bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of deterministic and stochastic processes on microbial community assembly during aerobic granulation
Authors: Liébana Raquel , Modin Oskar , Persson Frank , Szabó Enikö , Hermansson Malte , Wilén Britt-Marie
Published: June 2018

Aerobic granular sludge is an energy efficient and compact biofilm process for wastewater treatment which has received much attention during the last decades and is now being implemented in full-scale. However, the factors involved in microbial community assembly during formation of granules are poorly understood and little is known about the reproducibility in treatment performance and community structure. Here we show that both deterministic and stochastic factors exert a dynamic influence during microbial community assembly into granular sludge. During granulation, the microbial communities in three replicate sequencing batch reactors followed similar successional trajectories of the most abundant taxa and showed similar dynamics in diversity. Deterministic factors dominated the assembly of the most abundant community members as the microbial community transitioned from floccular to granular form. Stochastic factors mostly affected rare members of the communities and caused the microbial community structure to diverge in one of the reactors; however, this did not have an impact on the treatment performance. This demonstrates that the reactor function and the dynamics of the most abundant community members are in fact reproducible during the formation of aerobic granules.
Attention to a threat-related feature does not interfere with concurrent attentive feature selection
Authors: Boylan Maeve R. , Kelly Mia N. , Thigpen Nina N. , Keil Andreas
Published: June 2018

Visual features that are associated with a task and those that predict noxious events both prompt selectively heightened visuocortical responses. Conflicting views exist regarding how the competition between a task-related and a threat-related feature is resolved when they co-occur in time and space. Utilizing aversive differential Pavlovian conditioning, we investigated the visuocortical representation of two simultaneously presented, fully overlapping visual stimuli. Stimuli were isoluminant red and green random dot kinematograms (RDKs) which flickered at two tagging frequencies (8.57 Hz, 12 Hz) to elicit distinguishable steady-state visual evoked potentials (ssVEPs). Occasional coherent motion events prompted a motor response or predicted a noxious noise. These events occurred either in the green (task cue), the red (threat cue), or in both RDKs simultaneously. In an initial habituation phase, participants responded to coherent motion of the green RDK with a key press, but no loud noise was presented at any time. Here, selective amplification was seen for the task-relevant (green) RDK, but interference was observed when both RDKs simultaneously showed coherent motion. Upon pairing the threat cue with the noxious noise in the subsequent acquisition phase, the threat cue-evoked ssVEP (red RDK) was also amplified, but this amplification did not interact with amplification of the task cue, and did not alter the behavioral or visuocortical interference effect seen during simultaneous coherent motion. Results demonstrate that although competing feature conjunctions result in interference in visual cortex, the acquisition of a bias towards an individual threat-related feature does not result in additional cost effects.
Up, down, and out: optimized libraries for CRISPRa, CRISPRi, and CRISPR-knockout genetic screens
Authors: Sanson Kendall R , Hanna Ruth E , Hegde Mudra , Donovan Katherine F , Strand Christine , Sullender Meagan E , Vaimberg Emma W , Goodale Amy , Root David E , Piccioni Federica , Doench John G
Published: June 2018

Advances in CRISPR-Cas9 technology have enabled the flexible modulation of gene expression at large scale. In particular, the creation of genome-wide libraries for CRISPR knockout (CRISPRko), CRISPR interference (CRISPRi), and CRISPR activation (CRISPRa) has allowed gene function to be systematically interrogated. Here, we evaluate numerous CRISPRko libraries and show that our recently-described CRISPRko library (Brunello) is more effective than previously published libraries at distinguishing essential and non-essential genes, providing approximately the same perturbation-level performance improvement over GeCKO libraries as GeCKO provided over RNAi. Additionally, we developed genome-wide libraries for CRISPRi (Dolcetto) and CRISPRa (Calabrese). Negative selection screens showed that Dolcetto substantially outperforms existing CRISPRi libraries with fewer sgRNAs per gene and achieves comparable performance to CRISPRko in the detection of gold-standard essential genes. We also conducted positive selection CRISPRa screens and show that Calabrese outperforms the SAM library approach at detecting vemurafenib resistance genes. We further compare CRISPRa to genome-scale libraries of open reading frames (ORFs). Together, these libraries represent a suite of genome-wide tools to efficiently interrogate gene function with multiple modalities.tracr
Simulation-based approaches to characterize metagenome coverage as a function of sequencing effort and microbial community structure
Authors: Royalty Taylor , Steen Andrew D.
Published: June 2018

We applied simulation-based approaches to characterize how microbial community structure influences the amount of sequencing effort to reconstruct metagenomes that are assembled from short read sequences. An initial analysis evaluated the quantity, completion, and contamination of complete-metagenome-assembled genome (complete-MAG) equivalents, a bioinformatic-pipeline normalized metric for MAG quantity, as a function of sequencing effort, on four preexisting sequence read datasets taken from a maize soil, an estuarine sediment, the surface ocean, and the human gut. These datasets were subsampled to varying degrees of completeness in order to simulate the effect of sequencing effort on MAG retrieval. Modeling suggested that sequencing efforts beyond what is typical in published experiments (1 to 10 Gbp) would generate diminishing returns in terms of MAG binning. A second analysis explored the theoretical relationship between sequencing effort and the proportion of available metagenomic DNA sequenced during a sequencing experiment as a function of community richness, evenness, and genome size. Simulations from this analysis demonstrated that while community richness and evenness influenced the amount of sequencing required to sequence a community metagenome to exhaustion, the effort necessary to sequence an individual genome to a target fraction of exhaustion was only dependent on the relative abundance of the corresponding organism and its genome size. A software tool, GRASE, was created to assist investigators further explore this relationship. Re-evaluation of the relationship between sequencing effort and binning success in the context of the relative abundance of genomes, as opposed to base pairs, provides a framework to design sequencing experiments based on the relative abundance of microbes in an environment rather than arbitrary levels of sequencing effort.
Identification and characterization of a phase-variable element that regulates the autotransporter UpaE in uropathogenicEscherichia coli
Authors: Battaglioli E.J. , Goh K.G.K , Atruksang T. S. , Schwartz K. , Schembri M. A. , Welch R.A.
Published: June 2018

UropathogenicEscherichia coli(UPEC) are the most common etiological agent of uncomplicated urinary tract infection (UTI). An important mechanism of gene regulation in UPEC is phase variation that involves inversion of a promoter-containing DNA element via enzymatic activity of tyrosine recombinases, resulting in biphasic, ON or OFF expression of target genes. The UPEC reference strain CFT073 has five tyrosine site-specific recombinases that function at two previously characterized promoter inversion systems,fimSandhyxS. Three of the five recombinases are located proximally to their cognate target elements, which is typical of promoter inversion systems. The genes for the other two recombinases, IpuA and IpuB are located distal from these sites. Here, we identified and characterized a third phase variable invertible element in CFT073,ipuSlocated proximal toipuAandipuB. The inversion ofipuSis catalyzed by four of the five CFT073 recombinases. Orientation of the element drives transcription of a two-gene operon containingipuR, a predicted LuxR-type regulator, andupaE, a predicted autotransporter. We show that the predicted autotransporter UpaE is surface-located and facilitates biofilm formation as well as adhesion to extracellular matrix proteins in a K-12 recombinant background. Consistent with this phenotype, theipuSON condition in CFT073 results in defective swimming motility, increased adherence to human kidney epithelial cells, and a positive competitive kidney colonization advantage in experimental mouse UTI infections. Overall, the identification of a third phase-switch in UPEC that is regulated by a shared set of recombinases describes a complex phase-variable virulence network in UPEC.

Importance

UropathogenicEscherichia coli(UPEC) is the most common cause of urinary tract infection (UTI). ON versus OFF phase-switching by inversion of small DNA elements at two chromosome sites in UPEC regulates the expression of important virulence factors, including the type 1 fimbriae adhesion organelle. In this report, we describe a third invertible element,ipuS, in the UPEC reference strain CFT073. The inversion ofipuScontrols the phase variable expression ofupaE, an autotransporter gene that encodes a surface protein involved in adherence to extracellular matrix proteins and colonization of the kidneys in a murine model of UTI.
Inter-basin water transfers and the expansion of aquatic invasive species
Authors: Gallardo Belinda , Aldridge David C.
Published: June 2018

Inter-basin Water Transfers (IBWT) are recognized as one of the major pathways of freshwater invasion. They provide a direct link between previously isolated catchments and may modify the habitat conditions of the receiving waters such that they become more favourable for the establishment of invasive species. Combined, IBWT and invasive species will intensify the stress upon native species and ecosystems. Using the Severn and Thames Rivers-two of the largest river systems in Great Britain—as a case study, here we assess the potential influence of IBWT on the expansion of invasive species and thus their impact on biodiversity conservation. The Thames Valley is subject to extensive water abstraction, and an increasing population means that supplemented flow from the River Severn is being considered. Multi-scale Suitability Models, based on climate and water chemistry respectively, provided novel evidence that there is serious risk for further spread of invasive species in the focus area, particularly of the quagga mussel, a recent invader of the Thames River. Native freshwater mussels are particularly vulnerable to changing environmental conditions, and may suffer the decrease in alkalinity and increase in sedimentation associated with an IBWT from the lower Severn to the upper Thames. Regional models suggest considerable overlap between the areas suitable for three vulnerable native freshwater mussels and the expansion of invasive species that negatively impact upon the native mussels. This study illustrates the use of novel spatially-explicit techniques to help managers make informed decisions about the risks associated with introducing aquatic invasive species under different engineering scenarios. Such information may be especially important under new legislation (e.g. EU Invasive Species Regulation No 1143/2014) which increases the responsibility of water managers to contain and not transfer invasive species into new locations.
Resource co-limited growth in fluctuating environments
Authors: Koussoroplis Apostolos-Manuel , Schälicke Svenja , Raatz Michael , Bach Moritz , Wacker Alexander
Published: June 2018

Variability in the supply of limiting resources determines consumer-resource interactions. Yet, how consumers are affected by variability when multiple resources co-limit growth remains unknown. We use a two-resource DEB model to predict how consumer somatic growth rate responds to the temporal structure (i.e. fluctuation frequency, phase and covariance) of single and co-limiting resources supply. Subsequently, we experimentally test the model predictions usingDaphnia magna(co-)limited by dietary phosphorus and cholesterol supply. Both model and experiments indicate that for certain fluctuation frequencies, resource fluctuation phase and (co)variance can heavily affect somatic growth. The model suggests that dynamic resource storage and assimilation efficiency adjustment are key for predicting the frequencies at which the growth rate is mostly affected by (co)variance and phase. In a context of ongoing anthropogenic landscape homogenization, our results offer novel insights on how co-occurring perturbations to the temporal structure of resource supply can affect consumer performance.
Amyloid β oligomers constrict human capillaries in Alzheimer’s disease via signalling to pericytes
Authors: Nortley Ross , Mishra Anusha , Jaunmuktane Zane , Kyrargyri Vasiliki , Madry Christian , Gong Hui , Richard-Loendt Angela , Brandner Sebastian , Sethi Huma , Attwell David
Published: June 2018

Vascular compromise occurs early in Alzheimer’s disease (AD) and other dementias1–3. Amyloid β (Aβ) reduces cerebral blood flow4–6 and, as most of the cerebral vasculature resistance is in capillaries7, Aβ might mainly act on contractile pericytes on capillary walls8–10. Employing human tissue to establish disease-relevance, and rodent experiments to define mechanism, we now show that Aβ constricts brain capillaries at pericyte locations in human subjects with cognitive decline. Applying soluble Aβ1-42 oligomers to live human cortical tissue constricted capillaries. Using rat cortical slices, this was shown to reflect Aβ evoking capillary pericyte contraction, with an EC50 of 4.7 nM, via the generation of reactive oxygen species and activation of endothelin ET-A receptors. In freshly-fixed diagnostic biopsies from human patients investigated for cognitive decline, mean capillary diameters were less in subjects showing Aβ deposition than in subjects without Aβ deposition. For patients with Aβ deposition, the capillary diameter was 31% less at pericyte somata than away from somata, predicting a halving of blood flow. Constriction of capillaries by Aβ will contribute to the energy lack1–3 occurring in AD, which promotes further Aβ generation11,12. This mechanism reconciles the amyloid hypothesis13–15 with the earliest events in AD being vascular1.
Single molecule imaging reveals the concerted release of myosin from regulated thin filaments
Authors: Inchingolo A. V. , Mihailescu M. , Hongsheng D. , Kad N. M.
Published: June 2018

Regulated thin filaments (RTFs) tightly control striated muscle contraction through calcium binding to troponin, which in turn shifts the position of tropomyosin on actin to expose myosin binding sites. The binding of the first myosin holds tropomyosin in a position such that more myosin binding sites on actin are available, resulting in cooperative activation. Troponin and tropomyosin also act to turn off the thin filament; however, this is antagonized by the high local concentration of myosin, questioning how the thin filament relaxes. To provide molecular details of deactivation we use the RTF tightrope assay, in which single RTFs are suspended between pedestals above a microscope coverslip surface. Single molecule imaging of GFP tagged myosin-S1 (S1-GFP) is used to follow the activation of RTF tightropes. In sub-maximal activation conditions, S1-GFP molecules bind forming metastable clusters, from which release and rebinding of S1-GFP leads to prolonged activation in these regions. Because the RTFs are not fully active we are able to directly observe deactivation in real time. Using a Reversible Jump Markov Chain Monte Carlo model we are able to dynamically assess the fate of active regions. This analysis reveals that myosin binding occurs in a stochastic stepwise fashion; however, an unexpectedly large probability of multiple simultaneous detachments is observed. This suggests that deactivation of the thin filament is a coordinated, active process.
Paralogues of thePXYandERreceptor kinases enforce radial patterning in plant vascular tissue
Authors: Wang Ning , Bagdassarian Kristine S. , Doherty Rebecca E. , Wang Xiao Y. , Kroon Johannes T. , Wang Wei , Jermyn Ian H. , Turner Simon R. , Etchells J. Peter
Published: June 2018

Plant cell walls do not allow cells to migrate, thus plant growth and development is entirely the consequence of changes to cell division and cell elongation. Where tissues are arranged in concentric rings, expansion of inner tissue, such as that which occurs during vascular development, must be coordinated with cell division and/or expansion of the outer tissue layers, endodermis, cortex, and epidermis, in order for tissue integrity to be maintained. Little is known of how coordination between cell layers occurs, but non-cell autonomous signalling could provide an explanation. Endodermis-derived EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) ligands have been shown to signal to the ERECTA (ER) receptor kinase present in the phloem.ERinteracts withPHLOEM INTERCALLATED WITH XYLEM(PXY), a receptor present in the procambium. The PXY ligand, TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF) is derived fromCLE41which is expressed in the phloem. These factors therefore represent a mechanism by which intertissue signalling could occur to control radial expansion between vascular and non-vascular tissue in plant stems. Here we show thatERregulates expression ofPXYparalogues,PXL1andPXL2, and that in turnPXY,PXL1andPXL2together withER, regulate the expression ofERL1andERL2, genes paralogous toER.PXY,PXL1,PXL2andERalso regulate the expression of ER-ligands. Genetic analysis of these six receptor kinase genes demonstrated that they are required to control organisation, proliferation and cell size across multiple tissue layers. Taken together, our experiments demonstrate that ER signalling attenuatesPXLexpression in the stem, thus influencing vascular expansion and patterning. We anticipate that similar regulatory relationships, where tissue growth is controlled via cell signals moving across different tissue layers, will coordinate tissue layer expansion throughout the plant body.
Spatial Release from Informational Masking: Evidence from Functional Near Infrared Spectroscopy
Authors: Zhang Min , Ihlefeld Antje
Published: June 2018

Informational masking (IM) can greatly reduce speech intelligibility, but the neural mechanisms underlying IM are not understood. Binaural differences between target and masker can improve speech perception. In general, improvement in masked speech intelligibility due to provision of spatial cues is called spatial release from masking. Here, we focused on an aspect of spatial release from masking, specifically, the role of spatial attention. We hypothesized that in a situation with IM background sound 1) attention to speech recruits lateral frontal cortex (LFCx), and 2) LFCx activity varies with direction of spatial attention. Using functional near infrared spectroscopy (fNIRS), we assessed LFCx activity bilaterally in normal-hearing listeners. In experiment 1, two talkers were simultaneously presented. Listeners either attended to the target talker (speech task) or they listened passively to an unintelligible, scrambled version of the acoustic mixture (control task). Target and masker differed in pitch and interaural time difference (ITD). Relative to the passive control, LFCx activity increased during attentive listening. Experiment 2 measured how LFCx activity varied with ITD, by testing listeners on the speech task in experiment 1, except that talkers either were spatially separated by ITD or co-located. Results show that directing of auditory attention activates LFCx bilaterally. Moreover, right LFCx is recruited more strongly in the spatially separated as compared with co-located configurations. Findings hint that LFCx function contributes to spatial release from masking in situations with IM.
The gill-associated symbiont microbiome is a main source of woody-plant polysaccharide hydrolase genes and secondary metabolite gene clusters inNeoteredo reynei, a unique shipworm from south Atlantic mangroves
Authors: Brito Thais L. , Campos Amanda B. , von Meijenfeldt F.A. Bastiaan , Daniel Julio P. , Ribeiro Gabriella B. , Silva Genivaldo G. Z. , Wilke Diego V. , Morais Daniela , Dutilh Bas E. , Meirelles Pedro M. , Tridade-Silva Amaro E.
Published: June 2018

Teredinidae is a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract ofNeoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the symbiotic gammaproteobacterial community of gills of differentN. reyneispecimens, indicating closely related bacterial types are shared, while intestine and digestive glands presented related, and more diverse microbiomes that did not overlap with gills. Annotation of assembled metagenomic contigs revealed that the symbiotic community ofN. reyneigills was a hotspot of woody-polysaccharides degrading hydrolase genes, and Biosynthetic Gene Clusters (BGCs), while in contrast, the digestive tract microbiomes seems to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbioticTeredinibacterstrains from the gills, a representative ofTeredinibacter turnerae“clade I” strain, and a yet to be cultivatedTeredinibactersp. type. TheseTeredinibactergenomes, as well as unbinned gill-derived gammaproteobacteria contigs, code for novelty including an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Multivariate analyzes have shown that the secondary metabolome encoded on the genomes ofTeredinibacterrepresentatives, including the genomes binned fromN. reyneigill’s metagenomes, stand out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results grouped here add to the growing characterization of shipworm symbiotic microbiomes and indicate that theN. reyneigill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.
The integrated impact of new product and market flexibilities on operational performance
Authors: Alamro Ahmed Salameh , Awwad Abdulkareem Salameh , Anouze Abdel Latef M.
Published: June 2018

Purpose

The purpose of this paper is to investigate and test the relationship between a company’s strategic flexibility, as evidenced by new product development flexibility and market flexibility, and its operational performance (OP) in Jordanian manufacturing companies.

Design/methodology/approach

Using a survey questionnaire, data were collected against two strategic decisions market and new product flexibility (NPF) from 222 middle and senior managers belonging to 116 Jordanian manufacturing firms. Confirmatory factor analysis was employed to investigate the effects of these two strategic decisions on OP.

Findings

Results show a significant positive relationship between both NPF and market flexibility and OP. No significant differences between small and medium enterprises and large companies are found, indicating that the model is valid for both sizes. Also, the additional analyses suggest that the proposition that both NPF and market flexibility are important for OP was correct.

Research limitations/implications

Only two strategic flexibility decisions were considered in this paper, however, researcher could investigate other strategic flexibility decisions on OP.

Practical implications

The strategic flexibility level, in terms of NPF and market flexibility, that is needed for coping with uncertainty equips managers to handle challenges by enhancing the company’s controlled capacity through a considerable reduction in response time. An improvement in the company’s strategic flexibility enhances its overall performance and competitiveness and this, in turn, has a positive impact on its long-term sustainability.

Originality/value

The paper provides insights into the strategic flexibility decision practices in a Jordanian context. It provides further evidence that both market flexibility and NPF are significant in enhancing OP.
Adapting the scrum methodology for establishing the dynamic inter-organizational collaboration
Authors: Mollahoseini Ardakani Mohammad Reza , Hashemi Seyyed Mohsen , Razzazi Mohammadreza
Published: June 2018

Purpose

The purpose of this paper is to propose an applicable method for establishing the dynamic inter-organizational collaborations (DIOCs) based on the scrum methodology.

Design/methodology/approach

The scrum methodology embedded within the context of the DIOC project life cycle was used and adapted to being usable with specific characteristics of the project.

Findings

In order to succeed in the highly competitive, dynamic and changing business environments, the organizations need to change their view of business practices. The transition from the traditional status of manufacturing to the inter-organizational collaborations can be one of the fundamental changes in the modern business management. The proposed method has the capability to establish DIOCs effectively and efficiently whilst guaranteeing agility, competitiveness, and risk timely management.

Originality/value

Establishing collaborative alliances via association of various experienced and professional organizations and producing the value-added market’s need services is an effective and efficient solution for survival of SMEs in the current competitive, dynamic and changing business environment. So far, different frameworks, reference models/architectures, and many theoretical discussions have been presented for DIOCs context, but these representations are conceptual, empirical and generic. This paper aims to propose an applicable iterative and incremental method for establishing the DIOC which guarantees the agility and risk timely management of the establishment process and promotes competitiveness of partners.
The Dragon and the River: Poetic Parallelism in Hazardous Research
Authors: Zani Leah
Published: June 2018

I offer poetic parallelism as evidence for an ethnography of authoritarian power in Laos and as a conceptual frame for understanding hazards in ethnography and anthropological knowledge production. Parallel poems take the form of juxtaposed statements, often characterized by multiplicity and contradiction. In an authoritarian context marked by state violence, the very form of the parallels is data on Lao society. I examine poetic parallels as a provocation to write field poems rather than field notes.
At the “Love Commandos”: Narratives of Mobility Among Intercaste Couples in a Delhi Safe House
Authors: Sadana Rashmi
Published: June 2018

Meeting runaway intercaste couples hiding in a safe house in Delhi led me to reflect on the kinds of mobility at work in their lives and in the city today. By highlighting the social and physical parameters of their mobility in a single ethnographic context, I argue that it is the quest for mobility rather than an expression of individual choice that is most significant about their flouting of social norms.
Fiction/Creative Nonfiction First Prize
Authors: Yarbakhsh Elisabeth
Published: June 2018

Fiction provides a way through the ethical quagmire brought about by the necessity of providing both anonymity to research participants and an honest account of the field. Sheyda, the main protagonist in this short story, is a compilation of three Afghan women who make an appearance only in fragmentary form in my doctoral thesis. Her story, as it is told here, exposes the multiple tragedies and indignities that circumscribe Afghan life in contemporary Iran.
On a Hill with No Name
Authors: Champney Brynn
Published: June 2018

This narrative, based on fieldwork in Rwanda in 2008, shifts between two women who share the same physical space but lack the ability to communicate verbally: the novice anthropologist and the eldest woman in her host family's household. The Rwandan woman, Claire, speaks in the first person, while a third‐person narrative follows the student anthropologist, who is never named. I intend this choice to speak against the power inequity, select humanizing, and traditional focus on the Western protagonist. The anthropologist wants to hear this woman's voice but only hears her story told by more powerful male voices. Because Claire doesn't actually speak, her “voice” is only imagined, projected, and misrepresented through the words of a woman who is far removed from her. This is profoundly problematic. I have no solution, only a desire to grapple with the troubling questions surrounding speaking for the subaltern, versus not attempting to speak on behalf of anyone at all. This attempt to share Claire's voice falls short in every way, but the attempt is still important. Her story deserves to be heard and read, despite the inadequacies of the author. How can we co‐create more nuanced and transparent ways of doing this?
Collapse of farmland bird populations in an Eastern European country following its EU accession
Authors: Reif Jiří , Vermouzek Zdeněk
Published: June 2018

Eastern European countries are considered a stronghold for the continent's farmland biodiversity. The abundance of farmland birds is one important element of this biodiversity. At the end of the 20th century, member states of the European Union (EU) experienced serious population declines of farmland birds due to agricultural intensification, which was not observed in the Eastern European nonmember states. In 2004, 10 mostly Eastern European countries acceded to the EU. It is thus important to ask whether this historical step resulted in changes of agricultural production and, in turn, in farmland bird populations. Here we used annual crop yields and monitoring data on farmland bird abundance in an Eastern European new EU‐member state and showed that agricultural production intensified and farmland bird populations declined steeply after country's EU accession. These results indicate that entering EU's Common Agricultural Policy caused significant deterioration of farmland biodiversity in a once biodiversity‐rich region.
Synthesis and application of a novel, triphendioxazine‐based, phosphorus‐containing acid dye for wool
Authors: Cui Jinhai , Zhang Shufen
Published: June 2018

A novel phosphorus‐containing acid dye based on triphendioxazine was designed and synthesised from diphenylamine through a series of reactions. The dye has a navy‐blue colour, high molar extinction coefficient of 5.32 × 104 l/mol·cm, and high substantivity for dyeing wool in a salt‐free, aqueous dyebath. A high exhaustion value of 98.2% on wool fabrics was recorded at 3% omf and a liquor ratio of 1:20. The wash fastness values of the acid dye, including colour change and staining on cotton and wool, were grades 5, 4 and 4–5, respectively. The dry and wet fastness are grades 4–5 and 4, respectively. In addition, light fastness reaches grades 6–7 at 3% omf dye concentration. These dye properties are better than those of commercial triphendioxazine dyes, for example, CI Direct Blue 106 and CI Reactive Blue 198, under analogous dyeing conditions.
Leisure Experiences of Military Couples Postdeployment
Authors: Chandler Kelly D. , Dattilo John , Derrick Taff B. , Moeller Jeremy
Published: June 2018

Objective

This qualitative study was designed to explore how leisure is experienced by military couples postdeployment and the extent to which couples use leisure to cope with deployment or promote reintegration.

Background

To date, many studies have investigated how deployment affects relationship quality and stability. There is a dearth of literature on the leisure experiences of combat veterans and their spouses. Studying couples' leisure experiences may illuminate underlying processes that can explain couple relationship quality postdeployment.

Method

Ten combat veterans of Operation Iraqi Freedom or Operation Enduring Freedom (OIF/OEF) and their spouses/partners participated in separate in‐depth, face‐to‐face interviews about their perceptions of leisure and relationship experiences postdeployment.

Results

Four themes emerged: (a) deployment changes veterans and couples' leisure, (b) spouses support leisure and reintegration postdeployment, (c) leisure provides insight into military and deployment experiences, and (d) deployment helps couples cultivate appreciation.

Conclusion

This study provides evidence that everyday couple leisure experiences (e.g., watching movies, doing home projects) may be integral in fostering reintegration postdeployment.

Implications

Practitioners are encouraged to educate military couples about the potential of free or inexpensive leisure experiences to promote reintegration by providing daily opportunities for positive interactions and creating contexts to share enjoyable moments.
Hold on Tight: Coping Strategies of Persons With Bipolar Disorder and Their Partners
Authors: Granek Leeat , Danan Dor , Bersudsky Yuly , Osher Yamima
Published: June 2018

Objective

To explore coping strategies for persons with bipolar affective disorder and their partners.

Background

Bipolar disorder poses interpersonal and practical challenges for patients and their partners. Although the divorce rate is high among persons with bipolar disorder, few studies have examined how these people and their partners cope with the condition.

Method

11 persons with bipolar affective disorder and 10 partners of people with bipolar affective disorder were interviewed separately about coping. Data were analyzed using the grounded theory method.

Results

Both patients and partners reported that coping strategies included professional help, social support, and emotional, instrumental, and religious coping strategies.

Conclusions

Persons with bipolar disorder and their partners draw on similar coping strategies, but the former draw more on social support and instrumental coping strategies, and their partners draw on emotional coping strategies. Both members of the couple are dependent on the use of professional support—psychiatric, psychological, and psychosocial—when it is readily available and easily accessible, and this was a key aspect of coping with the disorder.

Implications

Clinical interventions should focus on providing support for partners, who are integral to the health and well‐being of persons with bipolar disorder and who experience substantial strain associated with their caregiving duties. Focusing on strategies to strengthen the spousal relationship is an essential aspect of care.
Health champions in South London: evaluation of training, and impact on public health
Authors: Micallef Ricarda , Grewal Jaspal Singh , Khan Sharifah , Wells Joshua , Kayyali Reem
Published: June 2018

Objectives

The Healthy Living Pharmacy framework, introduced in England in 2008, provides a tailored approach to the implementation of pharmacy services locally, facilitated by qualified ‘Health Champions’ (HCs). The study aimed to evaluate the perceived value of the 1-day level 2 HC training by assessing knowledge and confidence of HC pre- and post-training, and changes in practice. The views of additional stakeholders on factors that either obstructed or facilitated pharmacy engagement are also explored.

Methods

This study used a mixed method approach. Pre- and post-training surveys evaluating HC pre-existing knowledge and understanding of their role were used. Additionally, qualitative semi-structured interviews were undertaken with four key groups: participating pharmacists, non-participating pharmacists, Local Pharmaceutical Committee leads and Public Health Leads from Public Health England.

Key findings

A total of 354 pre-training evaluation surveys were completed on the training day (100%), compared to 54 post-evaluation postal surveys with a 19% (n = 54/282) response rate. The post-evaluation of the training indicated that 83% (n = 45) of qualified HC were actively implementing their new role, with observed increased confidence and service provision. From the 22 interviews conducted two major themes emerged including: Training and Impact. Training had a positive impact on staff knowledge and confidence plus service delivery.

Conclusion

An immediate impact was observed in increasing HC knowledge and confidence, service delivery and awareness of facilities for patient sign-posting. There was no statistical evidence to support a positive effect stemming from training on services. However, it was identified that time and further training were needed to both provide and assess value within local public health.
Colour pattern component phenotypic divergence can be predicted by the light environment
Authors: Kranz Alexandrea M. , Cole Gemma L. , Singh Priti , Endler John A.
Published: June 2018

The sensory drive hypothesis predicts that across different light environments sexually selected colour patterns will change to increase an animal's visual communication efficiency within different habitats. This is because individuals with more efficient signal components are likely to have more successful matings and hence produce more offspring. However, how colour pattern signals change over multiple generations under different light environmental conditions has not been tested experimentally. Here, we manipulated colour pattern signal efficiency by providing different ambient light environments over multiple generations to examine whether male colour pattern components change within large replicated populations of guppies (Poecilia reticulata). We report that colour patches change within populations over time and are phenotypically different among our three different light environments. Visual modelling suggests that the majority of these changes can be understood by considering the chroma, hue and luminance of each colour patch as seen by female guppies under each light environment. Taken together, our results support the hypothesis that different environmental conditions during signal reception can directly or indirectly drive the phenotypic diversification of visual signals within species.
Comparison of wiping and rinsing techniques after oral care procedures in critically ill patients during endotracheal intubation and after extubation: A prospective cross‐over trial
Authors: Muramatsu Keita , Matsuo Koichiro , Kawai Yusuke , Yamamoto Tsukasa , Hara Yoshitaka , Shimomura Yasuyo , Yamashita Chizuru , Nishida Osamu
Published: June 2018

Aim

Endotracheal intubation of critically ill patients increases the risk of aspiration pneumonia, which can be reduced by regular oral care. However, the rinsing of the residual oral contaminants after mechanical cleaning carries the risk of aspirating the residue during the intubation period. Removing the contaminants by wiping with mouth wipes could be an alternative to rinsing with water because of no additional fluid. This study tested: (i) the amount of oral bacteria during endotracheal intubation and after extubation; and (ii) the changes in the bacterial count during oral care procedures.

Methods

Thirty‐five mechanically ventilated patients in the intensive care unit were enrolled. The amount of bacteria on the dorsal tongue surface was counted before and following oral care and then after the elimination of contaminants either by rinsing with water and suctioning or by wiping with mouth wipes. The oral bacterial amount was compared statistically between the intubation and extubation status and among set time points during the oral care procedure.

Results

The oral bacterial count was significantly decreased after extubation. During the oral care procedure, the oral bacterial amount was significantly lower after eliminating the contaminants either by rinsing or wiping, with no remarkable difference between the elimination techniques.

Conclusions

The findings suggest that the oral bacterial amount is elevated during endotracheal intubation, which could increase the risk of aspiration pneumonia. The significant reduction in the bacterial count by wiping indicates that it might be a suitable alternative to rinsing for mechanically ventilated patients.
Geography, productivity, and trade: Does selection explain why some locations are more productive than others?
Authors: Accetturo Antonio , Di Giacinto Valter , Micucci Giacinto , Pagnini Marcello
Published: June 2018

Two main hypotheses are usually put forward to explain the productivity advantages of larger cities: agglomeration economies and firm selection. Combes et al. (2012) propose an empirical approach to disentangle these two effects and find no impact of selection on local productivity differences. We theoretically show that selection effects do emerge when heterogeneous trade costs and the different spatial scale at which agglomeration and selection may work are properly taken into account. Our empirical findings confirm that agglomeration effects play a major role. However, they also show a substantial increase in the importance of the selection effect.
The Mobilization of Evangelical Protestants in the Nonprofit Sector: Parachurch Foundings Across U.S. Counties, 1998–2016
Authors: Scheitle Christopher P. , McCarthy John D.
Published: June 2018

The political mobilization of evangelicals has been widely chronicled, but their mobilization in the civil sector has received far less attention. That mobilization is embodied in parachurch organizations, which are nonprofits infused with religious purpose but independent of congregations and denominations. Here we examine the features of local communities that account for variation in the creation of parachurch organizations. Drawing upon a broad number of theoretical approaches, we develop a series of expectations about the variation in parachurch foundings across counties. Using IRS registration records and a diverse set of other secondary data sources, we assess the impact of religious structures and cultures, organizational densities, and government and social movement contexts on parachurch foundings across U.S. counties. Our analysis finds that counties with higher rates of adherence to evangelical Protestantism generate more parachurch organizations, but only if the county is not too saturated by evangelicals. On the other hand, counties with higher rates of adherence to Catholic, mainline Protestant, and Latter‐Day Saint traditions generate fewer parachurch organizations.
Hybrid Probabilistic–Possibilistic Treatment of Uncertainty in
Building Energy Models: A Case Study of Sizing Peak Cooling
Loads
Authors: Khayatian Fazel , MeshkinKiya Maryam , Baraldi Piero , Di Maio Francesco , Zio Enrico
Published: June 2018

Optimal sizing of peak loads has proven to be an important factor affecting the overall energy consumption of heating ventilation and air-conditioning (HVAC) systems. Uncertainty quantification of peak loads enables optimal configuration of the system by opting for a suitable size factor. However, the representation of uncertainty in HVAC sizing has been limited to probabilistic analysis and scenario-based cases, which may limit and bias the results. This study provides a framework for uncertainty representation in building energy modeling, due to both random factors and imprecise knowledge. The framework is shown by a numerical case study of sizing cooling loads, in which uncertain climatic data are represented by probability distributions and human-driven activities are described by possibility distributions. Cooling loads obtained from the hybrid probabilistic–possibilistic propagation of uncertainty are compared to those obtained by pure probabilistic and pure possibilistic approaches. Results indicate that a pure possibilistic representation may not provide detailed information on the peak cooling loads, whereas a pure probabilistic approach may underestimate the effect of uncertain human behavior. The proposed hybrid representation and propagation of uncertainty in this paper can overcome these issues by proper handling of both random and limited data.
Opiates increase the number of hypocretin-producing cells in human and mouse brain and reverse cataplexy in a mouse model of narcolepsy
Authors: Thannickal Thomas C. , John Joshi , Shan Ling , Swaab Dick F. , Wu Ming-Fung , Ramanathan Lalini , McGregor Ronald , Chew Keng-Tee , Cornford Marcia , Yamanaka Akihiro , Inutsuka Ayumu , Fronczek Rolf , Lammers Gert Jan , Worley Paul F. , Siegel Jerome M.
Published: June 2018

Heroin addiction is accompanied by an increase in detected hypocretin (orexin) neurons, and in narcoleptic mice deficient in these neurons, morphine can reverse cataplexy.
Complete Genome Sequences of Two Chikungunya Viruses Imported into China
Authors: Zhang Xiaomin , Huang Yalan , Wang Miao , Yang Fan , Cheng Jinquan , Wan Chengsong , Zhang Renli
Published: June 2018

Here, we isolated two chikungunya virus strains (SZ1050 and SZ1239) from patients infected with chikungunya virus who were returning to China from India and Indonesia, respectively. Strain SZ1050 was classed in the Indian Ocean lineage, and strain SZ1239 belonged to the Asian lineage.
Draft Genome Assemblages of 10 Xanthomonas vasicola pv. zeae Strains, Pathogens Causing Leaf Streak Disease of Maize in South Africa
Authors: Sanko Tomasz J. , Kraemer Astrid S. , Niemann Niklaas , Gupta Arvind K. , Flett Bradley C. , Mienie Charlotte , Bezuidenhout Carlos C.
Published: June 2018

Maize bacterial leaf streak disease has spread across maize crops in South Africa and therefore potentially poses a threat to maize production and food security. Until recently, this pathogen was identified as a
Xanthomonas campestris
pathovar, whereas our South African genomes seem to be more divergent and create their own subclade.
Complete Genome Sequence of a Bluetongue Virus Serotype 15 Strain Isolated from China in 1996
Authors: Liao Defang , Yang Heng , Xiao Lei , Zhu Jianbo , Wang Jinpin , Li Zhanhong , Zhang Nianzu , Li Huachun
Published: June 2018

The full-genome sequence of bluetongue virus serotype 15 (BTV-15) strain B105/YN/1996 isolated in China was determined for the first time. The virus was isolated from sentinel cattle in Yunnan Province, China, in 1996.
Draft Genome Sequence of Bacillus altitudinis Lc5, a Biocontrol and Plant Growth-Promoting Endophyte Strain Isolated from Indigenous Black Rice of Manipur
Authors: Potshangbam Momota , Sahoo Dinabandhu , Verma Preveen , Verma Sandhya , Kalita Mohan Chandra , Indira Devi Sarangthem
Published: June 2018

We report here the 3.6-Mb draft genome of
Bacillus altitudinis
Lc5, a potential plant growth promoter and an active antagonistic endophyte of black rice. This genome study will provide better insights into the strain’s mechanisms for plant growth promotion and biocontrol, thus facilitating its application in organic agriculture.
Complete Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Senftenberg and Montevideo Isolates Associated with a 2016 Multistate Outbreak in the United States
Authors: Haendiges Julie , Blessington Tyann , Zheng Jie , Davidson Gordon , Miller Jesse D. , Hoffmann Maria
Published: June 2018

A multistate outbreak of 11
Salmonella
infections linked to pistachio nuts occurred in 2016. In this announcement, we report the complete genome sequences of four
Salmonella enterica
subsp.