bluuebunny/crossref_metadata_2025 huggingface dataset:
The ultrastructure ofShewanella oneidensisMR-1 nanowires revealed by electron cryo-tomography
Authors: Subramanian Poorna , Pirbadian Sahand , El-Naggar Mohamed Y. , Jensen Grant J.
Published: January 2017

Bacterial nanowires have garnered recent interest as a proposedExtracellularElectronTransfer (EET) pathway that links the bacterial electron transport chain to solid-phase electron acceptors away from the cell.In vivofluorescenceLightMicroscopy (fLM) imaging recently showed thatShewanella oneidensisMR-1 nanowires are extensions of the outer membrane that contain EET components. However, their fine structure and distribution of cytochrome electron carriers remained unclear, making it difficult to evaluate the electron transport mechanism along the nanowires. Here, we report high-resolution images of nanowires usingElectronCryo-Tomography (ECT). We developed a robust method for fLM imaging of nanowire growth onelectron microscopy grids and used correlative light and electron microscopy to identify and image the same nanowires by ECT. Our results confirm thatS. oneidensisnanowires are outer membrane extensions, and further reveal that nanowires are dynamic chains of interconnectedOuterMembraneVesicles (OMVs) with variable dimensions, curvature, and extent of tubulation. Junction densities that potentially stabilize OMV chains are seen between neighboring vesicles in cryotomograms. Our ECT results also provide the first hints of the positions and packing of periplasmic and outer membrane proteins consistent with cytochromes. We observe tight packing of putative cytochromes along lateral patches that extend tens of nanometers, but not across the micrometer scale of whole nanowires. We therefore propose that electron transfer along nanowires involves a combination of direct hopping and diffusive events that link neighboring redox proteins.
Longitudinal samples of bacterial genomes potentially bias evolutionary analyses
Authors: Arnold B.J. , Hanage W.P.
Published: January 2017

Samples of bacteria collected over a period of time are attractive for several reasons, including the ability to estimate the molecular clock rate and to detect fluctuations in allele frequencies over time. However, longitudinal datasets are occasionally used in analyses that assume samples were collected contemporaneously. Using both simulations and genomic data fromNeisseria gonorrhoeae, Streptococcus mutans, Campylobacter jejuni, and Helicobacter pylori, we show that longitudinal samples (spanning more than a decade in real data) may suffer from considerable bias that inflates estimates of recombination and the number of rare mutations in a sample of genomic sequences. While longitudinal data are frequently accounted for using the serial coalescent, many studies use other programs or metrics, such as Tajima’s D, that are sensitive to these sampling biases and contain genomic data collected across many years. Notably, longitudinal samples from a population of constant size may exhibit evidence of exponential growth. We suggest that population genomic studies of bacteria should routinely account for temporal diversity in samples or provide evidence that longitudinal sampling bias does not affect conclusions.
Word and sentence embedding tools to measure semantic similarity of Gene Ontology terms by their definitions
Authors: Duong Dat , Ahmad Wasi Uddin , Eskin Eleazar , Chang Kai-Wei , Li Jingyi Jessica
Published: January 2017

The Gene Ontology (GO) database contains GO terms that describe biological functions of genes. Previous methods for comparing GO terms have relied on the fact that GO terms are organized into a tree structure. Under this paradigm, the locations of two GO terms in the tree dictate their similarity score. In this paper, we introduce two new solutions for this problem, by focusing instead on the definitions of the GO terms. We apply neural network based techniques from the natural language processing (NLP) domain. The first method does not rely on the GO tree, whereas the second indirectly depends on the GO tree. In our first approach, we compare two GO definitions by treating them as two unordered sets of words. The word similarity is estimated by a word embedding model that maps words into an N-dimensional space. In our second approach, we account for the word-ordering within a sentence. We use a sentence encoder to embed GO definitions into vectors and estimate how likely one definition entails another. We validate our methods in two ways. In the first experiment, we test the model’s ability to differentiate a true protein-protein network from a randomly generated network. In the second experiment, we test the model in identifying orthologs from randomly-matched genes in human, mouse, and fly. In both experiments, a hybrid of NLP and GO-tree based method achieves the best classification accuracy.
Model communities hint to promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria
Authors: Garcia Sarahi L , Buck Moritz , Hamilton Joshua J. , Wurzbacher Christian , Rosenblad Magnus Alm , McMahon Katherine D. , Grossart Hans-Peter , Warnecke Falk , Eiler Alexander
Published: January 2017

Free-living microorganisms with streamlined genomes are very abundant in the environment. Genome streamlining results in losses in the cell’s biosynthetic potential generating physiological dependencies between microorganisms. However, there exists no consensus on the specificity of these microbial associations. To verify specificity and extent of these associations, mixed cultures were established from three different freshwater environments. These cultures contained free-living streamlined organisms lacking multiple biosynthetic pathways. Among the co-occurring members of the mixed cultures, there was no clear recurring pattern of metabolic complementarity and dependencies. This, together with weak temporal co-occurrence patterns observed using time-series metagenomics, suggests that free-living freshwater bacteria form loose and unspecific cooperative loops. Comparative genomics suggests that the proportion of accessory genes in populations of streamlined bacteria allows for flexibility in interaction partners. Altogether this renders these free-living bacterial lineages functionally versatile despite their streamlining tendencies.
No evidence for avoidance of black rat scent by the presumably less competitive Natal multimammate mouse in a choice experiment
Authors: Cuypers Laura N. , Cuypers Wim L. , Gildemyn-Blomme Amélie , Abraham Laura , Aertbeliën Senne , Massawe Apia W. , Borremans Benny , Gryseels Sophie , Leirs Herwig
Published: January 2017

In Africa, indigenous multimammate mice (Mastomys natalensis) only appear to live commensally in houses when invasive black rats (Rattus rattus) are absent, yet little is known about the underlying mechanism. Avoidance through smell may cause the absence ofM. natalensisfrom areas occupied byR. rattus, but this hypothesis has not yet been tested. We conducted a Y-maze choice experiment where 15M. natalensiswere offered a choice between corridors containing conspecific scent,R. rattusscent, and a control scent. Residence time in theR. rattuscorridor was greater than that in the control corridor but equal to that in theM. natalensiscorridor, suggesting that multimammate mice do not actively avoid the scent of their invasive competitor.
Marchantialiverworts as aproxyto plants basal microbiomes
Authors: Alcaraz Luis D. , Peimbert Mariana , Dorantes-Acosta Ana E. , Bowman John L. , Arteaga-Vázquez Mario A.
Published: January 2017

Microbiomes influence plant development, establishment, nutrient acquisition, pathogen defense, and the myriad of roles that ultimately impacts plant health. Plants microbiome are shaped through interactions between the microbes (ranging from cooperative functions to chemical warfare) and a selection process entailed by the host plants that distinguishes between pathogens, commensals, symbionts and transient bacteria. The soil is a primary source for microbes colonizing plants, along with other environmental sources including rain and interactions with other organisms. In this work, we explore the microbiomes through massive sequencing of the 16S rRNA gene in the eldest terrestrial plants:Marchantialiverworts. We compared microbiomes fromM. polymorpha, andM. paleaceaplants collected in the wild and their soils, all together luckily in the same geographical location (sympatric) thus reducing geographic effects; and also from plants grown in vitro and established from gemmae obtained from the same population of wild plants. Qualitative and quantitative microbiome analysis allowed us to identify microbes conserved in both native and in vitroMarchantiaspecies. WhileM. polymorphanative plants microbiomes richness is reduced about M.paleacea, containing almost half of the Operative Taxonomic Units (OTUs) observed inM. paleacea, M. polymorphagrown in vitro exhibits larger OTUs. This diversity differences might be the result of impairment to recognize their microbial partners and being an open niche for opportunistic bacteria. The main OTUs inMarchantiamicrobiomes were assigned to the genera:Methylobacterium, Rhizobium, Paenibacillus, Lysobacter, Pirellula, Steroidobacter, andBryobacter. The assigned genera correspond to bacteria capable of plant-growth promotion, complex exudates degradation, nitrogen fixation, methylotrophs, and disease-suppressive bacteria, all hosted in the relatively simple anatomy of the plant that provides refuge on their surfaces, rhizoids, and multiple gas chambers that work as specialized niches for different bacterial groups.Marchantiais a promising model to study not only long-term relationships between plants and their microbes but also the transgenerational impact of microbiomes because ofMarchantialong 450 million years under climate change conditions testing microbiome configurations.
A computational toolbox and step-by-step tutorial for the analysis of neuronal population dynamics in calcium imaging data
Authors: Romano Sebastián A. , Pérez-Schuster Verónica , Jouary Adrien , Candeo Alessia , Boulanger-Weill Jonathan , Sumbre Germán
Published: January 2017

The development of new imaging and optogenetics techniques to study the dynamics of large neuronal circuits is generating datasets of unprecedented volume and complexity, demanding the development of appropriate analysis tools. We present a tutorial for the use of a comprehensive computational toolbox for the analysis of neuronal population activity imaging. It consists of tools for image pre-processing and segmentation, estimation of significant single-neuron single-trial signals, mapping event-related neuronal responses, detection of activity-correlated neuronal clusters, exploration of population dynamics, and analysis of clusters’ features against surrogate control datasets. They are integrated in a modular and versatile processing pipeline, adaptable to different needs. The clustering module is capable of detecting flexible, dynamically activated neuronal assemblies, consistent with the distributed population coding of the brain. We demonstrate the suitability of the toolbox for a variety of calcium imaging datasets, and provide a case study to explain its implementation.
Joint estimation of relatedness coefficients and allele frequencies from ancient samples
Authors: Theunert Christoph , Racimo Fernando , Montgomery Slatkin
Published: January 2017

We develop and test a method to address whether DNA samples sequenced from a group of fossil hominin bone or teeth fragments originate from the same individual or from closely related individuals. Our method assumes low amounts of retrievable DNA, significant levels of sequencing error and contamination from one or more present-day humans. We develop and implement a maximum likelihood method that estimates levels of contamination, sequencing error rates and pairwise relatedness co-efficients in a set of individuals. We assume there is no reference panel for the ancient population to provide allele and haplotype frequencies. Our approach makes use of single nucleotide polymorphisms and does not make assumptions about the underlying demographic model. By artificially mating individual genomes from the 1000 Genomes Project, we determine the numbers of individuals at a given genomic coverage that are required to detect different levels of genetic relatedness with confidence.
De NovoPacBio long-read and phased avian genome assemblies correct and add to genes important in neuroscience research
Authors: Korlach Jonas , Gedman Gregory , Kingan Sarah B. , Chin Chen-Shan , Howard Jason , Cantin Lindsey , Jarvis Erich D.
Published: January 2017

Reference quality genomes are expected to provide a resource for studying gene structure and function. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional cloning efforts for the correct sequences. A promising solution to this problem is long-read sequencing. Here we tested PacBio-based long-read sequencing and diploid assembly for potential improvements to the Sanger-based intermediate-read zebra finch reference and Illumina-based short-read Anna’s hummingbird reference, two vocal learning avian species widely studied in neuroscience and genomics. With DNA of the same individuals used to generate the reference genomes, we generated diploid assemblies with the FALCON-Unzip assembler, resulting in contigs with no gaps in the megabase range (N50s of 5.4 and 7.7 Mb, respectively), and representing 150-fold and 200-fold improvements over the current zebra finch and hummingbird references, respectively. These long-read assemblies corrected and resolved what we discovered to be misassemblies, including due to erroneous sequences flanking gaps, complex repeat structure errors in the references, base call errors in difficult to sequence regions, and inaccurate resolution of allelic differences between the two haplotypes. We analyzed protein-coding genes widely studied in neuroscience and specialized in vocal learning species, and found numerous assembly and sequence errors in the reference genes that the PacBio-based assemblies resolved completely, validated by single long genomic reads and transcriptome reads. These findings demonstrate, for the first time in non-human vocal learning species, the impact of higher quality, phased and gap-less assemblies for understanding gene structure and function.
Understanding sequence conservation with deep learning
Authors: Li Yi , Quang Daniel , Xie Xiaohui
Published: January 2017

Motivation

Comparing the human genome to the genomes of closely related mammalian species has been a powerful tool for discovering functional elements in the human genome. Millions of conserved elements have been discovered. However, understanding the functional roles of these elements still remain a challenge, especially in noncoding regions. In particular, it is still unclear why these elements are evolutionarily conserved and what kind of functional elements are encoded within these sequences.

Results

We present a deep learning framework, called DeepCons, to uncover potential functional elements within conserved sequences. DeepCons is a convolutional neural net (CNN) that receives a short segment of DNA sequence as input and outputs the probability of the sequence of being evolutionary conserved. DeepCons utilizes hundreds of convolution kernels to detect features within DNA sequences, and automatically learns these kernels after training the CNN model using 887,577 conserved elements and a similar number of nonconserved elements in the human genome. On a balanced test dataset, DeepCons can achieve an accuracy of 75% in determining whether a sequence element is conserved or not, and the area under the ROC curve of 0.83, based on information from the human genome alone. We further investigate the properties of the learned kernels. Some kernels are directly related to well-known regulatory motifs corresponding to transcription factors. Many kernels show positional biases relative to transcriptional start sites or transcription end sites. But most of discovered kernels do not correspond to any known functional element, suggesting that they might represent unknown categories of functional elements. We also utilize DeepCons to annotate how changes at each individual nucleotide might impact the conservation properties of the surrounding sequences.

Availability

The source code of DeepCons and all the learned convolution kernels in motif format is publicly available online athttps://github.com/uci-cbcl/DeepCons.

Contact

xhx@ics.uci.edu
LET-99-dependent spatial restriction of active force generators makes spindle’s position robust
Authors: Bouvrais H. , Chesneau L. , Pastezeur S. , Delattre M. , Pécréaux J.
Published: January 2017

During the asymmetric division of theCaenorhabditis elegansnematode zygote, the polarity cues distribution and daughter cell fates depend on the correct positioning of the mitotic spindle, which results from both centering and cortical pulling forces. Revealed by anaphase spindle rocking, these pulling forces are regulated by the force generator dynamics, which are in turn consequent of mitotic progression. We found a novel, additional, regulation of these forces by the spindle position. It controls astral microtubule availability at the cortex, on which theactiveforce generators can pull. Importantly, this positional control relies on the polarity dependent LET-99 cortical band, which restricts or concentrates generators to a posterior crescent. After delaying anaphase onset, we detected this positional pulling force regulation inC. elegansas a precocious spindle rocking with respect to anaphase onset. We ascribed this control to the microtubule dynamics at the cortex. Indeed, in mapping the cortical contacts, we found a correlation between the centrosome–cortex distance and the microtubule contact density. In turn, it modulates pulling force generator activity. We modelled this control, predicting and experimentally validating that the posterior crescent extent controlled where the anaphase oscillations started, in addition to mitotic progression. We found in particular that the oscillation onset position resists changes in cellular geometry and moderate variations of active force generator count. Finally, we propose that spatially restricting force generator to a posterior crescent sets the spindle’s final position, reflecting polarity through the LET-99 dependent restriction of force generators to a posterior crescent. This regulation superimposes that of force generator processivity. This novel control confers a low dependence on microtubule and active force generator exact numbers or dynamics, provided that they exceed the threshold needed for posterior displacement. Interestingly, this robustness originates in cell mechanics rather than biochemical networks.
Antibiotic resistance genes in agriculture and urban influenced watersheds in southwestern British Columbia
Authors: Uyaguari-Díaz Miguel I. , Croxen Matthew A. , Luo Zhiyao , Cronin Kirby I. , Chan Michael , Baticados Waren N. , Nesbitt Matthew J. , Li Shaorong , Miller Kristi , Dooley Damion , Hsiao William , Isaac-Renton Judith L. , Tang Patrick , Prystajecky Natalie
Published: February 2017

Background

The dissemination of antibiotic resistance genes (ARGs) from anthropogenic activities into the environment poses an emerging public health threat. Water constitutes a major vehicle for transport of both biological material and chemical substances. The present study focused on putative antibiotic resistance and integrase genes present in the microbiome of agricultural, urban influenced and protected watersheds in southwestern British Columbia, Canada. A metagenomics approach and high throughput quantitative PCR (HT qPCR) were used to screen for elements of resistance including ARGs and integron-associated integrase genes (intI). Sequencing of bacterial genomic DNA was used to characterize the resistome of microbial communities present in watersheds over a one-year period.

Results

Data mining using CARD and Integrall databases enabled the identification of putative antibiotic resistance genes present in watershed samples. Antibiotic resistance genes presence in samples from various watershed locations was low relative to the microbial population (<1 %). Analysis of the metagenomic sequences detected a total of 78 ARGs andintI1across all watershed locations. The relative abundance and richness of antibiotic resistance genes was found to be highest in agriculture impacted watersheds compared to protected and urban watersheds. Gene copy numbers (GCNs) from a subset of 21 different elements of antibiotic resistance were further estimated using HT qPCR. Most GCNs of ARGs were found to be variable over time. A downstream transport pattern was observed in the impacted watersheds (urban and agricultural) during dry months. Urban and agriculture impacted sites had a higher GCNs of ARGs compared to protected sites. Similar to other reports, this study found a strong association betweenintI1and ARGs (e.g.,sul1), an association which may be used as a proxy for anthropogenic activities. Chemical analysis of water samples for three major groups of antibiotics was negative. However, the high richness and GCNs of ARGs in impacted sites suggest effects of effluents on microbial communities are occurring even at low concentrations of antimicrobials in the water column.

Conclusion

Antibiotic resistance and integrase genes in a year-long metagenomic study showed that ARGs were driven mainly by environmental factors from anthropogenized sites in agriculture and urban watersheds. Environmental factors accounted for almost 40% of the variability observed in watershed locations.
High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing
Authors: Lagarde Julien , Uszczynska-Ratajczak Barbara , Carbonell Silvia , Pérez-Lluch SÍlvia , Abad Amaya , Davis Carrie , Gingeras Thomas R. , Frankish Adam , Harrow Jennifer , Guigo Roderic , Johnson Rory
Published: February 2017

Accurate annotations of genes and their transcripts is a foundation of genomics, but no annotation technique presently combines throughput and accuracy. As a result, reference gene collections remain incomplete: many gene models are fragmentary, while thousands more remain uncatalogued–particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), combining targeted RNA capture with third-generation long-read sequencing. We present an experimental re-annotation of the GENCODE intergenic lncRNA population in matched human and mouse tissues, resulting in novel transcript models for 3574 / 561 gene loci, respectively. CLS approximately doubles the annotated complexity of targeted loci, outperforming existing short-read techniques. Full-length transcript models produced by CLS enable us to definitively characterize the genomic features of lncRNAs, including promoter- and gene-structure, and protein-coding potential. Thus CLS removes a longstanding bottleneck of transcriptome annotation, generating manual-quality full-length transcript models at high-throughput scales.

Abbreviations

bp

base pair

FL

full length

nt

nucleotide

ROI

read of insert,i.e.PacBio read

SJ

splice junction

SMRT

single-molecule real-time

TM

transcript model
Bayesian analysis of genetic association across tree-structured routine healthcare data in the UK Biobank
Authors: Cortes Adrian , Dendrou Calliope A. , Motyer Allan , Jostins Luke , Vukcevic Damjan , Dilthey Alexander , Donnelly Peter , Leslie Stephen , Fugger Lars , McVean Gil
Published: February 2017

Genetic discovery from the multitude of phenotypes extractable from routine healthcare data has the ability to radically transform our understanding of the human phenome, thereby accelerating progress towards precision medicine. However, a critical question when analysing high-dimensional and heterogeneous data is how to interrogate increasingly specific subphenotypes whilst retaining statistical power to detect genetic associations. Here we develop and employ a novel Bayesian analysis framework that exploits the hierarchical structure of diagnosis classifications to jointly analyse genetic variants against UK Biobank healthcare phenotypes. Our method displays a more than 20% increase in power to detect genetic effects over other approaches, such that we uncover the broader burden of genetic variation: we identify associations with over 2,000 diagnostic terms. We find novel associations with common immune-mediated diseases (IMD), we reveal the extent of genetic sharing between specific IMDs, and we expose differences in disease perception or diagnosis with potential clinical implications.
The mechanisms of regulatory focus
Authors: Zivnuska Suzanne , Kacmar K. Michele , Valle Matthew
Published: February 2017

Purpose

The purpose of this paper is to explore the mechanisms underlying prevention-focus and promotion-focus, two distinct dimensions of regulatory focus undertaken to fulfill different goals. The authors explore distinct triggers (mindfulness and leader-member exchange (LMX)) and outcomes (role overload and burnout) of each.

Design/methodology/approach

The model is grounded in regulatory focus theory (Higgins, 1997), and is tested with data collected at two times from 206 full-time workers.

Findings

Findings revealed mindfulness was positively related to prevention- and promotion-focus, while LMX was positively related to only promotion-focus. Prevention-focus mediated the relationship between mindfulness and role overload and burnout, while promotion-focus mediated the relationship between both mindfulness and LMX and role overload, but not burnout.

Originality/value

This research expands the nomological network describing individual and dyadic antecedents to regulatory focus. It also explores the nature of the relationships between regulatory focus and career management consequences, and may allow us to offer useful advice for practicing managers trying to understand employee career trajectories.
Managing business networks for value creation in facilities and their external environments
Authors: Artto Karlos , Ahola Tuomas , Kyrö Riikka , Peltokorpi Antti
Published: February 2017

Purpose

The purpose of this paper is to increase understanding of the logic of business network formation among the co-located and external actors of a facility.

Design/methodology/approach

The research adopts a theory-building approach through developing propositions inductively from the empirical case study on four purposefully sampled modern service station facilities. The focus is on analyzing how a facility and its inherent co-located actors represent an entity that forms a business network with external actors in the facility’s environment.

Findings

The findings propose that when co-located with a large number of actors, the facility and its actors represent an entity that is connected to a wide business network of multiple external actors. On the other hand, when co-located with a small number of actors, the facility becomes a part of the overall supply in the surrounding business environment with a differentiated offering for competitive advantage.

Practical implications

The research suggests that an appropriate co-locating strategy, for example, when planning the tenant mix of the facility, can contribute to creating a vivid business network in the external environment, which raises the facility to a role of a central entity in such a network.

Originality/value

The findings explaining how co-location affects the businesses within the facility and within a wider networked environment are novel to the scholarly knowledge on co-location. The research bridges the theories of co-location and business networks that have been treated as separate discourses in previous research.
When family businesses go international: management sets the path
Authors: Jorge Marta , Couto Maria , Veloso Tânia , Franco Mário
Published: February 2017

Purpose

The purpose of this study is to understand the characteristics and decision processes of small- and medium-sized family firms (FSMEs) regarding the internationalization process.

Design/methodology/approach

For this purpose, the authors decided on a qualitative approach and performed exploratory case studies of two small- and medium-sized firms (SMEs) in Portugal, one family and the other non-family.

Findings

The authors found that the internationalization of FSME is not entirely explained by gradual processes of commitment to international markets. Restricted access to resources (financial and human) is compensated for by specific factors of FSMEs.

Practical implications

This study shows the relevance of FSME management for the process that seems to be at the basis of the commitment to, and success in international markets, concerning both the risk taken on and its cultural mentality.

Originality/value

Although family firms are many in number and central in the dynamics of the world economy, the family factor has not been approached as a determinant characteristic in the internationalization process. This holds particularly for the realm of FSMEs.
Improving coating properties of shellac–epoxidised-novolac blends with melamine formaldehyde resin
Authors: Ansari Mohammad Fahim , Sarkhel Gautam
Published: February 2017

Purpose

The purpose of this study is to improve the coating properties of shellac–epoxidised novolac blends by treatment with melamine formaldehyde resin (MF) at ambient temperature for its use as a coating material.

Design/methodology/approach

Epoxidised-novolac resin was synthesised by epoxidation of novolac resin with epichlorohydrin. Novolac resin was synthesised by reaction of phenol with formaldehyde in acidic medium. Shellac was blended with the epoxidised-novolac resin in solution in varying ratios and treated the blends with MF resin in fixed ratio. Coating properties of the treated compositions were studied using a standard procedure. The compositions were characterised with Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA) and scanning electron microscopic (SEM) spectroscopy.

Findings

Treatment of shellac–epoxidised-novolac blends with MF resin improved water and alkali resistance of the blends, besides enhancing gloss. Gloss in all the blends was uniformly increased on treatment with MF resin. Water resistance of the blends tremendously improved after treatment with MF resin. Contact angle of the blends against water increased while decreased against ethylene glycol and dioxane. The compositions were more resistant to polar solvent than non-polar ones, suggesting that the compositions shifted to hydrophobic (lipophilic) nature on treatment with the MF resin.

Research limitations/implications

A specified concentration of MF resin was used in the study. Different concentrations of the MF resin can also be tried for treatment of shellac–epoxidised-novolac blends to see the effect of the resin on the blends.

Practical implications

Treatment of shellac–epoxidised-novolac blend with MF resin improved the coating properties of the blends. The formulation SeNB-64 is the best with high gloss, good impact, scratch hardness and water resistance, and hence can be used as coating material for metal surfaces.

Originality/value

Blending of shellac with epoxidised-novolac resin and treatment of the blends with the MF resin was done for the first time. The formulation SeNB-64 can be used as coating material for metal surfaces.
Changes of serum trace elements level in patients with alopecia areata: A meta‐analysis
Authors: Jin Waishu , Zheng Haibo , Shan Baihui , Wu Yi
Published: February 2017

Abnormalities of serum trace elements are involved in the etiology and pathogenesis of alopecia areata (AA); however, the results of published studies are controversial. The purpose of the present study is to investigate the alterations of serum level of trace elements and AA using a meta‐analysis approach. We searched all articles indexed in PubMed, Embase and Science Citation Index published up to 30 April 2016 concerning the association between serum level of zinc, copper, iron/ferritin, selenium or magnesium and AA. Ten eligible articles involving 764 subjects were identified. Overall, pooled analysis indicated that patients with AA had a lower serum level of zinc (P < 10−4) and selenium (P < 10−4) than the healthy controls. However, there was no significant difference between the AA patients and controls in the levels of serum copper (P = 0.81), serum iron (P = 0.36), serum ferritin (P = 0.37) and serum magnesium (P = 0.07). This meta‐analysis suggests that low serum levels of zinc and selenium seem to be important risk factors for AA.
The Tunisian Revolution: Neoliberalism, Urban Contentious Politics and the Right to the City
Authors: Zemni Sami
Published: January 2017

This article engages in the debate on urban contentious politics by returning to the Tunisian revolution. In the article, I chart movements provoked by neoliberal restructurings, and show how these ultimately came together to form a mass movement demanding radical political change. I first describe the socio‐spatial roots of the Tunisian revolution to understand its dynamics. Based on the chronology of the unfolding events I sketch the classes, social groups and movements that coalesced against authoritarian rule in early 2011. Although the Tunisian revolution started in rural environments, I focus more specifically on the role of urban social movements in the uprising to link questions of urbanism to what were clearly national revolts. Secondly, I outline the scope of neoliberal reforms in Tunisia by looking at the impact of these reforms to chart the resulting emergence of contentious politics in response to the increasing violence that characterized all levels of economic life during this period. I also consider the resulting uneven development and the changing relations between the state and the different social classes. This enables me to reflect on the politicization of the city with the aim of opening up new opportunities for engaging with a more comparative and cosmopolitan theory about cities around the world.
Staging Equality in Greek Squares: Hybrid Spaces of Political Subjectification
Authors: Karaliotas Lazaros
Published: January 2017

This article stages a dialogue between Jacques Rancière's political writings and the squares movement in Greece. From May to July 2011, a heterogeneous multitude of protesters reclaimed the squares of the country from their allocation in the police order and articulated a multiplicity of divergent discursive, organizational and spatial repertoires. This was an urban political event that reasserted the importance of urban spaces in expressing political dissent and experimented with new ways of being and acting in common. This article draws on Rancière's conceptualization of politics to read the squares movement as an opening of spaces of political subjectification. At the same time, through a close ethnography of the squares, it highlights the tensions that marked this process and focuses on two of these: the coexistence of nationalist and equalibertarian discursive and performative repertoires and the co‐implication of horizontal and vertical organizational practices. The article builds on this analysis to argue that the squares movement opened hybrid spaces of political subjectification and to explore some of the tensions in Rancière's political writings. This reading, in turn, informs a discussion of the legacies of the squares movement.
From Occupying Plazas to Recuperating Housing: Insurgent Practices in Spain
Authors: García‐Lamarca Melissa
Published: January 2017

Urban insurgencies have spread across the globe like wildfire in recent years. The indignado plaza occupations in Spain are often cited as beacons of popular and widespread dissent. This article argues that urban insurgencies with the highest emancipatory potential in Spain today are found in the practices of the housing rights movement—the Plataforma de Afectados por la Hipoteca (PAH, or Platform for Mortgage‐affected People)—that mainly entail blocking evictions and occupying empty bank‐owned housing. I elaborate on the notion of insurgent practice by examining how insurgency has been considered in relationship to citizenship, planning and public space. I propose insurgent practice as a way of articulating how people attempt to enact equality in everyday life and engage explicitly with socio‐spatial and political questions related to an emancipatory democratic politics. Based on a detailed analysis of two of the PAH's insurgent housing practices, I posit that recuperating empty bank‐owned housing with and for evicted families has the highest and most significant emancipatory potential, as it disrupts the core dynamics of urban capital accumulation and enacts equality for evicted households by directly contesting financial rent‐extraction mechanisms at multiple levels. In closing, I outline some conclusions that emerge from the Spanish housing case and from the concept of insurgent practice and urban politicizing practice in general.
The Work of a Few Trees: Gezi, Politics and Space
Authors: Erensü Sinan , Karaman Ozan
Published: January 2017

In June 2013, Istanbul and many cities across Turkey became stages of massive demonstrations and occupations, which were sparked by a conflict over Gezi Park in central Istanbul. For many, the ‘park issue' was simply the last straw, and it led to unprecedented revolt, reflecting a huge number of grievances against the government for some, while for others it emphasized the impoverishing consequences of the Justice and Development Party's (AKP's) urban policies. Instead of disentangling causes and effects, we think that a productive way of approaching the oppositional surge that erupted in Gezi Park is through the political work that space does in the context of the increasing prominence of speculation‐driven and authoritarian interventions in urban spaces. Gezi, as an event, not only disrupted the routinized scripts of an increasingly autocratic government and defied the presumed consensus over real‐estate and infrastructure‐led economic growth policies, but also helped to articulate a series of political agendas across the urban–rural continuum that came before it. Even after the occupation, the Gezi spirit continued to politicize space through various de‐localizations. By elaborating on a particular phrase popularized during Gezi, namely yaşam alanı (life space), the article discusses how the riot's political impact deepened and expanded not only through defending a space but also by creating new ones, both materially and conceptually.
Theorizing the Politicizing City
Authors: Dikeç Mustafa , Swyngedouw Erik
Published: January 2017

This introductory symposium article develops a framework for an urban political reading and a theorization of urban uprisings. We argue that there is a need to foreground the notion of the urban political as central to the theoretical and practical demands of urban research today. First, we revisit critical urban theory in light of recent urban insurrections and point out a lack of sustained theoretical engagement with the political. Second, based on this critique, we argue for what we call a ‘re‐centring of the urban political' to rethink urban theory in ways that consider the city as a site of political encounter, interruption and experimentation, even when, or perhaps especially when, these ways fall outside institutional forms or lack the organizational form or legitimacy of social movements. Thus, we attempt to place politics at the heart of radical urban political theory and practice today in order to make sense of urban subjects, events and claims that elude established government practices and institutionalized structures.
JUDICIAL ROTATION AS CENTRIPETAL FORCE: SENTENCING IN THE COURT COMMUNITIES OF SOUTH CAROLINA*
Authors: HESTER RHYS
Published: February 2017

Courts as communities theory emphasizes the sentencing differences that can arise between localities within a single state. The results of published studies have highlighted how local differences emerge based on informal sociological and political processes defined by the communities perspective. The findings from recent quantitative studies from South Carolina have revealed notably less county variation in sentencing than has been observed elsewhere. I use qualitative interviews with 13 South Carolina trial judges to investigate sentencing processes and to shed light on these findings. The interviews explore the state's legal structure and culture, including the practice of circuit rotation in which judges travel among counties holding court. The results suggest rotation serves as a centripetal force of sentencing culture, homogenizing what might otherwise be a more varied collection of county‐specific norms. Rotation leads to increased uniformity through judge shopping and the cross‐pollination of ideas and norms. Defendants can strategically judge shop and plead in front of a lenient judge—a process that gives rise to the term “plea judge,” which is a label for the most lenient judges who sentence a large number of defendants. Rotation also increases the interactions among judges and prosecutors, expanding networks and grapevines, and leading to cross‐pollination and the sharing of ideas.
Saponin Profile of Wild Asparagus Species
Authors: Jaramillo‐Carmona Sara , Rodriguez‐Arcos Rocío , Jiménez‐Araujo Ana , López Sergio , Gil Juan , Moreno Roberto , Guillén‐Bejarano Rafael
Published: February 2017

The aim of this work was to study the saponin profiles from spears of different wild asparagus species in the context of its genetic diversity aside from geographical seed origin. They included Asparagus pseudoscaber Grecescu, Asparagus maritimus (L.) Mill., Asparagus brachiphyllus Turcz., Asparagus prostrates Dumort., and Asparagus officinalis L. The saponin analysis by LC‐MS has shown that saponin profile from wild asparagus is similar to that previously described for triguero asparagus from Huétor‐Tájar landrace (triguero HT), which had not ever been reported in the edible part of asparagus. All the samples, except A. officinalis, were characterized for having saponins distinct to protodioscin and the total saponin contents were 10‐fold higher than those described for commercial hybrids of green asparagus. In particular, A. maritimus from different origins were rich in saponins previously found in triguero HT. These findings supported previous suggestion, based on genetic analysis, about A. maritimus being the origin of triguero HT. Multivariate statistics including principal component analysis and hierarchical clustering analysis were used to define both similarities and differences among samples. The results showed that the greatest variance of the tested wild asparagus could be attributed to differences in the concentration of particular saponins and this knowledge could be a tool for identifying similar species.
Personalized microbiome‐based approaches to metabolic syndrome management and prevention
Authors: Shapiro Hagit , Suez Jotham , Elinav Eran
Published: February 2017

Personalized or precision medicine is a novel clinical approach targeted to the individual patient and based on integration of clinical, genetic, and environmental factors that define a patient uniquely from other individuals featuring similar clinical symptoms. Such a personalized medicine approach is increasingly applied for diagnosis, clinical stratification, and treatment of metabolic syndrome (MetS)‐associated risks and diseases, including obesity, type 2 diabetes, non‐alcoholic fatty liver disease, and their complications. One emerging factor that governs MetS manifestations is the microbiome, the composition, function, growth dynamics, associated metabolite profile and diverse effects of which on host immune and metabolic systems can all significantly affect metabolic homeostasis. Interindividual differences in microbiome composition and function, as well as personal variations in microbial‐derived products, pave the way towards microbiome‐based personalized medicine in treating MetS‐related diseases.
Modulation of antiphospholipid antibodies‐induced trophoblast damage by different drugs used to prevent pregnancy morbidity associated with antiphospholipid syndrome
Authors: Alvarez Angela M. , Balcázar Norman , San Martín Sebastián , Markert Udo R. , Cadavid Angela P.
Published: January 2017

Problem

Women with antiphospholipid antibodies (aPLs) present a risk of pregnancy morbidity (PM), vascular thrombosis (VT), or both (PM/VT). aPLs affect trophoblast function, and the aim of this study was to determine the modulation of this aPL‐induced damage by different drugs.

Method of study

IgG was obtained from women with PM and PM/VT positive to aPLs. Binding of IgG to trophoblastic cells, proliferation, mitochondrial membrane integrity, and trophoblast invasion were assessed. The effect of enoxaparin, aspirin, and aspirin‐triggered lipoxin (ATL) were evaluated as well as signal transducer and activator of transcription 3 (STAT3) phosphorylation.

Results

IgG from women with aPLs strongly binds to trophoblastic cells. Integrity of mitochondrial membrane was reduced, and proliferation was increased by IgG‐PM/VT. Both IgG‐PM and IgG‐PM/VT decreased trophoblast invasion, which was restored by enoxaparin, aspirin, and ATL. IgG‐PM triggered reduction in STAT3 phosphorylation.

Conclusion

Some drugs used to prevent aPL‐induced PM modulated the alteration of trophoblast function.
Serologic markers of autoimmunity in women with recurrent pregnancy loss
Authors: Hefler‐Frischmuth Katrin , Walch Katharina , Hefler Lukas , Tempfer Clemens , Grimm Christoph
Published: January 2017

Problem

Various autoimmunologic mechanisms have been shown to be involved in recurrent pregnancy loss (RPL). This study aimed to evaluate whether women with RPL have elevated serum levels of common autoimmunologic parameters.

Method of Study

Serum levels of antinuclear antibodies (ANAs) were measured in 114 women with RPL, and 107 healthy controls using a qualitative immunometric enzyme immunoassay, serum levels of IgG class autoantibodies against histone, IgG class autoantibodies against nucleosomes, and IgG class autoantibodies against double‐stranded (ds) DNA were measured by quantitative enzyme immunoassays.

Results

No differences were ascertained regarding serum levels of ANAs (P=.9), serum levels of antibodies against histones (P=.1), antibodies against nucleosomes (P=.4) and antibodies against dsDNA (P=.6) between women with RPL and healthy controls. No associations were found between serum levels and clinical characteristics of affected women.

Conclusion

Our study shows that serologic parameters of autoimmunity are not elevated in women with RPL and are not associated with clinical characteristics of affected women.