bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping RNA-capsid interactions and RNA secondary structure within authentic virus particles using next-generation sequencing
Authors: Zhou Yiyang , Routh Andrew
Published: August 2019

To characterize RNA-capsid binding sites genome-wide within mature RNA virus particles, we have developed a Next-Generation Sequencing (NGS) platform: Photo-Activatable Ribonucleoside Cross-Linking (PAR-CL). In PAR-CL, 4-thiouracil is incorporated into the encapsidated genomes of authentic virus particles and subsequently UV-crosslinked to adjacent capsid proteins. We demonstrate that PAR-CL can readily and reliably identify capsid binding sites in genomic viral RNA by detecting crosslink-specific uridine to cytidine transitions in NGS data. Using Flock House virus (FHV) as a model system, we identified highly consistent and significant PAR-CL signals across virus RNA genome indicating a clear tropism of the encapsidated RNA genome. Certain interaction sites correlate to previously identified FHV RNA motifs. We additionally performed dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to generate a high-resolution profile of single-stranded genomic RNA inside viral particles. Combining PAR-CL and DMS-MaPseq reveals that the predominant RNA-capsid sites favor double-stranded RNA regions. We disrupted secondary structures associated with PAR-CL sites using synonymous mutations, resulting in varied effects to virus replication, propagation, and packaging. Certain mutations showed substantial deficiency in virus replication, suggesting these RNA-capsid sites are multifunctional. These provide further evidence to support that FHV packaging and replication are highly coordinated and inter-dependent events.

Importance

Icosahedral RNA viruses must package their genetic cargo into the restrictive and tight confines of the protected virions. High resolution structures of RNA viruses have been solved by Cryo-EM and crystallography, but the encapsidated RNA often eluded visualization due to the icosahedral averaging imposed during image reconstruction. Asymmetrical reconstructions of some icosahedral RNA virus particles have revealed that the encapsidated RNAs conform to specific structures, which may be related to programmed assembly pathway or an energy-minima for RNA folding during or after encapsidation. Despite these advances, determining whether encapsidated RNA genomes conform to a single structure and determining what regions of the viral RNA genome interact with the inner surface of the capsid shell remains challenging. Furthermore, it remains to be determined whether there exists a single RNA structure with conserved topology in RNA virus particles or an ensemble of genomic RNA structures. This is important as resolving these features will inform the elusive structures of the asymmetrically encapsidated genomic material and how virus particles are assembled.
Downscaling livestock census data using multivariate predictive models: sensitivity to modifiable areal unit problem
Authors: Da Re Daniele , Gilbert Marius , Chaiban Celia , Bourguignon Pierre , Thanapongtharm Weerapong , Robinson Timothy P. , Vanwambeke Sophie O.
Published: August 2019

The analysis of census data aggregated by administrative units introduces a statistical bias known as the modifiable areal unit problem (MAUP). Previous researches have mostly assessed the effect of MAUP on upscaling models. The present study contributes to clarify the effects of MAUP on the downscaling methodologies, highlighting how a priori scales and shapes choices could influence the results. We aggregated chicken and duck fine-resolution census in Thailand, using three administrative census levels in regular and irregular shapes. We then disaggregated the data within the Gridded Livestock of the World analytical framework, sampling predictors in two different ways. A sensitivity analysis on Pearson’srcorrelation statistics and RMSE were carried out to understand how size and shapes of the response variables affect the goodness-of-fit and downscaling performances. We showed that scale, rather than shapes and sampling methods, affected downscaling precision, suggesting that training the model using the finest administrative level available is preferable. Moreover, datasets showing non-homogeneus distribution but instead spatial clustering seemed less affected by MAUP, yielding higher Pearson’srvalues and lower RMSE compared to a more spatially homogenous dataset. Implementing aggregation sensitivity analysis in spatial studies could help to interpret complex results and disseminate robust products.
Crl activates transcription by stabilizing the active conformation of the master stress factor σS
Authors: Xu Juncao , Cui Kaijie , Shen Liqiang , Shi Jing , Li Lingting , You Linlin , Fang Chengli , Zhao Guoping , Feng Yu , Yang Bei , Zhang Yu
Published: August 2019

σS is a master transcription initiation factor that protects bacterial cells from various harmful environmental stresses and antibiotic pressure. Although its mechanism remains unclear, it is known that full activation of σS-mediated transcription requires a σS-specific activator, Crl. In this study, we determined a 3.80 Å cryo-EM structure of an E. coli transcription activation complex (E. coli Crl-TAC) comprising E. coli σS-RNAP holoenzyme, Crl, and a nucleic-acid scaffold. The structure reveals that Crl interacts with the domain 2 of σS (σS2), sharing no interaction with promoter DNA. Subsequent hydrogen-deuterium exchange mass spectrometry (HDX-MS) results indicate that Crl stabilizes key structural motifs of σS2 to promote the assembly of σS-RNAP holoenzyme and also to facilitate formation of the RNA polymerase-promoter DNA open complex (RPo). Our study demonstrates a unique DNA contact-independent mechanism of transcription activation, thereby defining a previously unrecognized mode of transcription activation in cells.
Grazer behavior can regulate large-scale patterning of community states
Authors: Karatayev Vadim A. , Baskett Marissa L. , Kushner David J. , Shears Nicholas T. , Caselle Jennifer E. , Boettiger Carl
Published: August 2019

Ecosystem patterning can arise from environmental heterogeneity, biological feedbacks that produce multiple persistent ecological states, or their interaction. One source of feed-backs is density-dependent changes in behavior that regulates species interactions. By fitting state-space models to large-scale (∼500km) surveys on temperate rocky reefs, we find that behavioral feedbacks best explain why kelp and urchin barrens form either reef-wide patches or local mosaics. Best-supported models in California include feedbacks where starvation intensifies grazing across entire reefs create reef-scale, alternatively stable kelp- and urchin-dominated states (32% of reefs). Best-fitting models in New Zealand include the feedback of urchins avoiding dense kelp stands that can increase abrasion and predation risk, which drives a transition from shallower urchin-dominated to deeper kelp-dominated zones, with patchiness at 3-8m depths with intermediate wave stress. Connecting locally-studied processes with region-wide data, we highlight how behavior can explain community patterning and why some systems exhibit community-wide alternative stable states.
Three-dimensional observations of an aperiodic oscillatory gliding motility behaviour inMyxococcus xanthususing confocal interference reflection microscopy
Authors: Rooney Liam M. , Kölln Lisa S. , Scrimgeour Ross , Amos William B. , Hoskisson Paul A. , McConnell Gail
Published: August 2019

The Delta-proteobacterium,Myxococcus xanthus, has been used as a model for bacterial motility and to provide insights of bacterial swarming behaviours. Fluorescence microscopy techniques have shown that various mechanisms are involved in gliding motility, but these have almost entirely been limited to 2D studies and there is currently no understanding of gliding motility in a 3D context. We present here the first use of confocal interference reflection microscopy (IRM) to study gliding bacteria, and we reveal aperiodic oscillatory behaviour with changes in the position of the basal membrane relative to the coverglass on the order of 90 nmin vitro. Firstly, we use a model plano-convex lens specimen to show how topological information can be obtained from the wavelength-dependent interference pattern in IRM. We then use IRM to observe glidingM. xanthusand show that cells undergo previously unobserved changes in their height as they glide. We compare the wild-type with mutants of reduced motility, which also exhibit the same changes in adhesion profile during gliding. We find that the general gliding behaviour is independent of the proton motive force-generating complex, AglRQS, and suggest that the novel behaviour we present here may be a result of recoil and force transmission along the length of the cell body following firing of the Type IV pili.
Fungal hyphae colonization byBacillus subtilisrelies on biofilm matrix components
Authors: Kjeldgaard Bodil , Listian Stevanus A. , Ramaswamhi Valliyammai , Richter Anne , Kiesewalter Heiko T. , Kovács Ákos T.
Published: August 2019

Bacteria interact with their environment including microbes and higher eukaryotes. The ability of bacteria and fungi to affect each other are defined by various chemical, physical and biological factors. During physical association, bacterial cells can directly attach and settle on the hyphae of various fungal species. Such colonization of mycelia was proposed to be dependent on biofilm formation by the bacteria, but the essentiality of the biofilm matrix was not represented before. Here, we demonstrate that secreted biofilm matrix components of the soil-dwelling bacterium,Bacillus subtilisare essential for the establishment of a dense bacterial population on the hyphae of the filamentous black mold fungus,Aspergillus nigerand the basidiomycete mushroom,Agaricus bisporus. We further illustrate that these matrix components can be shared among various mutants highlighting the community shaping impact of biofilm formers on bacteria-fungi interactions.
Pharmaco-genetic screen to uncover actin regulators targeted by prostaglandins duringDrosophilaoogenesis
Authors: Spracklen Andrew J. , Lamb Maureen C. , Groen Christopher M. , Tootle Tina L.
Published: August 2019

Prostaglandins (PGs) are lipid signaling molecules with numerous physiologic functions, including pain/inflammation, fertility, and cancer. PGs are produced downstream of cyclooxygenase (COX) enzymes, the targets of non-steroidal anti-inflammatory drugs (NSAIDs). In numerous systems, PGs regulate actin cytoskeletal remodeling, however, their mechanisms of action remain largely unknown. To address this deficiency, we undertook a pharmaco-genetic interaction screen during late-stageDrosophilaoogenesis.Drosophilaoogenesis is as an established model for studying both actin dynamics and PGs. Indeed, during Stage 10B, cage-like arrays of actin bundles surround each nurse cell nucleus, and during Stage 11, the cortical actin contracts, squeezing the cytoplasmic contents into the oocyte. Both of these cytoskeletal properties are required for follicle development and fertility, and are regulated by PGs. Here we describe a pharmaco-genetic interaction screen that takes advantage of the facts that Stage 10B follicles will mature in culture and COX inhibitors, such as aspirin, block thisin vitrofollicle maturation. In the screen, aspirin was used at a concentration that blocks 50% of the wild-type follicles from maturing in culture. By combining this aspirin treatment with heterozygosity for mutations in actin regulators, we quantitatively identified enhancers and suppressors of COX inhibition. Here we present the screen results and initial follow-up studies on three strong enhancers – Enabled, Capping protein, and non-muscle Myosin II Regulatory Light Chain. Overall, these studies provide new insight into how PGs regulate both actin bundle formation and cellular contraction, properties that are not only essential for development, but are misregulated in diseases.
Dopamine modulates the integrity of the perisynaptic extracellular matrix at excitatory synapses
Authors: Mitlöhner Jessica , Kaushik Rahul , Niekisch Hartmut , Blondiaux Armand , Gee Christine E. , Happel Max F.K. , Gundelfinger Eckart , Dityatev Alexander , Frischknecht Renato , Seidenbecher Constanze
Published: August 2019

In the brain, Hebbian-type and homeostatic forms of plasticity are affected by neuromodulators like dopamine (DA). Modifications of the perisynaptic extracellular matrix (ECM), controlling functions and mobility of synaptic receptors as well as diffusion of transmitters and neuromodulators in the extracellular space, are crucial for the manifestation of plasticity. Mechanistic links between synaptic activation and ECM modifications are largely unknown. Here, we report that neuromodulation via D1-type DA receptors can induce targeted ECM proteolysis specifically at excitatory synapses of rat cortical neurons via proteases ADAMTS-4 and -5. We show that receptor activation induces increased proteolysis of brevican (BC) and aggrecan, two major constituents of the adult ECM,in vivoandin vitro. ADAMTS immunoreactivity is detected near synapses, and shRNA-mediated knockdown reduced BC cleavage. We outline a molecular scenario how synaptic activity and neuromodulation are linked to ECM rearrangements via increased cAMP levels, NMDA receptor activation, and intracellular calcium signaling.
Spatial simulation of co-designed land-cover change scenarios in New England: Alternative futures and their consequences for conservation priorities
Authors: Thompson Jonathan R. , Plisinski Joshua , Lambert Kathy Fallon , Duveneck Matthew J. , Morreale Luca , McBride Marissa , MacLean Meghan Graham , Weis Marissa , Lee Lucy
Published: August 2019

To help prepare for an uncertain future, planners and scientists often engage with stakeholders to co-design alternative scenarios of land-use change. Methods to translate the resulting qualitative scenarios into quantitative simulations that characterize the future landscape condition are needed to understand consequences of the scenarios while maintaining the legitimacy of the process. We use the New England Landscape Futures (NELF) project as a case study to demonstrate a transparent method for translating participatory scenarios to simulations of Land-Use and Land-Cover (LULC) change and for understanding the major drivers of land-use change and diversity of plausible scenarios and the consequences of alternative land-use pathways for conservation priorities. The NELF project co-designed four narrative scenarios that contrast with a Recent Trends scenario that projects a continuation of observed changes across the 18-million-hectare region during the past 20 years. Here, we (1) describe the process and utility of translating qualitative scenarios into spatial simulations using a dynamic cellular land change model; (2) evaluate the outcomes of the scenarios in terms of the differences in the LULC configuration relative to the Recent Trends scenario and to each other; (3) compare the fate of forests within key areas of concern to the stakeholders; and (4) describe how a user-inspired outreach tool was developed to make the simulations and analyses accessible to diverse users. The four alternative scenarios populate a quadrant of future conditions that crosses high to low natural resource planning and innovation with local to global socio-economic connectedness. The associated simulations are strongly divergent in terms of the amount of LULC change and the spatial pattern of change. Features of the simulations can be linked back to the original storylines. Among the scenarios there is a fivefold difference in the amount of high-density development, and a twofold difference in the amount of protected land. Overall, the rate of LULC change has a greater influence on forestlands of concern to the stakeholders than does the spatial configuration. The simulated scenarios have been integrated into an online mapping tool that was designed via a user-engagement process to meet the needs of diverse stakeholders who are interested the future of the land and in using future scenarios to guide land use planning and conservation priorities.
Cross-feeding modulates the rate and mechanism of antibiotic resistance evolution in a model microbial community of Escherichia coli and Salmonella enterica
Authors: Adamowicz Elizabeth M. , Muza Michaela A. , Chacón Jeremey M. , Harcombe William R.
Published: August 2019

With antibiotic resistance rates on the rise, it is critical to understand how microbial species interactions influence the evolution of resistance. We have previously shown that in obligate mutualisms the survival of any one species (regardless of its intrinsic resistance) is contingent on the resistance of its cross-feeding partners, setting the community antibiotic tolerance at that of the ‘weakest link’ species. In this study, we extended that hypothesis to test whether obligate cross-feeding would limit the extent and mechanisms of antibiotic resistance evolution. In both rifampicin and ampicillin treatments, we observed that resistance evolved more slowly in obligate co-cultures of E. coli and S. enterica than in monocultures. While we observed similar mechanisms of resistance arising under rifampicin selection, under ampicillin selection different resistance mechanisms arose in co-cultures and monocultures. In particular, mutations in an essential cell division protein, ftsI, arose in S. enterica only in co-culture. A simple mathematical model demonstrated that reliance on a partner is sufficient to slow the rate of adaptation, and can change the distribution of adaptive mutations that are acquired. Our results demonstrate that cooperative metabolic interactions can be an important modulator of resistance evolution in microbial communities.

Significance statement

Little is known about how ecological interactions between bacteria influence the evolution of antibiotic resistance. We tested the impact of metabolic interactions on resistance evolution in an engineered two-species bacterial community. Through experimental and modeling work, we found that obligate metabolic interdependency slows the rate of resistance acquisition, and can change the type and magnitude of resistance mutations that evolve. This work suggests that resistance evolution may be slowed by targeting both a pathogen and its metabolic partners with antibiotics. Additionally, we showed that community context can generate novel trajectories through which antibiotic resistance evolves.
Visualising nascent chain dynamics at the ribosome exit tunnel by cryo-electron microscopy
Authors: Javed Abid , Wlodarski Tomasz , Cassaignau Anaïs. M.E. , Cabrita Lisa D. , Christodoulou John , Orlova Elena V.
Published: August 2019

Ribosomes maintain a healthy cellular proteome by synthesising proteins. The nascent chain (NC), emerges into the cellular milieu via the ribosomal exit tunnel, which is an active component that regulates the NC passage. How the NC dynamics at the exit tunnel affect NC folding remains to be an important question, the answer on which has strong implications to medicine. Here, we report high-resolution cryo-EM maps of ribosome nascent-chain complexes (RNCs) displaying distinct steps during biosynthesis. These RNC structures reveal a range of pathways adopted by the NC. The most pronounced diversity in the NC trajectories were found in the vestibule region. Rearrangements of several ribosomal components further suggest that these elements may actively monitor the emerging NC during translation. The ribosome-NC contacts within the vestibule define these NC pathways and modulate position of a folded immunoglobulin domain outside the ribosome.
Combining case-control status and family history of disease increases association power
Authors: Hujoel Margaux L.A. , Gazal Steven , Loh Po-Ru , Patterson Nick , Price Alkes L.
Published: August 2019

Family history of disease can provide valuable information about an individual’s genetic liability for disease in case-control association studies, but it is currently unclear how to best combine case-control status and family history of disease. We developed a new association method based on posterior mean genetic liabilities under a liability threshold model, conditional on both case-control status and family history (LT-FH); association statistics are computed via linear regression of genotypes and posterior mean genetic liabilities, equivalent to a score test. We applied LT-FH to 12 diseases from the UK Biobank (average N=350K). We compared LT-FH to genome-wide association without using family history (GWAS) and a previous proxy-based method for incorporating family history (GWAX). LT-FH was +63% (s.e. 6%) more powerful than GWAS and +36% (s.e. 4%) more powerful than the trait-specific maximum of GWAS and GWAX, based on the number of independent genome-wide significant loci detected across all diseases (e.g. 690 independent loci for LT-FH vs. 423 for GWAS); the second best method was GWAX for lower-prevalence diseases and GWAS for higher-prevalence diseases, consistent with simulations. We also confirmed that LT-FH was well-calibrated (assessed via stratified LD score regression attenuation ratio), consistent with simulations. When using BOLT-LMM (instead of linear regression) to compute association statistics for all three methods (increasing the power of each method), LT-FH was +67% (s.e. 6%) more powerful than GWAS and +39% (s.e. 4%) more powerful than the trait-specific maximum of GWAS and GWAX. In summary, LT-FH greatly increases association power in case-control association studies when family history of disease is available.
Fission yeast Pak1 phosphorylates anillin-like Mid1 for spatial control of cytokinesis
Authors: Magliozzi Joseph O. , Sears Jack , Cressey Lauren , Brady Marielle , Opalko Hannah E. , Kettenbach Arminja N. , Moseley James B.
Published: August 2019

Protein kinases direct polarized growth by regulating the cytoskeleton in time and space, and could play similar roles in cell division. We found that the Cdc42-activated polarity kinase Pak1 colocalizes with the assembling contractile actomyosin ring (CAR) and remains at the division site during septation. Mutations inpak1led to defects in CAR assembly and genetic interactions with cytokinesis mutants. Through a phosphoproteomic screen, we identified novel Pak1 substrates that function in polarized growth and cytokinesis. For cytokinesis, we found that Pak1 regulates the localization of its substrates Mid1 and Cdc15 to the CAR. Mechanistically, Pak1 phosphorylates the Mid1 N-terminus to promote its association with cortical nodes that act as CAR precursors. Defects in Pak1-Mid1 signaling lead to misplaced and defective division planes, but these phenotypes can be rescued by synthetic tethering of Mid1 to cortical nodes. Our work defines a new signaling mechanism driven by a cell polarity kinase that promotes CAR assembly in the correct time and place.

Magliozzi et al. show that fission yeast cell polarity kinase Pak1 regulates cytokinesis. Through a phosphoproteomic screen and subsequent mutant analysis, their work uncovers direct targets and mechanisms for Pak1 activity during cell division.
Measurement of Atom Resolvability in CryoEM Maps with Q-scores
Authors: Pintilie Grigore , Zhang Kaiming , Su Zhaoming , Li Shanshan , Schmid Michael F. , Chiu Wah
Published: August 2019

CryoEM density maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryoEM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands, and other solvent atoms, using models fitted to or derived from cryoEM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryoEM maps for both protein and RNA. Assuming the models they are calculated from are well-fitted to the map, Q-scores can thus be used as another measure to indicate resolvability of features in cryoEM maps at various scales, from entire complexes down to individual atoms. Q-score analysis of multiple cryoEM maps of the same proteins derived from different labs confirms reproducibility of structural features down to water and ion atoms.
Statistical modelling of bacterial promoter sequences for regulatory motif discovery with the help of transcriptome data: application to Listeria monocytogenes
Authors: Sultan Ibrahim , Fromion Vincent , Schbath Sophie , Nicolas Pierre
Published: August 2019

Automatic de novo identification of the main regulons of a bacterium from genome and transcriptome data remains a challenge. To address this task, we propose a statistical model of promoter DNA sequences that can use information on exact positions of the transcription start sites and condition-dependent expression profiles. Two main novelties are to allow overlaps between motif occurrences and to incorporate covariates summarising expression profiles (e.g. coordinates in projection spaces or hierarchical clustering trees). All parameters are estimated using a dedicated trans-dimensional Markov chain Monte Carlo algorithm that adjusts, simultaneously, for many motifs and many expression covariates: the width and palindromic properties of the corresponding position-weight matrices, the number of parameters to describe position with respect to the transcription start site, and the choice of relevant expression covariates. A data-set of transcription start sites and expression profiles available for the Listeria monocytogenes is analysed. The results validate the approach and provide a new global view of the transcription regulatory network of this important model food-borne pathogen. A previously unreported motif that may play an important role in the regulation of growth was found in promoter regions of ribosomal protein genes.
Land snail dispersal, abundance and diversity on green roofs
Authors: McKinney Michael L. , Gladstone Nicholas S. , Lentz Jillian G. , Jackson Faith A.
Published: August 2019

We present the first major systematic study of land snail diversity on green roofs. We surveyed 27 green roofs and the adjacent ground habitat in six major cities in the southeastern United States. We found a total of 18 species of land snails, with three considered to be non-native, invasive species. The majority of land snails encountered in surveys are widespread, generalist species, typically adapted to open habitats. Twelve of the land snails encountered are “greenhouse” species that are very commonly transported via the horticultural trade. Therefore, we infer that at least some land snail species are introduced to green roofs via initial green roof installation and associated landscaping. Additionally, some similarity between roof and ground populations indicates dispersal from nearby ground habitats. The major determinants of snail species diversity and community composition are largely derived from local environmental conditions that are significantly correlated to the quality of green roof maintenance regime and plant diversity. Roof area, height, and age are seemingly not significant characteristics that dictate land snail species richness.
Effects of trap confinement on personality measurements in two terrestrial rodents
Authors: Brehm Allison M. , Tironi Sara , Mortelliti Alessio
Published: August 2019

In recent years individual differences in the behavior of animals, or personalities, have been shown to influence the response of individuals to changing environments and have important ecological implications. As researchers strive to understand and predict the responses of individuals and populations to anthropogenic changes, personality studies in wild populations will likely continue to increase. Studies of personality in wild populations often require that animals are live-trapped before behavioral observation can occur; however, it is unknown what impact live trapping may have on the behavior of trapped individuals. Specifically, if the duration of trap confinement directly influences behavior, then by obtaining wild animals through live-trapping are we confounding the very measurements we are most interested in? To investigate this question, we performed a study using two small mammal species. We positioned high-definition trail cameras on Longworth small mammal traps in the field to observe capture events and record the time of capture. We then measured personality in captured deer mice (Peromyscus maniculatus) and southern red-backed voles (Myodes gapperi) using three standardized tests. With a repeatability analysis, we confirmed which behaviors could be considered personality traits, and through linear and generalized linear models, we found that the time an animal had spent confined to a trap before testing did not affect the majority of behaviors exhibited. Our results showed two weak behavioral effects of confinement duration on boldness and docility depending on whether an individual had been trapped previously. Our results suggest that personality measurements of wild, trapped small mammals are not determined by trapping procedures, but that researchers should control for whether an animal is naïve to trapping during analysis.
Cross-cultural adaptation and psychometric evaluation of the Yoruba version of Oswestry disability index
Authors: Mbada Chidozie Emmanuel , Oguntoyinbo Oluwabunmi Esther , Fasuyi Francis Oluwafunso , Idowu Opeyemi Ayodiipo , Odole Adesola Christiana , Ayanniyi Olusola , Johnson Olubusola Esther , Orimolade Elkanah Ayodele , Oladiran Ajibola Babatunde , Fatoye Francis
Published: August 2019

Introduction

Low Back Pain is a common public health problem worsened by maladaptive beliefs and incongruent back pain behaviour. It is imperative to develop outcome measures to assess these beliefs among patients with chronic LBP. This study aimed to cross-culturally adapt and determine the psychometric properties of the Yoruba version of the ODI (ODI-Y).

Methods

The ODI-Y was cross-culturally adapted following the process involving forward translation, synthesis, backward translation, expert review, and pilot testing. One hundred and thirty-six patients with chronic LBP took part in the validation of the ODI-Y; 86 of these individuals took part in the test-retest reliability (within 1-week interval) of the translated instrument. Internal consistency and test-retest reliability of the ODI-Y were determined using the Cronbach’s alpha and intra-class correlation. Other psychometric properties explored included the factor structure and fit, convergent validity, standard error of measurement and the minimal detectable change.

Results

The mean age of the respondents was 50.5±10.6years. The ODI-Y showed a high internal consistency, with a Cronbach’s alpha (α) of 0.81. Test-retest of the Yoruba version of the ODI within 1-week interval yielded an Intra-Class Correlation coefficient of 0.89. The ODI-Y yielded a two-factor structure which accounted for 51.7% of the variance but showed poor fit. Convergent of ODI-Y with the visual analogue scale was moderate (r=0.30; p=0.00). The standard error of measurement and minimal detectable change of the ODI-Y were 2.0 and 5.5.

Conclusions

The ODI was adapted into the Yoruba language and proved to have a good factor structure and psychometric properties that replicated the results of other obtainable versions. We recommend it for use among Yoruba speaking patients with low-back pain.
K-mer counting with low memory consumption enables fast clustering of single-cell sequencing data without read alignment
Authors: Shi Christina Huan , Yip Kevin Y.
Published: August 2019

K-mer counting has many applications in sequencing data processing and analysis. However, sequencing errors can produce many false k-mers that substantially increase the memory requirement during counting. We propose a fast k-mer counting method, CQF-deNoise, which has a novel component for dynamically identifying and removing false k-mers while preserving counting accuracy. Compared with four state-of-the-art k-mer counting methods, CQF-deNoise consumed 49-76% less memory than the second best method, but still ran competitively fast. The k-mer counts from CQF-deNoise produced cell clusters from single-cell RNA-seq data highly consistent with CellRanger but required only 5% of the running time at the same memory consumption, suggesting that CQF-deNoise can be used for a preview of cell clusters for an early detection of potential data problems, before running a much more time-consuming full analysis pipeline.
Segmentation in intangible heritage of humanity (ICH) events: the Oruro Carnival
Authors: Pérez-Gálvez Jesús Claudio , Gomez-Casero Gema , Choque Tito Juan , Jara Alba Carol Angélica
Published: August 2019

Purpose

The purpose of this paper is to characterize the international tourists who visit a cultural event, such as the Oruro Carnival (Bolivia), that is catalogued as Intangible Cultural Heritage of Humanity by UNESCO.

Design/methodology/approach

To achieve this purpose, a segmentation is made based on the combination of two theoretical models used and contrasted in similar research: the model of McKercher (2002), based on the cultural motivations to go to a destination, and that of Poriaet al.(2003), based on the emotional perception of the visitor in relation to the heritage they visit.

Findings

Four types of tourists are thus identified: alternative, cultural, emotional and patrimonial. Likewise, the research includes an assessment of the most relevant tourist attributes linked to the Oruro Carnival, which is much more positive among international tourists with greater cultural motivation and emotional bonding.

Originality/value

The principal originality factor and innovation is analysing the cultural motivations and the emotional perception of the visitor in relation to the heritage they visit.
Performance evaluation of hazelnut oil with copper nanoparticles - a new entrant for sustainable lubrication
Authors: Shafi Wani K. , Raina Ankush , Ul Haq Mir Irfan
Published: August 2019

Purpose

This paper aims to investigate the friction and wear performance of Hazelnut oil with copper (Cu) nano additives.

Design/methodology/approach

The experiments were performed on a pin-on-disc tribometer in boundary and mixed lubrication regimes. Copper nanoparticles were added in 0.5 and 1 Wt.% concentrations and corresponding Stribeck curves were generated with a base oil and with oil containing Cu nanoparticles. Surface analysis of aluminium 6061 pins was conducted using an optical microscope, scanning electron microscope and energy dispersive spectroscopy.

Findings

The lubricant with 0.5 Wt.% Cu nanoparticles exhibited better results. An improvement of around 80 per cent in coefficient of friction and around 99 per cent in specific wear rate was observed. The film formation capability of the Cu nanoparticles led to an overall improvement in tribological properties of the base oil.

Originality

Experiments were performed to evaluate the tribological performance of a new lubricant (Hazelnut oil) using Cu nanoparticles. The results obtained herein suggest that Hazelnut oil has a great potential to replace the conventional mineral oils in the field of industrial lubrication.
Study on the influence of round pits arrangement patterns on tribological properties of journal bearings
Authors: Mao Yazhou , Jianxi Yang , Wenjing Xu , Yonggang Liu
Published: August 2019

Purpose

The purpose of this paper is to investigate the effect of round pits arrangement patterns on tribological properties of journal bearing. In this paper, the tribological behaviors of journal bearing with different arrangement patterns under lubrication condition were studied based on M-2000 friction and wear tester.

Design/methodology/approach

The friction and wear of journal bearing contact surface were simulated by ANSYS. The wear mechanism of bearing contact surfaces was investigated by the means of energy dispersive spectrum analysis on the surface morphology and friction and wear status of the journal bearing specimens by Scanning Electron Microscopy (SEM) and Energy Dispersive Spectrometer (EDS). Besides, the wearing capacity of the textured bearing was predicted by using the GM (1,1) and Grey–Markov model.

Findings

As the loads increase, the friction coefficient of journal bearing specimens decrease first and then increase slowly. The higher rotation speed, the lower friction coefficient and the faster temperature build-up. The main friction method of the bearing sample is three-body friction. The existence of texture can effectively reduce friction and wear. In many arrangement patterns, the best is 4# bearing with round pits cross-arrangement pattern. Its texturing diameters are 60 µm and 125 µm, and the spacing and depth are 200 µm and 25 µm, respectively. In addition, the Grey–Markov model prediction result is more accurate and fit the experimental value better.

Originality/value

The friction and wear mechanism is helpful for scientific research and engineers to understand the tribological behaviors and engineering applications of textured bearing. The wear capacity of textured bearing is predicted by using the Grey–Markov model, which provides technical help and theoretical guidance for the service life and reliability of textured bearing.
Effect of non-Newtonian magneto-elastohydrodynamic on performance characteristics of slider-bearings
Authors: Mouda Mouhcine , Nabhani Mohamed , El Khlifi Mohamed
Published: August 2019

Purpose

This study aims to examine the magneto-elastohydrodynamic effect on finite-width slider-bearings lubrication using a non-Newtonian lubricant.

Design/methodology/approach

Based on the magneto-hydrodynamic (MHD) theory and Stokes micro-continuum mechanics, the modified two-dimensional Reynolds equation including bearing deformation was derived.

Findings

It is found that the bearing deformation diminishes the load-capacity and increases the friction coefficient in comparison with the rigid case. However, the non-Newtonian effect increases load-capacity but decreases the friction coefficient. Moreover, the use of a transverse magnetic field increases both the friction coefficient and load capacity.

Originality/value

This study combines for the first time MHD and elastic deformation effects on finite-width slider-bearings using a non-Newtonian lubricant.
CPG-fuzzy-based control of a cownose-ray-like fish robot
Authors: Cao Yong , Lu Yang , Cai Yueri , Bi Shusheng , Pan Guang
Published: August 2019

Purpose

This paper aims to imitate a cownose ray to develop a fish robot with paired flexible multi-fin-ray oscillating pectoral fins (OPFs) and control it to accomplish vivid stable 3-D motions using central pattern generators (CPGs) and fuzzy algorithm.

Design/methodology/approach

The cownose ray’s asymmetric sine-like oscillations were analyzed. Then a cownose-ray-like fish robot named Robo-ray was developed, which has paired flexible multi-fin-ray OPFs to actively control the fin shape and two tail fins to control the depth. To solve the problem of coordinated control for multi-degree-of-freedom Robo-ray, CPGs were adopted. An improved phase oscillator as a CPG unit with controlled amplitude, phase lag, smooth frequency transition and asymmetric oscillation characteristic was established. Furthermore, the CPG-fuzzy algorithm was developed for vivid stable 3-D motions. The open-loop speed control, the closed-loop control of depth and yaw were established.

Findings

The kinematic comparisons indicate that Robo-ray imitates the cownose ray realistically. The experimental results of closed-loop are obtained that the depth error of Robo-ray is less than ±100 mm and the course error is less than ±3°. Furthermore, the comprehensive experiments demonstrate that Robo-ray has high mobility, stability and robustness.

Originality/value

This research makes the fish robot with OPF propulsion closer to practical applications in complex underwater environment, for instance, ocean explorations, water quality monitoring and stealth military reconnaissance. In addition, Robo-ray can be taken as a scientific tool for better understanding of the hydrodynamics of OPF batoid.
NCSS notable trade book lesson plan: Windows written by Julia Denos
Authors: Evans Dana Michelle , Robertson William Boden , Swain Holly Hilboldt
Published: August 2019

Purpose

The purpose of this paper, notable trade lesson plan, is to utilize a notable picture book in an early childhood application.

Design/methodology/approach

The approach of this notable trade book lesson plan is that of a hands-on interactive reading leading to a cultural exploration.

Findings

Young learners communicated connections with global communities, as they expressed similarities found between their evening routines and those of Germany. Opportunities arose for prekindergarten students to converse in a foreign language through a familiar song, as they discovered similarities and differences found in evening routines such as meals, games, family conversations and preparing for bedtime.

Originality/value

The value of this notable trade plan submission is in its ability to integrate geographical and cultural lessons into literacy contexts.
Teaching about American slavery and its connections to Christianity and the Bible
Authors: Shepherd Dan
Published: August 2019

Purpose

A reluctance of social studies teachers to address religious matters prevents students from understanding the intersection of two important American institutions: slavery and Christianity. The continuing importance of religion in American life and the tension centered around race relations in this country make instruction in the connections between these two institutions invaluable. Evidence for the rich spiritual experience of enslaved African Americans is both ample and easily accessed; conversely, the misuse of Christianity by the oppressors and the biblical support for abolition commonly referenced during that period can be easily explored. The paper aims to discuss these issues.

Design/methodology/approach

In addition to these historical matters, modern results of the intersection of slavery and religion prove beneficial for study. While slavery itself is an irredeemable wound on American history, one that has repercussions even to this day, the encouraging impact of Christianity in the lives of enslaved African American and their progeny is worth noting.

Findings

Finally, this topic lends itself to progressive and engaging learning activities that are cooperative, project-based and authentic.

Originality/value

The teaching of history, which wrongly has a reputation for being lifeless and dull, can be improved and energized with this content of two topics still vital in America today: race and religion.
Interplay between paternal germline and maternal effects in shaping development: The overlooked importance of behavioural ecology
Authors: Champagne Frances A.
Published: August 2019

Environmental conditions can have a lasting epigenetic impact on development, and there is increasing evidence that these effects can be transmitted across generations. Evidence for parental transmission of epigenetic variation to offspring has been primarily focused on paternal epigenetic influences induced by a male's experience of nutritional, social and toxicological exposures.

There is an assumption in the literature that paternal influence on offspring in non‐biparental species is mediated exclusively through epigenetic transmission via the germline. However, integration of concepts from behavioural ecology into the study of parental transmission of environmental effects reveals the importance of mating tactics and maternal–paternal interplay in shaping resource allocation towards offspring in considering the mechanism(s) of epigenetic transmission.

This paper describes the current state of knowledge regarding paternal epigenetic germline effects, the interplay between maternal and paternal influences and the importance of considering the complex nature of reproduction when predicting the transmission of phenotype across generations. Further, this paper highlights how incorporating concepts from behavioural ecology into the study of epigenetic transmission can refine predictions of phenotypes that emerge and create a more integrated notion of development and inheritance.

It is proposed that theoretical and methodological approaches that consider the impact of reproductive context, which include mating dynamics, fertility, variation in parental life history and assessment of maternal effects, could improve the predictions made within studies of paternal epigenetic effects on offspring development.

A free Plain Language Summary can be found within the Supporting Information of this article.
Floral volatiles structure plant–pollinator interactions in a diverse community across the growing season
Authors: Burkle Laura A. , Runyon Justin B.
Published: August 2019

While the importance of floral odours for pollinator attraction relative to visual cues is increasingly appreciated, how they structure community‐level plant–pollinator interactions is poorly understood. Elucidating the functional roles of flowering plant species with respect to their floral volatile organic compounds (VOCs) and how those roles vary over the growing season is an initial step towards understanding the contribution of floral VOCs to plant–pollinator interaction structure.

We sampled the floral VOCs, phenologies and bee visitors of naturally growing plants in a montane meadow in the Northern Rocky Mountains of USA in order to acquire a base understanding of how floral VOCs and other plant traits may structure plant–pollinator interactions across the growing season. We expected forb species with floral VOCs that were original (far from the community mean) and unique (far from the nearest neighbour) would have few pollinating partners (i.e. specialists), while forbs with non‐original or highly variable floral VOCs would form the generalist core of interactors, thereby contributing to network nestedness (specialists interacting with nested subsets of generalists). Network modularity (patterns of distinct, highly connected subnetworks) could be influenced by groups of pollinators that are attracted to or repelled by certain floral bouquets.

Species blooming in early spring emitted similar floral VOC blends containing generalist attractants, whereas floral VOC complexity was highest in mid to late summer. Forb species varied in the originality, uniqueness, and intraspecific variation (i.e. dispersion) of their floral VOCs, indicating the potential for different functional roles in plant–pollinator networks. Specifically, the originality, uniqueness and dispersion of forb species’ floral VOCs increased across the growing season.

Floral VOCs influenced forb interactions with pollinators. Floral VOCs contributed to the nested structure, but not modular structure, of community‐level plant–pollinator network structure. Forb species with more original floral VOCs were less connected, while forb species emitting more compounds and with higher intraspecific variation in floral VOCs were more connected to pollinators.

These findings show that floral scent plays important roles in structuring bee–forb interactions and guiding seasonal patterns in complex communities. Understanding seasonal patterns in floral VOCs may have important implications for plant–pollinator interactions among communities differing in species composition, or as shifts occur in suites of co‐flowering species due to climate change.

A free Plain Language Summary can be found within the Supporting Information of this article.