bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractVisual 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

ABSTRACTAdvances 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

AbstractWe 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

AbstractUropathogenicEscherichia 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.ImportanceUropathogenicEscherichia 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

AbstractInter-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

AbstractVariability 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.
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

AbstractRegulated 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

AbstractPlant 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

ABSTRACTInformational 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

AbstractTeredinidae 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

PurposeThe 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/approachUsing 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.FindingsResults 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/implicationsOnly two strategic flexibility decisions were considered in this paper, however, researcher could investigate other strategic flexibility decisions on OP.Practical implicationsThe 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/valueThe 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.