bluuebunny/crossref_metadata_2025 huggingface dataset:
Co-outbreak of ST37 and a novel ST3006 Klebsiella pneumoniae from multi-site infection in a neonatal intensive care unit: a retrospective study
Authors: Chen Dongjie , Hu Xinlan , Chen Falin , Li Hongru , Wang Daxuan , Li Xiaoqin , Wu Changsheng , Li Ning , Wu Shaolian , Li Zhen , Chen Liqing , Chen Yusheng
Published: May 2018

Background

The outbreak of carbapenems resistant Klebsiella pneumoniae (K. pneumoniae) is a serious public health problem, especially in the neonatal intensive care unit (NICU).

Methods

Fifteen strains of K. pneumoniae were isolated from seven neonates during June 3–28, 2017 in a NICU. Antimicrobial susceptibility was determined by the Vitek 2 system and micro-broth dilution method. Multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were used to analyse the genetic relatedness of isolates. Genome sequencing and gene function analyses were performed for investigating pathogenicity and drug resistance and screening genomic islands.

Findings

Two K. pneumoniae clones were identified from seven neonates, one ST37 strain and another new sequence type ST3006. The ST37 strain exhibited multi-drug resistance genes and resistance to carbapenem. MLST and PFGE showed that 15 strains were divided into three groups, with a high level of homology. Gene sequencing and analysis indicated that KPN1343 harboured 12 resistance genes, 15 genomic islands and 205 reduced virulence genes. KPN1344 harboured four resistance genes, 19 genomic islands and 209 reduced virulence genes.

Conclusion

Co-outbreak of K. pneumoniae involved two clones, ST36 and ST3006, causing multi-site infection. Genome sequencing and analysis is an effective method for studying bacterial resistance genes and their functions.
Diagnosing Bacterial Vaginosis with a Novel, Clinically-Actionable Molecular Diagnostic Tool
Authors: Jarvis Joseph P. , Rains Doug , Kradel Steven J. , Elliott James , Diamond Evan E. , Avaniss-Aghajani Erik , Yasharpour Farid , Shaman Jeffrey A.
Published: May 2018

Abstract/Summary

Bacterial vaginosis is a common condition among women of reproductive age and is associated with potentially serious side-effects, including an increased risk of preterm birth. Recent advancements in microbiome sequencing technologies have produced novel insights into the complicated mechanisms underlying bacterial vaginosis and have given rise to new methods of diagnosis. Here we report on the validation of a quantitative, molecular diagnostic algorithm based on the relative abundances of ten potentially pathogenic bacteria and four commensal Lactobacillus species in research subjects (n = 172) classified as symptomatic (n = 149) or asymptomatic (n = 23). We observe a clear and reinforcing pattern among patients diagnosed by the algorithm that is consistent with the current understanding of biological dynamics and dysregulation of the vaginal microbiome during infection. Using this enhanced assessment of the underlying biology of infection, we demonstrate improved diagnostic sensitivity (93%) and specificity (90%) relative to current diagnostic tools. Our algorithm also appears to provide enhanced diagnostic capabilities in ambiguous classes of patients for whom diagnosis and medical decision-making is complicated, including asymptomatic patients and those deemed “intermediate” by Nugent scoring. Ultimately, we establish CLS2.0q as a quantitative, sensitive, specific, accurate, robust, and flexible algorithm for the clinical diagnosis of bacterial vaginosis – importantly, one that is also ideal for the differential diagnosis of non-BV infections with clinically similar presentations.
Antimicrobial Activity of Tetrabromobisphenol A (TBBPA) against Staphylococcus aureus Skin Infections
Authors: Wang Chang , Ji Fang , Chen Fengjie , Chen Bolei , Zhou Zhen , Li Zhi , Liang Yong
Published: May 2018

Tetrabromobisphenol A (TBBPA) is a brominated flame retardant with selective antimicrobial activity against Gram-positive bacteria. We show that TBBPA exerts bactericidal effects by damaging the cell wall and membrane of Staphylococcus aureus (SA) without inducing antimicrobial resistance. In vivo skin infection assays indicate that a low dose of TBBPA could contribute to wound closure and attenuate SA infection and inflammatory infiltration. TBBPA has potential for use as an antimicrobial agent against Gram-positive pathogens.
Genetic variant pathogenicity prediction trained using disease-specific clinical sequencing datasets
Authors: Evans Perry , Wu Chao , Lindy Amanda , McKnight Dianalee A. , Lebo Matthew , Sarmady Mahdi , Abou Tayoun Ahmad N.
Published: May 2018

Recent advances in DNA sequencing technologies have expanded our understanding of the molecular underpinnings for several genetic disorders, and increased the utilization of genomic tests by clinicians. Given the paucity of evidence to assess each variant, and the difficulty of experimentally evaluating a variant’s clinical significance, many of the thousand variants that can be generated by clinical tests are reported as variants of unknown clinical significance. However, the creation of population-scale variant databases can significantly improve clinical variant interpretation. Specifically, pathogenicity prediction for novel missense variants can now utilize features describing regional variant constraint. Constrained genomic regions are those that have an unusually low variant count in the general population. Several computational methods have been introduced to capture these regions and incorporate them into pathogenicity classifiers, but these methods have yet to be compared on an independent clinical variant dataset. Here we introduce one variant dataset derived from clinical sequencing panels, and use it to compare the ability of different genomic constraint metrics to determine missense variant pathogenicity. This dataset is compiled from 17,071 patients surveyed with clinical genomic sequencing for cardiomyopathy, epilepsy, or RASopathies. We further utilize this dataset to demonstrate the necessity of disease-specific classifiers, and to train PathoPredictor, a disease-specific ensemble classifier of pathogenicity based on regional constraint and variant level features. PathoPredictor achieves an average precision greater than 90% for variants from all 99 tested disease genes while approaching 100% accuracy for some genes. Accumulation of larger clinical variant datasets and their utilization to train existing pathogenicity metrics can significantly enhance their performance in a disease and gene-specific manner.
Extracellular Degradation into Adenosine and the Activities of Adenosine Kinase and AMPK Mediate Extracellular NAD+-produced increases in the Adenylate Pool of BV2 Microglia under Basal Conditions
Authors: Zhang Jie , Wang Caixia , Wu Danhong , Ying Weihai
Published: May 2018

Cumulating evidence has indicated NAD+ deficiency as a common central pathological factor of multiple diseases and aging. NAD+ supplement is highly protective in various disease and aging models, while two key questions remain unanswered: 1) Does extracellular NAD+ also produce its effects through its degradation product adenosine? 2) Does extracellular NAD+ produce the protective effects by affecting cells under pathological insults only, or by affecting both normal cell and cells under pathological insults? Since extracellular NAD+ can be degraded into adenosine, and endogenous adenosine levels are in the nanomolar range under physiological conditions, extracellular NAD+ may produce its effects through its degradation into adenosine. In this study we used BV2 microglia as a cellular model to test our hypothesis that NAD+ treatment can increase the intracellular adenylate pool under basal conditions through its extracellular degradation into adenosine. Our study has shown that extracellular NAD+ increases the adenylate pool of BV2 microglia under basal conditions through its degradation into adenosine that enters the cells through equilibrative nucleoside transporters. The intracellular adenosine is converted to AMP by adenosine kinase, which increases intracellular ATP by both activating AMPK and increasing ADP that drives mitochondrial FoF1-ATP synthase. Collectively, our study has suggested that extracellular NAD+ can enhance defensive capacity of normal cells through a novel pathway, which includes extracellular NAD+ degradation into adenosine and the activities of adenosine kinase and AMPK. Our findings have also suggested that NAD+ administration in various disease and aging models may significantly affect the microglia under basal conditions.
Redefining mesothelioma types as a continuum uncovers the immune and vascular systems as key players in the diagnosis and prognosis of this disease
Authors: Alcala Nicolas , Caux Christophe , Girard Nicolas , McKay J.D. , Galateau-Salle Francoise , Foll Matthieu , Fernandez-Cuesta Lynnette
Published: May 2018

Malignant Pleural Mesothelioma (MPM) is an aggressive disease related to asbestos exposure, which incidence is expected to increase in the future, and with no effective therapeutic options. We have performed unsupervised analyses of publicly available RNAseq data for 297 MPM. We found that the molecular profile and the prognosis of this disease is better explained by a continuous model rather than by the current WHO classification into the epitheloid, biphasic and sarcomatoid histological types. The main source of variation of this continuum was explained by the immune and vascular pathways, with strong differences in the expression of pro-angiogenic genes and immune checkpoint inhibitors across samples. These data may inform future classifications of MPM and may also guide personalised therapeutic approaches for this disease.

Significance

Malignant Pleural Mesothelioma (MPM) is an aggressive disease with no effective therapeutic options. Unsupervised transcriptomic analyses of 297 MPM unveiled the vascular and the immune systems as key players in the prognosis of this disease, and identified potential therapeutic approaches for this disease targeting these pathways.
Chorioamnionitis Is a Risk Factor for Intraventricular Hemorrhage in Preterm Infants: A Systematic Review and Meta-Analysis
Authors: Villamor-Martinez Eduardo , Fumagalli Monica , Rahim Owais Mohammed , Passera Sofia , Cavallaro Giacomo , Degraeuwe Pieter , Mosca Fabio , Villamor Eduardo
Published: May 2018

Although chorioamnionitis (CA) is a well-known risk factor for white matter disease of prematurity, the association with intraventricular hemorrhage (IVH) is controversial and has not been yet systematically reviewed. We performed a systematic review and meta-analysis of studies exploring the association between CA and IVH. A comprehensive literature search was conducted using PubMed/MEDLINE and EMBASE, from their inception to 1 July 2017. Studies were included if they examined preterm infants and reported primary data that could be used to measure the association between exposure to CA and the presence of IVH. A random-effects model was used to calculate odds ratios (OR) and 95% confidence intervals (CI). We found 1284 potentially relevant studies, of which 85 met the inclusion criteria (46,244 infants, 13,432 CA cases). Meta-analysis showed that CA exposure was significantly associated with all grades IVH (OR 1.88, 95% CI 1.61-2.19), with grades 1-2 IVH (OR 1.69, 95% CI 1.22-2.34), and with grades 3-4 IVH (OR 1.62, 95% CI 1.42-1.85). Both clinical and histological CA were associated with an increased risk for developing IVH in very preterm infants. In contrast, the presence of funisitis did not increase IVH risk when compared to CA in the absence of funisitis (OR 1.22, 95% CI 0.89-1.67). Further meta-analyses confirmed earlier findings that CA-exposed infants have significantly lower gestation age (GA; mean difference [MD] −1.20 weeks) and lower birth weight (BW; MD −55g) than the infants not exposed to CA. However, meta-regression and subgroup analysis could not demonstrate an association between the lower GA and BW and the risk of IVH in the CA-exposed infants. In conclusion, our data show that CA is a risk factor for IVH, but also a risk factor for greater prematurity and more clinical instability. In contrast to other complications of prematurity, such as patent ductus arteriosus, retinopathy of prematurity, or bronchopulmonary dysplasia, the effect of CA on IVH appears to be independent of CA as causative factor for very preterm birth.
The interaction of p130Cas with PKN3 promotes malignant growth
Authors: Gemperle Jakub , Dibus Michal , Koudelková Lenka , Rosel Daniel , Brábek Jan
Published: May 2018

Protein p130Cas constitutes an adaptor protein mainly involved in integrin signaling downstream of Src kinase. Owing to its modular structure, p130Cas acts as a general regulator of cancer cell growth and invasiveness induced by different oncogenes. However, other mechanisms of p130Cas signaling leading to malignant progression are poorly understood. Here, we show a novel interaction of p130Cas with Ser/Thr kinase PKN3, which is implicated in prostate and breast cancer growth downstream of phosphoinositide 3-kinase. This direct interaction is mediated by the p130Cas SH3 domain and the centrally located PKN3 polyproline sequence. PKN3 is the first identified Ser/Thr kinase to bind and phosphorylate p130Cas and to colocalize with p130Cas in cell structures that have a pro-invasive function. Moreover, the PKN3-p130Cas interaction is important for mouse embryonic fibroblast growth and invasiveness independent of Src transformation, indicating a distinct mechanism from that previously characterized for p130Cas. Together, our results suggest that the PKN3-p130Cas complex may represent an attractive therapeutic target in late-stage malignancies.

Gemperle et al. present the first report of an interaction between p130Cas with the serine/threonine kinase PKN3, implicated in prostate and breast cancer growth. They show that p130Cas colocalizes with PKN3 in cell structures that have a pro-invasive function and enhance our understanding of PKN3-mediated signaling and tumor growth.
ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy
Authors: Vimont Noémie , Quah Fu Xiang , Guillaume-Schöpfer David , Roudier François , Dirlewanger Elisabeth , Wigge Philip A. , Wenden Bénédicte , Cortijo Sandra
Published: May 2018

Chromatin immunoprecipitation-sequencing (ChIP-seq) is a robust technique to study interactions between proteins, such as histones or transcription factors, and DNA. This technique in combination with RNA-sequencing (RNA-seq) is a powerful tool to better understand biological processes in eukaryotes. We developed a combined ChIP-seq and RNA-seq protocol for tree buds (Prunus avium L., Prunus persica L Batch, Malus x domestica Borkh.) that has also been successfully tested on Arabidopsis thaliana and Saccharomyces cerevisiae. Tree buds contain phenolic compounds that negatively interfere with ChIP and RNA extraction. In addition to solving this problem, our protocol is optimised to work on small amounts of material. Furthermore, one of the advantages of this protocol is that samples for ChIP-seq are cross-linked after flash freezing, making it possible to work on trees growing in the field and to perform ChIP-seq and RNA-seq on the same starting material. Focusing on dormant buds in sweet cherry, we explored the link between expression level and H3K4me3 enrichment for all genes, including a strong correlation between H3K4me3 enrichment at the DORMANCY-ASSOCIATED MADS-box 5 (PavDAM5) loci and its expression pattern. This protocol will allow analysis of chromatin and transcriptomic dynamics in tree buds, notably during its development and response to the environment.
The in situ structures of mono-, di-, and tri-nucleosomes in human heterochromatin
Authors: Cai Shujun , Böck Désirée , Pilhofer Martin , Gan Lu
Published: May 2018

Thein situ3-D organization of chromatin at the nucleosome and oligonucleosome levels is unknown. Here we use cryo-electron tomography (cryo-ET) to determine thein situstructures of HeLa nucleosomes, which have canonical core structures and asymmetric, flexible linker DNA. Subtomogram remapping suggests that sequential nucleosomes in heterochromatin follow irregular paths at the oligonucleosome level. This basic principle of higher-order repressive chromatin folding is compatible with the conformational variability of the two linker DNAs at the single-nucleosome level.
Deciphering the targets of retroviral protease inhibitors in Plasmodium berghei
Authors: Machuki Noah , Mogire Reagan , Ndung’u Loise , Mwitari Peter , Kimani Francis , Matoke-Muhia Damaris , Kiboi Daniel , Magoma Gabriel
Published: May 2018

Retroviral protease inhibitors (RPIs) such as lopinavir (LP) and saquinavir (SQ) are active against Plasmodium parasites. However, the exact molecular target(s) for these RPIs in the Plasmodium parasites remains poorly understood. We hypothesised that LP and SQ suppress parasite growth through inhibition of aspartyl proteases. Using reverse genetics approach, we embarked on separately generating knockout (KO) parasite lines lacking Plasmepsin 4 (PM4), PM7, PM8, or DNA damage-inducible protein 1 (Ddi1) in the rodent malaria parasite Plasmodium berghei ANKA. We then tested the suppressive profiles of the LP/Ritonavir (LP/RT) and SQ/RT as well as antimalarials; Amodiaquine (AQ) and Piperaquine (PQ) against the KO parasites in the standard 4-day suppressive test. The Ddi1 gene proved refractory to deletion suggesting that the gene is essential for the growth of the asexual blood stage parasites. Our results revealed that deletion of PM4 significantly reduces normal parasite growth rate phenotype (P = 0.003). Unlike PM4_KO parasites which were less susceptible to LP and SQ (P = 0.036, P = 0.030), the suppressive profiles for PM7_KO and PM8_KO parasites were comparable to those for the WT parasites. This finding suggests a potential role of PM4 in the LP and SQ action. On further analysis, modelling and molecular docking studies revealed that both LP and SQ displayed high binding affinities (-6.3 kcal/mol to -10.3 kcal/mol) towards the Plasmodium aspartyl proteases. We concluded that PM4 plays a vital role in assuring asexual stage parasite fitness and might be mediating LP and SQ action. The essential nature of the Ddi1 gene warrants further studies to evaluate its role in the parasite asexual blood stage growth as well as a possible target for the RPIs.

Author summary

The antiretroviral drugs (ARVs) such as LP or SQ that inhibit viral proteases reduce the rate of multiplication of the malaria parasites. The mode of action of these drugs against the parasites is however poorly understood. The proteases are among the enzymes that play essential roles in Plasmodium parasites. We sought to investigate the possible mode of action of these drugs by generating mutant parasites lacking specific aspartyl proteases namely PM4, PM7, PM8 or Ddi1 and then evaluate the susceptibility of the mutants to LP and SQ. We successfully generated parasites lacking either PM4, PM7 or PM8 but Ddi1 gene was refractory to deletion. From our data, we demonstrate that, unlike PM7 and PM8, the PM4 and Ddi1 are essential enzymes for asexual blood stage parasite fitness and survival and that the PM4 might be a target for the viral protease inhibitors in reducing parasite growth and multiplication. Further experiments using molecular docking tools show that LP or SQ have a high binding affinity for the Plasmodium aspartyl proteases.
Statistical Investigations of Protein Residue Direct Couplings
Authors: Neuwald Andrew F. , Altschul Stephen F.
Published: May 2018

Protein Direct Coupling Analysis (DCA), which predicts residue-residue contacts based on covarying positions within a multiple sequence alignment, has been remarkably effective. This suggests that there is more to learn from sequence correlations than is generally assumed, and calls for deeper investigations into DCA and perhaps into other types of correlations. Here we describe an approach that enables such investigations by measuring, as an estimated p-value, the statistical significance of the association between residue-residue covariance and structural interactions, either internal or homodimeric. Its application to thirty protein superfamilies confirms that DCA scores correlate with 3D pairwise contacts with very high significance. This method also permits quantitative assessment of the relative performance of alternative DCA methods, and of the degree to which they detect direct versus indirect couplings. We illustrate its use to assess, for a given protein, the biological relevance of alternative conformational states, to investigate the possible mechanistic implications of differences between these states, and to characterize subtle aspects of direct couplings. Our analysis indicates that direct pairwise correlations may be largely distinct from correlated patterns associated with functional specialization, and that the joint analysis of both types of correlations can yield greater power. Our approach might be applied effectively to assessing multiple alignment quality, eliminating the need for benchmark alignments. Data, programs, and source code are freely available at http://evaldca.igs.umaryland.edu.

Author Summary

The success of Direct Coupling Analysis (DCA) for protein structure prediction suggests that multiple sequence alignments implicitly contain more structural information than had previously been realized, and prompts deeper investigations of the sequence correlations uncovered by either DCA or other approaches. To aid such investigations and thereby broaden the utility of and improve DCA, we describe an approach that measures the statistical significance of the association between DCA and either 3D structure or correlated patterns associated with functional specialization. This approach can be used to obtain better input alignments, and to evaluate the relative performance of DCA methods, their ability to distinguish direct from indirect couplings, and the potential biological relevance and mechanistic implications of alternative conformations and homodimeric interactions.
Detection of cellular microRNAs with programmable DNA nanoswitches
Authors: Chandrasekaran Arun Richard , MacIsaac Molly , Dey Paromita , Levchenko Oksana , Zhou Lifeng , Andres Madeline , Dey Bijan K. , Halvorsen Ken
Published: May 2018

MicroRNAs are short non-coding regulatory RNAs that are increasingly used as disease biomarkers. Detection of microRNAs can be arduous and expensive, and often requires amplification, labeling, or radioactive probes. Here we report a single-step, non-enzymatic detection assay using conformationally responsive DNA nanoswitches. Termed miRacles (microRNAactivatedconditionallooping ofengineeredswitches), our assay has sub-attomole sensitivity and single-nucleotide specificity using an agarose gel electrophoresis readout. We detect cellular microRNAs from nanogram-scale RNA extracts of differentiating muscle cells, and demonstrate multiplexed detection of several microRNAs from one biological sample. We demonstrate one-hour detection without expensive equipment or reagents, making this assay a compelling alternative to qPCR and Northern blotting.

Significance statement

Detection of microRNAs play a key role in biological research and medical diagnostics, and current detection methods are expensive and require sophisticated processes. We presentmicroRNAactivatedconditionallooping ofengineeredswitches (miRacles), a mix-and-read strategy that is based on conformational changes of DNA nanoswitches upon binding a target microRNA. MiRacles has a sensitivity of ∼4 copies/cell and specificity of a single nucleotide, and can be performed in one hour at a fraction of the cost of traditional microRNA detection techniques. Our method can also be multiplexed to detect multiple microRNAs from one biological sample. The minimalistic miRacles assay has immediate application in biomedical research and longer term potential as a clinical tool.
Properties of cell signaling pathways and gene expression systems operating far from steady-state
Authors: Di Bella Juan Pablo , Colman-Lerner Alejandro , Ventura Alejandra C.
Published: May 2018

Ligand-receptor systems, covalent modification cycles, and transcriptional networks are basic units of signaling systems and their steady-state properties are well understood. However, the behavior of such systems before steady-state is poorly characterized. Here, we analyzed the properties of the input-output curves for each of these systems as they approach steady-state. In ligand-receptor systems, the EC50(concentration of the ligand that occupies 50% of the receptors) is higher before the system reaches steady-state. Based on this behavior, we have previously defined PRESS (for pre-equilibrium sensing and signaling), a general “systems level” mechanism cells may use to overcome input saturation. Originally, we showed that, given a step stimulation, PRESS operates when the kinetics of ligand-receptor binding are slower than the downstream signaling steps. Now, we show that, provided the input increases slowly, it is not essential for the ligand binding reaction itself to be slow. In addition, we demonstrate that covalent modification cycles and gene expression systems may also operate in PRESS mode. Thus, nearly all biochemical processes may operate in PRESS mode, suggesting that this mechanism may be ubiquitous in cell signaling systems.
Genetic, biochemical, and molecular characterization ofMethanosarcina barkerimutants lacking three distinct classes of hydrogenase
Authors: Mand Thomas D. , Kulkarni Gargi , Metcalf William W.
Published: May 2018

The methanogenic archaeonMethanosarcina barkeriencodes three distinct types of hydrogenase, whose functions vary depending on the growth substrate. These include the F420-dependent (Frh), methanophenazine-dependent (Vht), and ferredoxin-dependent (Ech) hydrogenases. To investigate their physiological roles, we characterized a series of mutants lacking each hydrogenase in various combinations. Mutants lacking Frh, Vht, or Ech in any combination failed to grow on H2/CO2, whereas only Vht and Ech were essential for growth on acetate. In contrast, a mutant lacking all three grew on methanol with a final growth yield similar to wild-type, produced methane and CO2in the expected 3:1 ratio, but had aca.33% slower growth rate. Thus, hydrogenases play a significant, but non-essential, role during growth on this substrate. As previously observed, mutants lacking Ech fail to grow on methanol/H2unless supplemented with biosynthetic precursors. Interestingly, this phenotype was abolished in the Δech/Δfrhand Δech/Δfrh/Δvhtmutants, consistent with the idea that hydrogenases inhibit methanol oxidation in the presence of H2, which prevents production of reducing equivalents needed for biosynthesis. Quantification of methane and CO2produced from methanol by resting cell suspensions of various mutants supports this conclusion. Based on global transcriptional profiles, none of the hydrogenases are upregulated to compensate for loss of the others. However, transcript levels of the F420 dehydrogenase operon were significantly higher in all strains lackingfrh, suggesting a mechanism to sense the redox state of F420. The roles of the hydrogenases in energy conservation during growth with each methanogenic pathway are discussed.
Exploring the archaeome: detection of archaeal signatures in the human body
Authors: Pausan Manuela R. , Csorba Cintia , Singer Georg , Till Holger , Schöpf Veronika , Santigli Elisabeth , Klug Barbara , Högenauer Christoph , Blohs Marcus , Moissl-Eichinger Christine
Published: May 2018

Due to their fundamentally different biology, archaea are consistently overlooked in conventional microbiome surveys. Using amplicon sequencing, we evaluated methodological set-ups to detect archaea in samples from five different body sites: respiratory tract (nose), digestive tract (mouth, appendix, and stool) and skin. With the optimized protocols, the detection of archaeal ribosomal sequence variants (RSVs) was increased from one (found in currently used, so-called “universal” approach) to 81 RSVs in a representative sample set. In order to assess the archaeome diversity, a specific archaea-targeting methodology is required, for which we propose a standard procedure. This methodology might not only prove useful for analyzing the human archaeome in more detail but could also be used for other holobionts’ samples.
Protein Gradients on the Nucleoid Position the Carbon-fixing Organelles of Cyanobacteria
Authors: MacCready Joshua S. , Hakim Pusparanee , Young Eric J. , Hu Longhua , Liu Jian , Osteryoung Katherine W. , Vecchiarelli Anthony G. , Ducat Daniel C.
Published: May 2018

In Brief

We describe a novel positioning system that utilizes the cyanobacterial nucleoid to segregate, transport and equidistantly position the carbon-fixation machinery (carboxysomes).

Carboxysomes are protein-based bacterial organelles that encapsulate a key enzyme of the Calvin-Benson-Bassham cycle. Previous work has implicated a ParA-like protein (hereafter McdA) as important for spatially organizing carboxysomes along the longitudinal axis of the model cyanobacterium Synechococcus elongatus PCC 7942. Yet, how self-organization of McdA emerges and contributes to carboxysome positioning is unknown. Here, we show that a small protein, termed McdB, localizes to carboxysomes through interactions with carboxysome shell proteins to drive emergent oscillatory patterning of McdA on the nucleoid. Our results demonstrate that McdB directly interacts to stimulate McdA ATPase activity, and indicate that carboxysome-dependent McdA depletion zone formation on the nucleoid is required for directed motion of carboxysomes towards increased concentrations of McdA. We propose that McdA and McdB are a new class of self-organizing proteins that follow a Brownian-ratchet mechanism, challenging the cytoskeletal model of organelle transport, for equidistant positioning of carboxysomes in cyanobacteria. These results have broader implications for understanding spatial organization of protein mega-complexes and organelles in bacteria more broadly.
Different states of priority recruit different neural codes in visual working memory
Authors: Yu Qing , Postle Bradley R.
Published: May 2018

We tracked the neural representation of the orientation and the location of stimuli held in working memory at different levels of priority (“attended” and “unattended” memory items -- AMI and UMI), using multivariate inverted encoding models of human fMRI. Although representation of the orientation of the AMI and of the UMI could be reconstructed in several brain regions, including in early visual and parietal regions, the identity of the UMI was actively represented in early visual cortex in a distinct “reversed” code, suggesting this region as a site of the focus of attention to nonspatial stimulus information. The location of stimuli was also broadly represented, although only in parietal cortex was the location of the UMI represented in a reversed code. Our results suggest that a common recoding operation may be engaged, across stimulus dimensions and brain areas, to retain information in working memory while outside the focus of attention.
The inhibition of automatic imitation: a meta-analysis and synthesis of fMRI studies
Authors: Darda Kohinoor M. , Ramsey Richard
Published: May 2018

Humans copy other people without their conscious awareness, a behaviour known as automatic imitation. Although automatic imitation forms a key part of daily social interactions, we do not copy other people indiscriminately. Instead, we control imitative tendencies by prioritising some actions and inhibiting others. To date, neuroimaging studies investigating the control of automatic imitation have produced inconsistent findings. Some studies suggest that imitation control relies on a domain-specific neural circuit related to social cognition (the theory-of-mind network). In contrast, other studies show engagement of a domain-general neural circuit that is engaged during a diverse range of cognitive control tasks (the multiple demand network). Given the inconsistency of prior findings, in the current paper we avoided problems associated with interpreting individual studies by performing a meta-analysis. To do so, we used a multi-level kernel density analysis to quantitatively identify consistent patterns of activation across functional magnetic resonance imaging studies investigating the control of imitation. Our results show clear and consistent evidence across studies that the control of automatic imitation is guided by brain regions in the multiple demand network including dorsolateral frontoparietal cortex. In contrast, there was only limited evidence that regions in the theory of mind network were engaged. Indeed, medial prefrontal cortex showed no consistent engagement and right temporoparietal junction engagement may reflect spatial rather than imitative control. As such, the current meta-analysis reinforces the role of domain-general control mechanisms and provides limited evidence in support of the role of domain-specific processes in regulating imitative tendencies. Consequently, neurocognitive models of imitation need updating to place more emphasis on domain-general control mechanisms, as well as to consider more complex organisational structures of control, which may involve contributions from multiple cognitive systems.
Industrial relations in Poland
Authors: Czarzasty Jan , Mrozowicki Adam
Published: May 2018

Purpose

The purpose of this paper is to examine the interrelations between the evolution of industrial relations (IR) and IR research in Poland in the historical context. Two questions are put forward: How was the evolution of the IR system in Poland influenced by the re-constitution of a particular model of the capitalism and the strategies and struggle of IR actors? How were the ways of approaching and theorizing IR influenced by the aforementioned evolution?

Design/methodology/approach

The paper draws upon academic literature, secondary data on actors and processes of IR as well as four expert interviews with the representatives of the first generation of IR scholars in Poland.

Findings

The paper suggests that the development of the IR system and the related scholarship can be divided into three phases: the pre-1989 period characterised by the lack of autonomous interests representation and rather limited IR research; the early development of the post-1989 IR system marked by the debates on the integrative role of IR as peacekeeping mechanism in the period of deep economic and political changes (1989-2004); the post-EU accession consolidation of the IR system characterised by the weakness of the IR actors vis-à-vis the state and increasing neo-etatist tendencies.

Originality/value

This paper contributes to the ongoing debate on the relationships between the emergent models of Eastern European capitalism and the evolution of IR systems. It critically analyses the state of the discussion on the IR field Poland emphasising the relevance of political-economic factors as well as the ideology of “social peace” for both the evolution of the IR system in the country and the state of the IR debate.
Integrating affect, cognition, and culture in Hispanic financial planning
Authors: Weisfeld-Spolter Suri , Sussan Fiona , Rippé Cindy , Gould Stephen
Published: May 2018

Purpose

Debt is at a peak and consumers purport needing help with financial planning. To better understand the antecedents of financial planning behavior, the purpose of this paper is to examine the importance of cultural values in financial decision making within the context of Hispanic American consumers. A new conceptual model is proposed to integrate affect (cultural value) and cognition (financial knowledge) in financial planning.

Design/methodology/approach

To uncover respondents’ views on cultural values, financial knowledge, financial attitude, and financial planning behavior, an online survey hosted on a business school’s website was distributed to members of two Hispanic Chambers of Commerce. The survey consisted of five parts, and took each respondent an average of 15 minutes to complete. The final data set has 158 observations.

Findings

Results analyzed using structural equation modeling confirmed the hypotheses that financial knowledge, attitude, and perceived control simultaneously influence Hispanic consumers’ intentions to purchase financial planning products or services. More interestingly, these results confirm that multiple different routes coexist in the decision-making process, especially within the Hispanic financial planning context.

Originality/value

Key contributions of this paper include the conceptualization of cultural value as an antecedent to Hispanic financial behavior; detailing the different routes to financial decision making for US Hispanic consumers; and informing financial service managers on marketing strategies toward Hispanic consumers.
The innovation process impact on the new product performance: a case study
Authors: Fouad Fatimaezzahra , Tourabi Amina , Lakhnati Ghizlane
Published: May 2018

Purpose

In the presence of a low rate of investment in research and development in the fish industry, the Moroccan government launched in 2009 a new fisheries program which directs fish processing companies towards a non-price competitiveness strategy. These companies are driving to establish a modernized value chain that supports product innovation in its performance generation. This study therefore aims at measuring the impact of this value chain on the performance of a new product taking into account the early stages of development, namely prototyping.

Design/methodology/approach

First, the authors tried to collect the data in a dichotomous qualitative form for the structure of the innovation process which reflects the measure of elapsed time for each stage of the innovation process in the two cases, namely, sequentiality and parallelism of the steps. The authors then addressed a second time to the quality managers to provide them with quantitative data. Nevertheless, the evaluation of the improvement of the innovative product had remained qualitative.

Findings

The study shows that there is a positive and significant relationship between the partially parallel structure and the internal improvement objectives of the new prototype.

Research limitations/implications

The main limitation of this study was the very small sample of firms operating in innovation, which did not allow us to apply a parametric analysis such as logistic or linear regression according to a normal law on a sufficient number of observations according to the transversal approach. As theoretical implications of this study, Davila et al. (2006) argue that to succeed in a product development process, it must be possible to measure the resulting performance. Assessing performance in the product development process is particularly important for managers and decision makers to address key management issues such as “what we do”, “what we have learned” and “what should we do in the future” (Tatikonda, 2007).

Practical implications

The empirical implications of this study have shown that accelerating the execution of innovation activity is enormously favored to increase the performance of the innovative product over the medium term. This will enable the company to be efficient in terms of market entry time with good quality and as soon as possible mainly in the early stages of development of the new product.

Originality/value

Compared with previous studies, the originality of this study is to answer two inadequacies in the theory of performance of the new product, namely, the objective/quantitative nature of the practice measured in the innovation process and the use of a holistic approach based on the performance indicators of the innovative product at each stage of the innovation process.
Supporting non-native university lecturers with English-medium instruction
Authors: Tuomainen Satu
Published: May 2018

Purpose

The purpose of this paper is to describe a support course for English-medium instruction (EMI) which continues to expand in European higher education (HE). While the phenomenon of teaching through English is not novel, support for university teachers appears to remain limited despite recognised challenges of EMI such as language proficiency and pedagogical considerations.

Design/methodology/approach

In the course non-native university lecturers in Finland were provided a course to practice various elements of English for academic purposes and receive feedback on their teaching. A pre-course needs analysis was used to determine the main causes for EMI concerns with non-native lecturers, and which elements of English they wished to develop during the course. The course itself consisted of six joint meetings, followed by individual teaching demonstrations, and concluded with a post-course analysis.

Findings

Findings suggest that Finnish university lecturers were pre-course most concerned about the accuracy, fluency and pronunciation of their academic English. Based on the post-course analysis, the most beneficial elements of the EMI support course were the reflective discussions about EMI, the language practice and receiving individual feedback.

Practical implications

The study suggests that support courses for university lecturers involved with EMI should not cover only language but allow lecturers to share their concerns and experiences and to practice in authentic teaching situations in English.

Originality/value

This study describes a pedagogically effective method to assist and encourage lecturers in HE to the use of English in their instruction.
Relational university, learning and entrepreneurship ecosystems for sustainable tourism
Authors: Torres Valdés Rosa María , Lorenzo Álvarez Carolina , Castro Spila Javier , Santa Soriano Alba
Published: May 2018

Purpose

This paper aims to offer a conceptual model for the development of a teaching–learning experiential ecosystem which favors university entrepreneurship in the area of sustainable tourism and innovation acceleration.

Design/methodology/approach

The methodology is carried out in two phases. First, participatory action research in the context of the “Protocol and Event Organization” subject, included in the Tourism degree taught at the University of Alicante, analyzing a didactic experience as a case study. Second, primary qualitative and quantitative research.

Findings

Although at a small scale, it is shown that the relational approach for university management fosters entrepreneurship and generates social awareness regarding the sustainable tourism business.

Research limitations/implications

This is a local simulatory case on relational university and is based on only one subject. However, as a starting point, it has the following implications.

Practical implications

The authors contribute in a practical manner to model a learning and entrepreneurship ecosystem for configuring an education innovation agenda in the field of tourism, with the cooperation of all agents involved in this sector to accelerate novel entrepreneurships, as well as transitions, toward sustainability.

Social implications

The model is useful to accelerate new entrepreneurship and transitions toward sustainable regional development.

Originality/value

Students have led the process and have become quintessential relationatory agents, creating their own career opportunities on sustainable tourism, in addition to creating society–university links.
Improving patient flow through applying lean concepts to emergency department
Authors: Elamir Hossam
Published: May 2018

Purpose

This paper aims to propose lean-based interventions that address the main causes of emergency department overcrowding. Emergency department overcrowding (EDOC) and increased length of stay (LOS) have been key global issues for more than 20 years, as they have serious repercussions. No measurements have been done to assess the situation nationally. Expanding emergency departments (EDs) and adding more beds have never succeeded in eliminating wastes and targeting the root causes of the problem.

Design/methodology/approach

This paper is a quantitative analytical applied research. The paper used direct observation for seven days to collect patient flow data on ED patients at a secondary care hospital in Kuwait. It calculated wait times and services to identify the major causes of EDOC and increased LOS.

Findings

Around one-third of the ED design capacity was used by 12 per cent of the patients who stayed >6 h each. The wasted waiting time represents 56.2 per cent of the aggregated LOS, which puts lean management (LM) on the top of the process reengineering approaches suitable for improving overcrowding by reducing waste. Guided by the LM concepts, the paper proposes solutions that fall into three themes. The selected solutions address the vital few causes of the EDOC and prolonged EDLOS.

Originality/value

This paper is the first study of its kind in Kuwait, and one of the most outstanding studies in the Gulf region, in terms of the number of the daily ED visits and the comprehensive multi-level proposed interventions.
Assessment’s role in building student support to facilitate change
Authors: Thompson Susan Meredith
Published: May 2018

Purpose

The California State University Library successfully improved its library’s hours, including introducing 24-hour access, thanks in part to an assessment process that helped the University Library to develop a partnership with the students. The paper aims to discuss this issue.

Design/methodology/approach

In order to understand the need for expanded operational hours, students’ were surveyed on their satisfaction with current library hours, suggestions on how best to meet their actual hour needs, and interest in 24-hour access. Efforts to solicit student input included involving the student government in promoting the survey and reviewing its results, a decision that later had a major impact on the success of the project.

Findings

The survey identified days with problematic hours and which hours student suggested changes to that would best fit most students’ needs. In response to the findings, the library immediately implemented incremental changes that fit within current library resources. The survey’s most significant finding was that 94 percent of students wanted 24-hour study in the library.

Originality/value

An unexpected benefit of the library making immediate, incremental changes was that students could see the results of their input and feel a sense of ownership. The findings also led to the library making 24-hour access a top priority. When university funding was not available, the university’s student government approached the library with a unique proposal to include funding for 24-hour library access in their proposed student fee increase. The student body showed its willingness to invest in the library by passing the fee increase. California State University San Marco’s library began 24/5 hours in Fall 2017.