and life history strategies of freshwater fish assemblages in the Ohio River Basin. We found significant changes in taxonomic and trophic composition of freshwater fishes in the Ohio River Basin. Annual species richness varied from 31 to 90 species and generally increased with year. Temporal trajectories were present for taxonomic and trophic assemblages. Assemblage structure based on taxonomy was correlated with land use change (decrease in agriculture and increase in forest). Taxonomic assemblage structure was also correlated with altered hydrology variables of increased minimum discharge, decreased fall rate, and increased rise rate. Trophic composition of fish catch correlated with land use change (decrease in agriculture and increase in forest) and altered hydrology. Altered hydrology of increased minimum discharge, increased fall discharge, decreased base flows, and increased number of high pulse events was correlated with increased counts of herbivore-detritivores and decreased counts of piscivores and planktivores. We did not find directional changes in life history composition. We hypothesized a shift occurred from benthic to phytoplankton production throughout the basin that may have decreased secondary production of benthic invertebrates. This may also be responsible for lower trophic position of invertivore and piscivore fishes observed in other studies.
An analytical solution for consolidation of PVD-installed deposit considering nonlinear distribution of hydraulic conductivity and compressibility
Authors: Nguyen Ba-Phu , Kim Yun-Tae
Published: January 2019

Purpose

It is well known that the prefabricated vertical drain (PVD) installation process generates a significant soil disturbance around PVD. This disturbed zone significantly affects the rate of settlement and excess pore pressure dissipation. However, the characteristics of these zones were still uncertain and difficult to quantify; there remains large discrepancy among researchers. This study aims to develop a simple analytical solution for radial consolidation analysis of PVD-installed deposit considering mandrel-induced disturbance.

Design/methodology/approach

The proposed solution takes into account the nonlinear distributions of both horizontal hydraulic conductivity and compressibility toward the drain. The proposed solution was applied to analyze field behavior of test embankment in New South Wales, Australia.

Findings

Both effects significantly increased the time required to achieve a certain degree of consolidation. The effect of hydraulic conductivity on the consolidation rate was more significant than the effect of compressibility variation. And, the increased compressibility in the soil-disturbed zone due to mandrel installation significantly increased vertical strain of the PVD-improved soil deposit. The predicted results using the proposed analytical solution were in good agreement with the field measurements.

Practical implications

A geotechnical engineer could use the proposed analytical solution to predict consolidation behavior of drainage-installed ground.

Originality/value

Consolidation behavior of PVD-installed ground could be reasonably predicted by using the proposed solution with considering variations of both hydraulic conductivity and compressibility due to PVD installation.
Cytosolic DNA‐sensing immune response and viral infection
Authors: Abe Takayuki , Marutani Yuki , Shoji Ikuo
Published: January 2019

How host cells recognize many kinds of RNA and DNA viruses and initiate innate antiviral responses against them has not yet been fully elucidated. Over the past decade, investigations into the mechanisms underlying these antiviral responses have focused extensively on immune surveillance sensors that recognize virus‐derived components (such as lipids, sugars and nucleic acids). The findings of these studies have suggested that antiviral responses are mediated by cytosolic or intracellular compartment sensors and their adaptor molecules (e.g., TLR, myeloid differentiation primary response 88, retinoic acid inducible gene‐I, IFN‐β promoter stimulator‐1, cyclic GMP‐AMP synthase and stimulator of IFN genes axis) for the primary sensing of virus‐derived nucleic acids, leading to production of type I IFNs, pro‐inflammatory cytokines and chemokines by the host cells. Thus, host cells have evolved an elaborate host defense machinery to recognize and eliminate virus infections. In turn, to achieve sustained viral infection and induce pathogenesis, viruses have also evolved several counteracting strategies for achieving immune escape by targeting immune sensors, adaptor molecules, intracellular kinases and transcription factors. In this review, we discuss recent discoveries concerning the role of the cytosolic nucleic acid‐sensing immune response in viral recognition and control of viral infection. In addition, we consider the regulatory machinery of the cytosolic nucleic acid‐sensing immune response because these immune surveillance systems must be tightly regulated to prevent aberrant immune responses to self and non‐self‐nucleic acids.
Dominance of wine Saccharomyces cerevisiae strains over S. kudriavzevii in industrial fermentation competitions is related to an acceleration of nutrient uptake and utilization
Authors: Alonso‐del‐Real Javier , Pérez‐Torrado Roberto , Querol Amparo , Barrio Eladio
Published: January 2019

Grape must is a sugar‐rich habitat for a complex microbiota which is replaced by Saccharomyces cerevisiae strains during the first fermentation stages. Interest on yeast competitive interactions has recently been propelled due to the use of alternative yeasts in the wine industry to respond to new market demands. The main issue resides in the persistence of these yeasts due to the specific competitive activity of S. cerevisiae. To gather deeper knowledge of the molecular mechanisms involved, we performed a comparative transcriptomic analysis during fermentation carried out by a wine S. cerevisiae strain and a strain representative of the cryophilic S. kudriavzevii, which exhibits high genetic and physiological similarities to S. cerevisiae, but also differences of biotechnological interest. In this study, we report that transcriptomic response to the presence of a competitor is stronger in S. cerevisiae than in S. kudriavzevii. Our results demonstrate that a wine S. cerevisiae industrial strain accelerates nutrient uptake and utilization to outcompete the co‐inoculated yeast, and that this process requires cell‐to‐cell contact to occur. Finally, we propose that this competitive phenotype evolved recently, during the adaptation of S. cerevisiae to man‐manipulated fermentative environments, since a non‐wine S. cerevisiae strain, isolated from a North American oak, showed a remarkable low response to competition.
Reframing health and illness: a collaborative autoethnography on the experience of health and illness transformations in the life course
Authors: Nowakowski Alexandra C.H. , Sumerau J.E.
Published: January 2019

In this collaborative autoethnography, we examine the processes whereby people may reframe their interpretations and understandings of health and illness as a result of new diagnostic information. In so doing, we utilise the first author's experience receiving a conclusive diagnosis of cystic fibrosis after years of misdiagnosis to outline some ways changes in diagnosis facilitate shifts in illness management, the nature of health and illness and the experience of the self in relation to health and medicine. Furthermore, we discuss the ways this case reveals the importance of examining and comparing the social construction and transformation of health and illness within and between different individual and collective lived experiences over time. In closing, we draw out theoretical and empirical implications for understanding transformations in the nature of health and illness over the life course as well as future directions for research investigating shifts in illness management and understanding over time (A virtual abstract of this paper is available to view at:https://www.youtube.com/channel/UC_979cmCmR9rLrKuD7z0ycA).
Physicalizations of Big Data in Ethnographic Context
Authors: BUUR JACOB , MOSLEH SARA SAID , FYHN CHRISTINA
Published: January 2019

With the Big Data hype, making digital data accessible and relatable for non‐data experts is becoming an increasing challenge. In this paper we suggest Data Physicalization as a novel approach to facilitate conversations with collaborators about the meaning of data. While this challenge has been approached with data visualizations before, we propose that Data Physicalizations can bring stronger engagement and even more depth to the data than visualizations can offer. Based on four design examples, we investigate how data, when made physical, can be used to instigate valuable reflections between field researchers and non‐data experts, and can serve as a platform for design. In all cases we worked with Data Physicalization to enhance our own understanding of the field, to engage collaborators in sense‐making, and to move towards design proposals. In the concluding section we discuss the intricate process of developing such Data Physicalizations and suggest traits that make them successful.
Evidence outside the Frame: Interpreting Participants’ “Framing” of Information when Using Participatory Photography
Authors: STEAGER TABITHA
Published: January 2019

This paper discusses the benefits and challenges of participatory photography as ethnographic evidence and how as researchers we can “read” the evidence our participants create. Drawing on examples from an ethnographic study examining concepts and constructions of community on Salt Spring Island, British Columbia, I examine how we can interrogate photographs as data rather than factual evidence. Adages such as “the camera doesn't lie” support the view of photography as a purveyor of truth. Photos accompanying journalistic dispatches from far‐flung outposts around the world are seen as authentic evidence of real‐world situations. Amateur videos of people's life experiences are filmed on smart phones and then posted to YouTube to be taken as authentic representations of life events. Early ethnographic uses celebrated photography as the ultimate tool for showing that anthropologists had actually “been there,” displaying the exoticism of other cultures in factual black and white. However, photography has never been a simple representation of the truth—it is not cameras that make photos but people, with all their personal quirks, cultural beliefs, and subjective experiences in tow. Photographs always provide at least two kinds of evidence—what is inside the frame and what is outside the frame. As researchers working with participatory photography, one of our roles is to determine the importance of what is outside the frame. We must ask whether this unseen evidence is as valid—or more so?—than what participants keep inside the frame. In the age of Snapchat, Instagram and other social media, researchers need to interrogate participant‐created photography carefully and methodically. We must question how we interpret photographic evidence that has been manipulated by its creators and how that manipulation affects our interpretations of the evidence. Participant‐created photographs add valuable depth and complexity to ethnographic research but we need to ask how participants may conceptualize their photographic creations and how context—culture, socioeconomic status, gender, location, etc—impacts the evidence participants create. And in turn, how those same contexts influence our interpretations of participatory photographic evidence.
Ethanol Extract of Chinese Propolis Attenuates Early Diabetic Retinopathy by Protecting the Blood–Retinal Barrier in Streptozotocin‐Induced Diabetic Rats
Authors: Shi Yi‐zhen , Liu Yi‐chen , Zheng Yu‐fei , Chen Yi‐fan , Si Juan‐juan , Chen Min‐li , Shou Qi‐yang , Zheng Huo‐qing , Hu Fu‐liang
Published: January 2019

Propolis has been shown to reduce the level of blood glucose and suppress the histopathological changes in diabetics. However, it still remains unknown if propolis has a similar effect on diabetic retinopathy (DR). Our study aimed to evaluate the effect of the ethanol extract of Chinese propolis (EECP) on early DR in streptozotocin (STZ)‐induced diabetic rats. EECP was given to diabetic rats by oral intubation for 12 weeks. The concentrations of fasting blood glucose (FBG), glycated hemoglobin (HbA1c), malondialdehyde (MDA), reactive oxygen species (ROS), and reactive nitrogen species (RNS) were measured. Pathological examinations, including hematoxylin and eosin (HE) staining, transmission electron microscopy (TEM), and immunofluorescence, were also conducted to provide further evidence of EECP's effect on early DR. EECP was able to attenuate diabetes via directly decreasing the levels of FBG and HbA1c, which also resulted in the reduction of MDA, ROS, and RNS. Furthermore, EECP could protect against the damages of photoreceptor cells, as well as retinal thickening. And the inhibition of blood–retinal barrier (BRB) leakage was also observed in EECP‐treated diabetic rats, along with the inhibition the loss of tight junction proteins (occludin, ZO‐1). These results suggest that EECP has an ameliorating effect on early DR by inhibition of blood–retinal barrier breakdown.

Practical Application

This study sheds light on the protective effect of the ethanol extract of Chinese propolis on early diabetic retinopathy and the molecular actions underlying the inhibition of blood–retinal barrier breakdown. Our study suggests that ethanol extract of Chinese propolis can be considered as a potential therapeutic agent in the treatment of early diabetic retinopathy.
Ultralong telomeres shorten with age in nestling great tits but are static in adults and mask attrition of short telomeres
Authors: Atema Els , Mulder Ellis , van Noordwijk Arie J. , Verhulst Simon
Published: January 2019

Telomere length (TL) is increasingly being used as a biomarker of senescence, but measuring telomeres remains a challenge. Within tissue samples, TL varies between cells and chromosomes. Class I telomeres are (presumably static) interstitial telomeric sequences, while terminal telomeres have been divided in shorter (Class II) telomeres and ultralong (Class III) telomeres, and the presence of the latter varies strongly between species. Class II telomeres typically shorten with age, but little is known of Class III telomere dynamics. Using multiple experimental approaches, we show great tits to have ultralong telomeres, and we investigated age effects on Class II and III telomeres using a longitudinal approach (our method excludes Class I telomeres). In adults, TL averaged over the whole distribution did not significantly change with age. However, more detailed analyses showed that Class II TL did shorten with age, and, as in other species, the longest Class II telomeres within individuals shortened more quickly with age. In contrast, Class III TL did not shorten with age within individual adults. Surprisingly, we found the opposite pattern in nestlings: Class III TL shortened significantly with age, while the age effect on Class II TL was close to zero. Thus, Class III TL may provide information on developmental history, while Class II TL provides information on telomere dynamics in adulthood. These findings have practical implications for telomere studies and raise the interesting question of what causes variation in TL dynamics between chromosomes within individuals and how this is related to development.
Feminist Economics: Theoretical and Political Dimensions
Authors: Agenjo‐Calderón Astrid , Gálvez‐Muñoz Lina
Published: January 2019

Feminist economics is a school of economic thought and political action that gained important visibility during the 1990s, although its origins can be dated back to the mid‐19th century. Since then, feminist economics has developed its own concepts, analytical frameworks, and methodologies. With gender as a central category, it seeks a more integral and humane comprehension of the economy and of the processes of inclusion and exclusion taking place in it. In addition, feminist economics has grown into a political practice that aims at improving the functioning of the economic system so that all people can have access to a dignified life on the basis of equality. This article presents a general systematization of these theoretical and political dimensions, particularly focusing on the critique of the neoclassical paradigm and its political correlates. We connect the epistemological, methodological, and conceptual contributions of feminist economics, as well as its propositions for transformative action, to specific debates on economic issues, such as the ecological emergency, crisis and austerity, the commodification of life, and the liberalization of trade.
Pru p 7 sensitization is a predominant cause of severe, cypress pollen‐associated peach allergy
Authors: Klingebiel Caroline , Chantran Yannick , Arif‐Lusson Rihane , Ehrenberg Angelica E. , Östling Jonas , Poisson Alain , Liabeuf Valérie , Agabriel Chantal , Birnbaum Joëlle , Porri Françoise , Sarrat Anne , Apoil Pol‐André , Vivinus Mylène , Garnier Lorna , Chiriac Anca Mirela , Caimmi Davide‐Paolo , Bourrain Jean‐Luc , Demoly Pascal , Guez Stéphane , Boralevi Franck , Lovato Bertrand , Palussière Céline , Leroy Sylvie , Bourrier Thierry , Giovannini‐Chami Lisa , Gouitaa Marion , Aferiat‐Derome Agnès , Charpin Denis , Sofalvi Tünde , Cabon‐Boudard Isabelle , Massabie‐Bouchat Yann‐Patrick , Hofmann Bernard , Bonardel Nathalie , Dron‐Gonzalvez Mireille , Sterling Benoît , Carsin Ania , Vivinus Serge , Poitevin Bernard , Nicolau Laureline , Liautard Geneviève , Soler Christophe , Mezouar Soraya , Annesi‐Maesano Isabella , Mège Jean‐Louis , Lidholm Jonas , Vitte Joana ,   and the ANAFORCAL and AllergoBioNet Networks
Published: January 2019

Background

Peach is a common elicitor of food allergic reactions. Peach‐induced immediate reactions may occur as benign pollen‐food syndromes, usually due to birch pollen‐related PR‐10 cross‐reactivity in temperate climates, and as potentially severe primary food allergies, predominantly related to nsLTP Pru p 3 in Mediterranean regions. The newly described peach allergen Pru p 7 has gained recent attention as a potential peach allergy severity marker. Sensitization to Pru p 7 and its allergenic homologues of the gibberellin‐regulated protein family occurs in areas with high Cupressaceae tree pollen exposure.

Objective

We sought to investigate the distribution, clinical characteristics and molecular associations of Pru p 7 sensitization among subjects with suspected peach allergy in different regions of France.

Methods

Subjects with suspected peach allergy (n = 316) were included. Diagnostic work‐up was performed according to current guidelines, including open food challenge when required. IgE antibody measurements and competition experiments were performed using the ImmunoCAP assay platform.

Results

Sensitization to Pru p 7 was present in 171 (54%) of all subjects in the study and in 123 of 198 (62%) diagnosed as peach allergic, more than half of whom were sensitized to no other peach allergen. Frequency and magnitude of Pru p 7 sensitization were associated with the presence of peach allergy, the clinical severity of peach‐induced allergic reactions and the level of cypress pollen exposure. Cypress pollen extract completely outcompeted IgE binding to Pru p 7. Pru p 7 was extremely potent in basophil activation tests.

Conclusion and Clinical Relevance

A subtype of Cupressaceae pollinosis, characterized by Pru p 7 sensitization, can be an underlying cause of severe peach allergy.