bluuebunny/crossref_metadata_2025 huggingface dataset:
Data-driven re-referencing of intracranial EEG based on independent component analysis (ICA)
Authors: Michelmann Sebastian , Treder Matthias S. , Griffiths Benjamin , Kerrén Casper , Roux Frédéric , Wimber Maria , Rollings David , Sawlani Vijay , Chelvarajah Ramesh , Gollwitzer Stephanie , Kreiselmeyer Gernot , Hamer Hajo , Bowman Howard , Staresina Bernhard , Hanslmayr Simon
Published: June 2017

Intracranial recordings from patients implanted with depth electrodes are a valuable source of information in cognitive neuroscience. They allow for the unique opportunity to record brain activity with a high spatial and temporal resolution. To extract the local signal of interest in stereotactic EEG (S-EEG) data, a common pre-processing choice is to re-reference the data with a bipolar montage.

With bipolar reference, each channel is subtracted from its neighbour in order to reduce commonalities between channels and isolate activity that is spatially confined. We here challenge the assumption that bipolar reference can effectively perform this task. We argue that in order to extract local activity, the distribution of the signal source of interest, as well as the distribution of interfering distant signals and noise sources need to be considered. Those can have a variable spatial extent and are modulated by electrode spacing, location and anatomical characteristics. Those factors are not accounted for by a fixed referencing scheme and bipolar reference can therefore not only decrease the signal to noise ratio (SNR) of the data, but also lead to mislocalization of activity and consequently to misinterpretation of results.

We promote the perspective of regarding referencing as a spatial filtering operation with fixed coefficients. As an alternative, we propose to use Independent Component Analysis (ICA), to derive filter coefficients that reflect the statistical dependencies of the data at hand. We argue that ICA performs the same task that bipolar referencing pursues, namely undoing the linear superposition of activity and can therefore be used to identify activity that is local. We first describe and demonstrate this procedure on human S-EEG recordings. In a simulation with real data, we then quantitatively show that ICA outperforms the bipolar referencing operation in sensitivity and importantly in specificity when it comes to revealing local time series from the superposition of neighbouring channels.
Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes
Authors: He Shaomei , Stevens Sarah LR , Chan Leong-Keat , Bertilsson Stefan , del Rio Tijana Glavina , Tringe Susannah G , Malmstrom Rex R , McMahon Katherine D
Published: June 2017

Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions, and greatly expand the known genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly)saccharide-degraders in freshwater, uncovered interesting genomic features for this life style, and suggested their adaptation to nutrient availabilities in their environments. Between the two lakes, Verrucomicrobia populations differ significantly in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially-derived allochthonous carbon sources of the two ecosystems respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochromeccomplex and might be involved in extracellular electron transfer in the anoxic humic-rich environment. Notably, most epilimnion genomes have large numbers of so-called “Planctomycete-specific” cytochromec-containing genes, which exhibited nearly opposite distribution patterns with glycoside hydrolase genes, probably associated with the different environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes are a major step towards understanding the role, ecophysiology and distribution of Verrucomicrobia in freshwater.

IMPORTANCE

Freshwater Verrucomicrobia are cosmopolitan in lakes and rivers, yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia are restricted to one subdivision of this phylum. Here, we greatly expand the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia as potential (poly)saccharide-degraders, and suggested their adaptation to carbon source of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called “Planctomycete-specific” cytochromec-containing genes, and found their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.
Maternal loading of a small heat shock protein increases embryo thermal tolerance inDrosophila melanogaster
Authors: Lockwood Brent L. , Julick Cole R. , Montooth Kristi L.
Published: June 2017

Maternal investment is likely to have direct effects on offspring survival. In oviparous animals whose embryos are exposed to the external environment, maternal provisioning of molecular factors like mRNAs and proteins may help embryos cope with sudden changes in the environment. Here we sought to modify the maternal mRNA contribution to offspring embryos and test for maternal effects on acute thermal tolerance in early embryos ofDrosophila melanogaster. We drove in vivo overexpression of a small heat shock protein gene (Hsp23) in female ovaries and measured the effects of acute thermal stress on offspring embryonic survival and larval development. We report that overexpression of theHsp23gene in female ovaries produced offspring embryos with increased thermal tolerance. We also found that brief heat stress in the early embryonic stage (0 to 1 hour-old) caused decreased larval performance later in life (5 to 10 days-old), as indexed by pupation height, as well as increased development time to pupation. Maternal overexpression ofHsp23protected embryos against these heat-induced larval defects. Our data demonstrate that transient products of single genes have large and lasting effects on whole-organism environmental tolerance. Further, our results suggest that maternal effects have a profound impact on offspring survival in the context of thermal variability.

SUMMARY STATEMENT

A gene-specific maternal effect confers thermal tolerance to offspring embryos in the fruit flyDrosophila melanogaster.
Leukocyte counts based on site-specific DNA methylation analysis
Authors: Frobel Joana , Božić Tanja , Lenz Michael , Uciechowski Peter , Han Yang , Herwartz Reinhild , Strathmann Klaus , Isfort Susanne , Panse Jens , Esser André , Birkhofer Carina , Gerstenmaier Uwe , Kraus Thomas , Rink Lothar , Koschmieder Steffen , Wagner Wolfgang
Published: June 2017

The composition of white blood cells is usually assessed by histomorphological parameters or flow cytometric measurements. Alternatively, leukocyte differential counts (LDCs) can be estimated by deconvolution algorithms for genome-wide DNA methylation (DNAm) profiles. We identified cell-type specific CG dinucleotides (CpGs) that facilitate relative quantification of leukocyte subsets. Site-specific analysis of DNAm levels by pyrosequencing provides similar precision of LDCs as conventional methods, whereas it is also applicable to frozen samples and requires only very small volumes of blood. Furthermore, we describe a new approach for absolute quantification of cell numbers based on a non-methylated reference DNA. Our “Epi-Blood-Count” facilitates robust and cost effective analysis of blood counts for clinical application.
Data-based, synthesis-driven: setting the agenda for computational ecology
Authors: Poisot Timothée , Labrie Richard , Larson Erin , Rahlin Anastasia
Published: June 2017

Computational thinking is the integration of algorithms, software, and data, to solve general questions in a field. Computation ecology has the potential to transform the way ecologists think about the integration of data and models. As the practice is gaining prominence as a way to conduct ecological research, it is important to reflect on what its agenda could be, and how it fits within the broader landscape of ecological research. In this contribution, we suggest areas in which empirical ecologists, modellers, and the emerging community of computational ecologists could engage in a constructive dialogue to build on one another’s expertise; specifically, about the need to make predictions from models actionable, about the best standards to represent ecological data, and about the proper ways to credit data collection and data reuse. We discuss how training can be amended to improve computational literacy.
In spoken word recognition the future predicts the past
Authors: Gwilliams Laura , Linzen Tal , Poeppel David , Marantz Alec
Published: June 2017

Speech is an inherently noisy and ambiguous signal. In order to fluently derive meaning, a listener must integrate contextual information to guide interpretations of the sensory input. While many studies have demonstrated the influence ofpriorcontext on speech perception, the neural mechanisms supporting the integration ofsubsequentcontext remain unknown. Using magnetoencephalography, we analysed responses to spoken words with a varyingly ambiguous onset phoneme, the identity of which is later disambiguated at the lexical uniqueness point1. Our findings suggest that primmary auditory cortex is sensitive to phonological ambiguity very early during processing — at just 50 ms after onset. Subphonemic detail is preserved in auditory cortex over long timescales, and re-evoked at subsequent phoneme positions. Commitments to phonological categories occur in parallel, resolving on the shorter time-scale of ~450 ms. These findings provide evidence that future input determines the perception of earlier speech sounds by maintaining sensory features until they can be integrated with top down lexical information.

Significance statement

The perception of a speech sound is determined by its surrounding context, in the form of words, sentences, and other speech sounds. Often, such contextual information becomes availablelaterthan the sensory input. The present study is the first to unveil how the brain uses this subsequent information to aid speech comprehension. Concretely, we find that the auditory system supports prolonged access to the transient acoustic signal, while concurrently making guesses about the identity of the words being said. Such a processing strategy allows the content of the message to be accessed quickly, while also permitting re-analysis of the acoustic signal to minimise parsing mistakes.
Space, Time and Episodic Memory: the Hippocampus is all over the Cognitive Map
Authors: Ekstrom Arne D. , Ranganath Charan
Published: June 2017

In recent years, the field has reached an impasse between models suggesting that the hippocampus is fundamentally involved in spatial processing and models suggesting that the hippocampus automatically encodes all dimensions of experience in the service of memory. Here, we consider key conceptual issues that have impeded progress in our understanding of hippocampal function, and we review findings that establish the scope and limits of hippocampal involvement in navigation and memory. We argue that space and time serve as a primary scaffold to break up experiences into specific contexts, and to organize multimodal input that is to be associated within a context. However, the hippocampus is clearly capable of incorporating additional dimensions into the scaffold if they are determined to be relevant in the event-defined context. Conceiving of the hippocampal representation as constrained by immediate task demands—yet preferring axes that involve space and time—helps to reconcile an otherwise disparate set of findings on the core function of the hippocampus.
The rodent hippocampus as a bilateral structure: A review of hemispheric lateralization
Authors: Jordan Jake T.
Published: June 2017

The left and right rodent hippocampi exhibit striking lateralization in some of the very neural substrates considered to be critical for hippocampal cognitive function. Despite this, there is an overwhelming lack of consideration for hemispheric differences in studies of the rodent hippocampus. Asymmetries identified so far suggest that a bilateral model of the hippocampus will be essential for an understanding of this brain region, and perhaps of the brain more widely. Although hypotheses have been proposed to explain how the left and right hippocampi contribute to behavior and cognition, these hypotheses have either been refuted by more recent studies or have been limited in the scope of data they explain. Here, I will first review data on human and rodent hippocampal lateralization. The implications of these data suggest that considering the hippocampus as a bilateral structure with functional lateralization will be critical moving forward in understanding the function and mechanisms of this brain region. In exploring these implications, I will then propose a hypothesis of the hippocampus as a bilateral structure. This discrete-continuous (DC) hypothesis proposes that the left and right hippocampi contribute to spatial memory and navigation in a complementary manner. Specifically, the left hemisphere stores spatial information as discrete, salient locations and that the right hemisphere represents space continuously, contributing to route computation and flexible spatial navigation. Consideration of hippocampal lateralization in designing future studies may provide insight into the function of the hippocampus and resolve debates concerning its function.
Modeling of cytometry data in logarithmic space: when is a bimodal distribution not bimodal?
Authors: Erez Amir , Vogel Robert , Mugler Andrew , Belmonte Andrew , Altan-Bonnet Grégoire
Published: June 2017

Recent efforts in systems immunology lead researchers to build quantitative models of cell activation and differentiation. One goal is to account for the distributions of proteins from single-cell measurements by flow cytometry or mass cytometry as a readout of biological regulation. In that context, large cell-to-cell variability is often observed in biological quantities. We show here that these readouts, viewed in logarithmic scale may result in two easily-distinguishable modes, while the underlying distribution (in linear scale) is unimodal. We introduce a simple mathematical test to highlight this mismatch. We then dissect the flow of influence of cell-to-cell variability proposing a graphical model which motivates higher-dimensional analysis of the data. Finally we show how acquiring additional biological information can be used to reduce uncertainty introduced by cell-to-cell variability, helping to clarify whether the data is uni- or bimodal. This communication has cautionary implications for manual and automatic gating strategies, as well as clustering and modeling of single-cell measurements.
Astrocytes release prostaglandin E2 to modify respiratory network activity
Authors: Forsberg David , Ringstedt Thomas , Herlenius Eric
Published: June 2017

Prostaglandin E2 (PGE2) released during hypercapnic challenge increases Ca2+oscillation frequency in the chemosensitive parafacial respiratory group (pFRG/RTN). Here, we demonstrate that pFRG/RTN astrocytes are the PGE2 source. Two distinct astrocyte subtypes were found using transgenic mice expressing GFP and MrgA1 receptors in astrocytes. Although most astrocytes appeared dormant during time-lapse calcium imaging, a subgroup displayed persistent, rhythmic oscillating calcium activity. These active astrocytes formed a subnetwork within the respiratory network distinct from the neuronal network. Activation of exogenous MrgA1 receptors expressed in astrocytes tripled their calcium oscillation frequency activity in both the preBötzinger complex and pFRG/RTN. However, neurons in the preBötC were unaffected, whereas neuronal calcium oscillatory frequency in pFRG/RTN doubled. Notably, astrocyte activation in pFRG/RTN triggered local PGE2 release and blunted the hypercapnic response. Thus, astrocytes play an active role in respiratory rhythm modulation, modifying respiratory-related behaviorthrough PGE2 release in the pFRG/RTN.
Reducing resistance allele formation in CRISPR gene drives
Authors: Champer Jackson , Liu Jingxian , Oh Suh Yeon , Reeves Riona , Luthra Anisha , Oakes Nathan , Clark Andrew G. , Messer Philipp W.
Published: June 2017

CRISPR gene drives can efficiently convert heterozygous cells with one copy of the drive allele into homozygotes, thereby enabling super-Mendelian inheritance. This mechanism could be used, for example, to rapidly disseminate a genetic payload through a population, promising novel strategies for the control of vector-borne diseases. However, all CRISPR gene drives tested have produced significant quantities of resistance alleles that cannot be converted to drive alleles and would likely prevent these drives from spreading in a natural population. In this study, we assessed three strategies for reducing resistance allele formation. First, we directly compared drives with thenanosandvasapromoters, which showed that thevasadrive produced high levels of resistance alleles in somatic cells. This was not observed in thenanosdrive. Another strategy was the addition of a second gRNA to the drive, which both significantly increased the drive conversion efficiency and reduced the formation rate of resistance alleles. Finally, to minimize maternal carryover of Cas9, we assessed the performance of an autosomal drive acting in the male germline, and found no subsequent formation of resistance alleles in embryos. Our results mark a step toward developing effective gene drives capable of functioning in natural populations and provide several possible avenues for further reduction of resistance rates.
Numerical simulations of the hard X-ray pulse intensity distribution at the Linac Coherent Light Source
Authors: Pardini Tom , Aquila Andrew , Boutet Sébastien , Cocco Daniele , Hau-Riege Stefan P.
Published: June 2017

Numerical simulations of the current and future pulse intensity distributions at selected locations along the Far Experimental Hall, the hard X-ray section of the Linac Coherent Light Source (LCLS), are provided. Estimates are given for the pulse fluence, energy and size in and out of focus, taking into account effects due to the experimentally measured divergence of the X-ray beam, and measured figure errors of all X-ray optics in the beam path. Out-of-focus results are validated by comparison with experimental data. Previous work is expanded on, providing quantitatively correct predictions of the pulse intensity distribution. Numerical estimates in focus are particularly important given that the latter cannot be measured with direct imaging techniques due to detector damage. Finally, novel numerical estimates of improvements to the pulse intensity distribution expected as part of the on-going upgrade of the LCLS X-ray transport system are provided. We suggest how the new generation of X-ray optics to be installed would outperform the old one, satisfying the tight requirements imposed by X-ray free-electron laser facilities.
(R)-3-(tert-Butoxycarbonyl)-5-methyl-1,2,3-oxathiazolidine 2,2-dioxide
Authors: Laus Gerhard , Wurst Klaus , Nerdinger Sven , Richter Frank , Schottenberger Herwig
Published: June 2017

The chiral title compound, C8H15NO5S, was obtained by cyclization of (R)-1-(tert-butoxycarbonylamino)-2-propanol with thionyl chloride and subsequent oxidation with sodium metaperiodate/ruthenium(IV) oxide. It crystallizes with two independent molecules in the asymmetric unit. In the crystal, C—H...O interactions link the molecules into a three-dimensional network.
Difficulty identifying universal high-efficacy locations for public access defibrillators
Authors: Somers Scott , LoGiudice Anthony
Published: June 2017

Purpose

This paper reports on an investigation of spatial patterns of out-of-hospital cardiac arrest (OHCA) incidence in a large American city. The purpose of this paper is to identify neighborhoods and public occupancies with highest risk in order to develop an evidence-based strategy to promote cardiac health and improve survival.

Design/methodology/approach

Two-tailed bivariate analysis was conducted using a Spearman correlation coefficient to check the covariance of census variables that were expected to relate to OHCA incidence. A principal component analysis was conducted on the remaining variables that statistically correlated with OHCA. Local indicators of spatial analysis was conducted to test the OHCA risk index and assess how well it predicts the observed OHCA incidence.

Findings

Clusters of OHCA events were found in neighborhoods with socially isolated older persons, as well as low-income minority populations. However, while past research has documented high-risk OHCA locations, these were not the case in this community.

Originality/value

The results highlight the importance of using local data to develop public health policies. Understanding neighborhood-level risks invariably guides resource allocation, service provision, and policy decisions to improve community public health and safety outcomes.
UK ambulance service complaints: a review of the literature
Authors: Brady Mike
Published: June 2017

Purpose

Complaints are an integral element of the quality control and clinical governance process of UK ambulance services, and form a valid and reliable way of identifying areas of practice that require improvement. The purpose of this paper is to assess to what extent such complaints and their possible causes are researched; to identify any possible areas of practice requiring further investigation.

Design/methodology/approach

A computerised literature search was conducted using the online databases Science Direct, Cochrane library, and Web of Science, as well as specific searches of the Journal of Paramedic Practice and the International Journal of Paramedic Practice database. Online databases were searched for peer-reviewed full research articles between January 2012 and May 2016.

Findings

A total of 125 papers were identified and after further screening 90 articles were excluded. Additional screening using the critical appraisal skills programme (2014) criterions excluded a further 21 papers, leaving 14 studies for inclusion within the review.

Originality/value

This review found no specific research focussing on any causes of complaints made to UK ambulance services. Moreover, no research was identified specifically investigating the top three cited themes of complaints made in the last three years. More research is required both in researching those themes of complaints already known but also determining any other possible causes of complaints made. This review has evidenced that studies investigating response times improvement strategies, ambulance staff attitudes, and educational assessments of errors, all have findings which are meaningful and valid to determining the possible causes of complaints and possible improvement strategies. Ambulance services, commissioners, practitioners, and clinical academics should endeavour to research and share causes of complaints made to improve the quality of patient care.
Determinants of SME integration into global value chains
Authors: Kotturu Chandra Mouli V.V. , Mahanty Biswajit
Published: June 2017

Purpose

In recent years, due to intense competition, small and medium-sized enterprises (SMEs) are unable to meet performance expectations and find difficulty in fulfilling the needs of the original equipment manufacturers (OEMs). Consequently, the growth of the SMEs has slowed down considerably. Constrained by their infrastructural resources, SMEs’ participation in global value chains (GVCs) has the potential to bring significant benefits, such as enhancing technological learning and innovation and generating positive contributions to the development of the SMEs. The purpose of this paper is to explore competitive priorities, key factors, and causal relationships influencing SMEs to enter GVCs.

Design/methodology/approach

In this paper, the GVC framework is adopted and qualitative feedback loop analysis is used to identify the key factors influencing the competitive factors. A questionnaire survey was carried out with the automotive component manufacturers of a transnational corporation in India.

Findings

The survey in the automotive component manufacturing industry reveals product quality standards as the most important priority for joining global production networks, followed by price competitiveness, timely delivery, innovativeness, manufacturing flexibility, service, and dependability. The qualitative findings reveal continuous personnel training, capacity expansion, research development, and others as key factors influencing competitiveness.

Practical implications

To retain SMEs’ role in economic development and to accelerate the growth of global production networks in India, thereby realizing opportunities from the emerging GVCs, support is needed for SMEs regarding the aspects identified in this study.

Originality/value

The study explores the dynamics of each competitive priority of SMEs in Indian automotive component manufacturing industry to enter the GVCs. No study has explored the dynamics of SMEs competitiveness to enter GVCs in the automotive manufacturing industry.
A longitudinal study into the effectiveness of the HPO Framework
Authors: de Waal André
Published: June 2017

Purpose

The academic and management literature offers an abundance of techniques for helping organizations improve their performance. Generally, though, these techniques have not been subjected to rigorous, evidence-based evaluation or have been tested in practice over time. The purpose of this paper is to describe a longitudinal study into the effectiveness of the High Performance Organization (HPO) Framework at a social care and rehabilitation organization.

Design/methodology/approach

The HPO Framework was applied at LIMOR in the Netherlands. The longitudinal nature of the study consisted of conducting an “HPO diagnosis” twice at the organization, in 2012 and 2015. In the second diagnosis, the effectiveness of the interventions the organization undertook to address the recommendations originating from the first HPO diagnosis was also measured.

Findings

The study aimed to discover whether the HPO Framework was a suitable improvement technique with which to increase the performance of a social care and rehabilitation organization in a sustainable way. The results showed that it was used to ward off and contain the negative effects of external turbulent developments, and thereby helped LIMOR to perform better than comparable organizations.

Originality/value

As a longitudinal study of the workings and effects of the HPO Framework at a social care and rehabilitation organization, this study is the first of its kind. Moreover, it addresses two gaps in the current literature, by contributing longitudinal evidence to the body of knowledge on improvement techniques, specifically in the non-profit sector, and by adding insights on the practical workings of the HPO Framework in a non-profit context, specifically the social care and rehabilitation sector.
Cedratvirus lausannensis – digging into Pithoviridae diversity
Authors: Bertelli Claire , Mueller Linda , Thomas Vincent , Pillonel Trestan , Jacquier Nicolas , Greub Gilbert
Published: June 2017

Amoeba‐infecting viruses have raised scientists’ interest due to their novel particle morphologies, their large genome size and their genomic content challenging previously established dogma. We report here the discovery and the characterization of Cedratvirus lausannensis, a novel member of the Megavirales, with a 0.75–1 µm long amphora‐shaped particle closed by two striped plugs. Among numerous host cell types tested, the virus replicates only in Acanthamoeba castellanii leading to host cell lysis within 24 h. C. lausannensis was resistant to ethanol, hydrogen peroxide and heating treatments. Like 30 000‐year‐old Pithovirus sibericum, C. lausannensis enters by phagocytosis, releases its genetic content by fusion of the internal membrane with the inclusion membrane and replicates in intracytoplasmic viral factories. The genome encodes 643 proteins that confirmed the grouping of C. lausannensis with Cedratvirus A11 as phylogenetically distant members of the family Pithoviridae. The 575,161 bp AT‐rich genome is essentially devoid of the numerous repeats harbored by Pithovirus, suggesting that these non‐coding repetitions might be due to a selfish element rather than particular characteristics of the Pithoviridae family. The discovery of C. lausannensis confirms the contemporary worldwide distribution of Pithoviridae members and the characterization of its genome paves the way to better understand their evolution.
Low‐abundant species facilitates specific spatial organization that promotes multispecies biofilm formation
Authors: Liu Wenzheng , Russel Jakob , Røder Henriette L. , Madsen Jonas S. , Burmølle Mette , Sørensen Søren J.
Published: June 2017

Microorganisms frequently co‐exist in matrix‐embedded multispecies biofilms. Within biofilms, interspecies interactions influence the spatial organization of member species, which likely play an important role in shaping the development, structure and function of these communities. Here, a reproducible four‐species biofilm, composed of Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus, was established to study the importance of individual species spatial organization during multispecies biofilm development. We found that the growth of species that are poor biofilm formers, M. oxydans and P. amylolyticus, were highly enhanced when residing in the four‐species biofilm. Interestingly, the presence of the low‐abundant M. oxydans (0.5% of biomass volume) was observed to trigger changes in the composition of the four‐species community. The other three species were crucially needed for the successful inclusion of M. oxydans in the four‐species biofilm, where X. retroflexus was consistently positioned in the top layer of the mature four‐species biofilm. These findings suggest that low abundance key species can significantly impact the spatial organization and hereby stabilize the function and composition of complex microbiomes.
Loss of the ssrA genome island led to partial debromination in the PBDE respiring Dehalococcoides mccartyi strain GY50
Authors: Ding Chang , Rogers Matthew J. , Yang Kun‐Lin , He Jianzhong
Published: June 2017

Polybrominated diphenyl ethers (PBDEs), chemicals commonly used as flame‐retardants in consumer products, are emerging persistent organic pollutants that are ubiquitous in the environment. In this study, we report a PBDE‐respiring isolate – Dehalococcoides mccartyi strain GY50, which debrominates the most toxic tetra‐ and penta‐BDE congeners (∼1.4 µM) to diphenyl ether within 12 days with hydrogen as the electron donor. The complete genome sequence revealed 26 reductive dehalogenase homologous genes (rdhAs), among which three genes (pbrA1, pbrA2 and pbrA3) were highly expressed during PBDE debromination. After 10 transfers of GY50 with trichloroethene or 2,4,6‐trichlorophenol as the electron acceptor instead of PBDEs, the ssrA‐specific genome island (ssrA‐GI) containing pbrA1 and pbrA2 was deleted from the genome of strain GY50, leading to two variants (strain GY52 with trichloroethene, strain GY55 with 2,4,6‐trichlorophenol) with identically impaired debromination capabilities (debromination of penta‐/tetra‐BDEs ceased at di‐BDE 15). Through analysis of Illumina paired‐end sequencing data, we identified read pairs that probably came from variants that contain ssrA‐GI deletions, indicating their possible presence in the original strain GY50 culture. The two variant strains provide real‐time examples on rapid evolution of organohalide‐respiring organisms. As PBDE‐respiring organisms, GY50‐like strains may serve as key players in detoxifying PBDEs in contaminated environments.
Creating Space For Citizenship: The Liminal Politics of Undocumented Activism
Authors: Swerts Thomas
Published: June 2017

Since the turn of the century, urban scholars have argued that cities are the sites par excellence where new political subjects are emerging and changing the face of citizenship. Undocumented activism is often invoked as an example of this phenomenon and an object of renewed interest. What remains unclear, however, is how these precarious actors, who are barred from institutional channels for voicing their grievances and who have little access to resources, become political. This article argues that the urban interstices—or the spaces in between legality and illegality, visibility and invisibility and formality and informality—offer strategic opportunities for undocumented activism. I introduce a theoretical understanding of liminal politics that focuses on the spatial and symbolic practices by means of which the undocumented, who find themselves betwixt and between statuses, develop innovative methods of political expression. Based on a multi‐sited ethnography, I demonstrate that undocumented activists craft urban space as a ‘backstage' as well as a ‘frontstage' for their struggles over citizenship. On the one hand, undocumented immigrants build safe spaces in which they can (re)imagine their subjectivities and develop political scripts. On the other hand, they stage and enact these political scripts by appropriating public space. This study therefore highlights the spatiality, theatricality and performativity of emerging forms of urban citizenship.
Pelvic trauma mortality reduced by integrated trauma care
Authors: Fitzgerald Mark , Esser Max , Russ Matthias , Mathew Joseph , Varma Dinesh , Wilkinson Andrew , Mannambeth Rejith V , Smit Devilliers , Bernard Stephen , Mitra Biswadev
Published: June 2017

Objectives

A multidisciplinary approach that emphasised improved triage, early pelvic binder application, early administration of blood and blood products, adherence to algorithmic pathways, screening with focused sonography (FAST), early computed tomography scanning with contrast angiography, angio‐embolisation and early operative intervention by specialist pelvic surgeons was implemented in the last decade to improve outcomes after pelvic trauma. The manuscript evaluated the effect of this multi‐faceted change over a 12‐year period.

Methods

A retrospective cohort study was conducted comparing patients presenting with serious pelvic injury in 2002 to those presenting in 2013. The primary exposure and comparator variables were the year of presentation and the primary outcome variable was mortality at hospital discharge. Potential confounders were evaluated using multivariable logistic regression analysis.

Results

There were 1213 patients with a serious pelvic injury (Abbreviated Injury Scale ≥3), increasing from 51 in 2002 to 156 in 2013. Demographics, injury severity and presenting clinical characteristics were similar between the two time periods. There was a statistically significant difference in mortality from 20% in 2002 to 7.7% in 2013 (P = 0.02). The association between the primary exposure variable of being injured in 2013 and mortality remained statistically significant (adjusted odds ratio 0.10; 95% confidence interval: 0.02–0.60) when adjusted for potential clinically important confounders.

Conclusions

Multi‐faceted interventions directed at the spectrum of trauma resuscitation from pre‐hospital care to definitive surgical management were associated with significant reduction in mortality of patients with severe pelvic injury from 2002 to 2013. This demonstrates the effectiveness of an integrated, inclusive trauma system in achieving improved outcomes.
Dominance of Sulfuritalea species in nitrate‐depleted water of a stratified freshwater lake and arsenate respiration ability within the genus
Authors: Watanabe Tomohiro , Miura Aya , Iwata Tomoya , Kojima Hisaya , Fukui Manabu
Published: June 2017

Facultative autotrophs of the genus Sulfuritalea within the class Betaproteobacteria have been predicted to be an important bacterial population in stratified freshwater lakes based on previous PCR‐based studies. Here, we designed a new probe specific for the genus Sulfuritalea and performed catalysed reporter deposition‐fluorescence in situ hybridisation to enumerate cells of Sulfuritalea species throughout the water column in a stratified freshwater lake. The cells stained with the Sulfuritalea‐specific probe were detected in all hypoxic water samples collected in different seasons and years. Their abundance ranged from 1.4 × 104 to 2.1 × 105 cells ml−1, corresponding to 0.5–5.5% of the total DAPI‐stained cells and 2.3–15% of the total bacterial cells. A high abundance of Sulfuritalea species was recorded in hypoxic water samples without nitrate, which is the only known anaerobic electron acceptor for Sulfuritalea. Nitrate‐independent anaerobic respiration was further investigated using a single cultured representative of this genus, and its growth via arsenate respiration was experimentally demonstrated. In conclusion, Sulfuritalea species were found to be a major component of the planktonic bacterial community in nitrate‐depleted hypoxic water, where arsenate respiration is one of the possible energy metabolisms of Sulfuritalea.
Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes
Authors: Li Minjing , Gao Yuqian , Qian Wei‐Jun , Shi Liang , Liu Yuanyuan , Nelson William C. , Nicora Carrie D. , Resch Charles T. , Thompson Christopher , Yan Sen , Fredrickson James K. , Zachara John M. , Liu Chongxuan
Published: June 2017

Microbial enzymes catalytically drive biogeochemical processes in environments. The dynamic linkage between functional enzymes and biogeochemical species transformation has, however, rarely been investigated for decades because of the challenges to directly quantify enzymes in environmental samples. The diversity of microorganisms, the low amount of available biomass and the complexity of chemical composition in environmental samples represent the main challenges. To address the diversity challenge, we first identify several signature peptides that are conserved in the targeted enzymes with the same functionality across many phylogenetically diverse microorganisms using metagenome‐based protein sequence data. Quantification of the signature peptides then allows estimation of the targeted enzyme abundance. To achieve analyses of the requisite sensitivity for complex environmental samples with low available biomass, we adapted a recently developed ultrasensitive targeted quantification technology, termed high‐pressure high‐resolution separations with intelligent selection and multiplexing (PRISM) by improving peptide separation efficiency and method detection sensitivity. Nitrate reduction dynamics catalyzed by dissimilatory and assimilatory enzymes in a hyporheic zone sediment was used as an example to demonstrate the application of the enzyme quantification approach. Together with the measurements of biogeochemical species, the approach enables investigating the dynamic linkage between functional enzymes and biogeochemical processes.
A statistical methodology for estimating assortative mating for phenotypic traits that are labile or measured with error
Authors: Class Barbara , Dingemanse Niels J. , Araya‐Ajoy Yimen G. , Brommer Jon E.
Published: June 2017

Assortative mating in wild populations is commonly reported as the correlation between males’ and females’ phenotypes across mated pairs. Theories of partner selection and quantitative genetics assume that phenotypic resemblance of partners captures associations in “intrinsically determined” trait values. However, when considering traits with a repeatability below one (labile traits or traits measured with error), the correlation between phenotypes of paired individuals can arise from shared environmental effects on the phenotypes of paired individuals or correlated measurement error.

We introduce statistical approaches to estimate assortative mating in labile traits or traits measured with error in the presence of shared environmental effects. These approaches include (1) the correlation between the mean phenotypes of males and females, (2) the correlation between randomized values of individuals and (3) the between‐pair correlation derived from a bivariate mixed model.

We use simulations to show that the performance of these different approaches depends on the number of repeated measures within individuals or pairs, which is determined by study design, and rates of survival and divorce.

We conclude that short‐term environmental effects on phenotypes of paired individuals likely inflate estimates of assortative mating when not statistically accounted for. Our approach allows investigation of this important issue in assortative mating studies for labile traits (e.g. behaviour, physiology, or metabolism) in both socially monogamous and other mating systems, and groupings of individuals outside a mating context.
Alcohol Consumption Decreases Oxytocin Neurons in the Anterior Paraventricular Nucleus of the Hypothalamus in Prairie Voles
Authors: Stevenson Jennie R. , Young Katelyn A. , Bohidar Amelia E. , Francomacaro Lisa M. , Fasold Terra R. , Buirkle Julia M. , Ndem Jackie R. , Christian Sara C.
Published: June 2017

Background

Alcohol use disorders are associated with dysfunctional social relationships and stress responses. The neuropeptides oxytocin (OT) and vasopressin (AVP) are known to orchestrate or mediate many aspects of social behavior, stress responses, and ingestive behaviors. Because of the overlap between the effects of alcohol and the roles of OT and AVP, we sought to determine whether alcohol consumption altered expression of OT and AVP in the paraventricular nucleus (PVN) of the hypothalamus, one of the key sites for OT and AVP synthesis.

Methods

Pair‐housed adult male prairie voles were allowed to consume 15% ethanol versus water in the home cage continuously (Continuous‐Access [CA] group) or every other day for 4 hours (Intermittent‐Access [IA] group). Control animals never had access to alcohol. After 7 weeks, animals were sacrificed and their brains were removed and immunohistochemical analysis of OT‐ and AVP‐immunopositive neurons was performed.

Results

OT‐immunopositive neurons were significantly decreased in the anterior PVN in the CA but not IA group, relative to Control animals, suggesting that continuous alcohol consumption decreases the number of OT neurons. There was no effect of alcohol consumption on posterior PVN OT neurons, and no effect on PVN AVP neurons.

Conclusions

These data show that continuous‐access voluntary alcohol consumption is associated with decreased OT neurons in the anterior PVN, suggesting that alcohol‐induced alterations in the OT system should be investigated as a mechanism for alcohol‐related changes in social behavior, stress responses, and exacerbation of alcohol use disorders.
Electrical storm in a patient with Duchenne muscular dystrophy cardiomyopathy triggered by abrupt β‐blocker interruption
Authors: Fragakis Nikolaos , Sotiriadou Melani , Krexi Lydia , Vassilikos Vassilios
Published: June 2017

We present a case of a young man with Duchenne muscular dystrophy cardiomyopathy (DMDC) having an implantable cardioverter defibrillator for secondary prevention, who presented with electrical storm shortly after β‐blocker interruption. The patient was stabilized and remained free of ventricular arrhythmias soon after reinitiating b‐adrenoreceptor antagonists. The present case highlights the importance of sympathetic blockage in patients with DMDC due to existing pathophysiology of excess diastolic Ca2+ leak from sarcoplasmic reticulum as a result of ryanodine receptor dysfunction.
Experiencing and practising inclusion through friendships
Authors: Korkiamäki Riikka , Kallio Kirsi Pauliina
Published: June 2017

The late modern change in young people's community life has meant moving from traditional, place‐based communities towards more fluid and situational contexts of belonging. These youth‐initiated attachments often build on amiable relationships that fall under the umbrella of “friendship”. This paper analyses Finnish early youths’ friendship narratives that were produced by sequential participatory methods. It introduces the dimensional and flexible spaces created in and through the participants’ friendships. These indicate relational spheres of actual and imagined activities where young people engage with people and places important to them. As a result, the paper first shows how young people together with their peers develop committed ties of belonging that reach beyond physical connection, and how these ties constitute experiential spatial attachments. Second, it demonstrates how they also make friends with kin and non‐kin adults and how these intergenerational friendships expand the variety of inclusionary spaces available to them. The findings provide alternative insights into young people's experiences and the practices of social and spatial inclusion. We hope they help to develop cross‐generational inclusionary policies that acknowledge youths’ amiable relationships as important potential in their lived communities.
“Less‐than‐fluent” and culturally connected: Language learning and cultural fluency as research methodology
Authors: Drozdzewski Danielle
Published: June 2017

The purpose of this paper is to critically explore language learning and cultural fluency as a research methodology. Deploying an auto‐ethnographic approach, I scrutinise my programme of language learning and forays into the cultural to highlight how knowledge of the cultural contexts of a language, and not just the language itself, have provided nuanced insights into Polish cultural memory and identity. The paper's specific contribution is to agitate for a greater recognition of the value of cultural understanding and language learning as a distinct methodological approach. I track how the process of learning the Polish language and its cultural intricacies has included both acts of speaking and comprehending how words are (re)presented in their cultural contexts.
Commentary on Cross‐Cultural Perspectives on Positive Youth Development With Implications for Intervention Research
Authors: Koller Silvia H. , Verma Suman
Published: June 2017

There is a growing focus on youth positive development issues among researchers and practitioners around the world. In this special issue of Child Development, each of the international authors provides new perspectives and understanding about youth developmental assets in different cultural settings. The present commentary (a) examines some of the cross‐cultural themes that emerge from the four articles by international authors in this issue with implications for positive youth development (PYD) and (b) how intervention science can benefit by incorporating a PYD approach. As evident, youth involved in contexts that provide positive resources from significant others not only were less likely to exhibit negative outcomes, but also were more likely to show evidence of positive development.