bluuebunny/crossref_metadata_2025 huggingface dataset:
Concurrence of Porin Loss and Modular Amplification of β-Lactamase Encoding Genes Drives Carbapenem Resistance in a Cohort of Recurrent Enterobacterales Bacteremia
Authors: Shropshire William C. , Aitken Samuel L. , Pifer Reed , Kim Jiwoong , Bhatti Micah M. , Li Xiqi , Kalia Awdhesh , Galloway-Peña Jessica , Sahasrabhojane Pranoti , Arias Cesar A. , Greenberg David E. , Hanson Blake M. , Shelburne Samuel A.
Published: April 2019

Background

Carbapenem resistant Enterobacterales (CRE) remain urgent antimicrobial resistance threats. Approximately half of CRE clinical isolates lack carbapenem hydrolyzing enzymes and develop carbapenem resistance through alternative mechanisms. The purpose of this study was to elucidate the development of carbapenem resistance mechanisms from clonal, recurrent extended-spectrum β-lactamase positive Enterobacterales (ESBL-E) bacteremia isolates in a vulnerable patient population.

Methods

This study investigated a historical, retrospective cohort of ESBL-E bacteremia cases in the University of Texas MD Anderson Cancer Center (MDACC) from January 2015 to July 2016. Phylogenetic and comparative genomic analyses were performed to identify clonal, recurrent ESBL-E isolates developing carbapenem resistance. Oxford Nanopore Technology (ONT) long-read and Illumina short-read sequencing data were used to generate consensus assemblies and to identify signatures of mobile genetic element mediated amplification and transposition of antimicrobial resistance genes. Serial passaging experiments were performed on a set of clinical ST131 ESBL-E isolates to recapitulate in vivo observations. qPCR and qRT-PCR were used to determine respective copy number and transcript levels of β-lactamase genes.

Results

116 ESBL-E bacteremia cases were identified, 16 of which had documented recurrent infections. Four serial, recurrent isolates displayed a carbapenem resistant phenotype, three without the acquisition of a known carbapenemase. These three isolates had non-carbapenemase-producing CRE (non-CP-CRE) mechanisms driven by IS26- and ISEcp1-mediated amplification of respective translocatable units (TU) and transposition units (TPU) harboring both blaOXA-1 and blaCTX-M variants with concomitant outer membrane porin disruption. The TU and TPU structures inserted into the open reading frames of outer membrane porin genes in a subset of non-CP-CRE isolates. Serial passage of an index ST131 ESBL-E isolate under selective carbapenem exposure resulted in chromosomal amplification of modular, TUs harboring β-lactamase genes with concomitant porin inactivation, recapitulating the in vivo carbapenem resistance progression. Long-read sequencing of two additional MDACC bacteremia strains identified similar non-CP-CRE mechanisms observed in the serial isolates.

Conclusions

Non-CP-CRE de novo mechanisms were the primary driver of CRE development in recurrent bacteremia cases within this vulnerable patient population. The incorporation of long-read ONT data into AMR surveillance platforms is critical to identify high-risk CRE isolates that are difficult to identify with low-resolution phenotypic and molecular characterization methods.
Distinct Structural Features of the Lon Protease Drive Conserved Hand-over-Hand Substrate Translocation
Authors: Shin Mia , Asmita Ananya , Puchades Cristina , Adjei Eric , Wiseman R. Luke , Karzai A. Wali , Lander Gabriel C.
Published: April 2019

Hand-over-hand translocation is emerging as the conserved mechanism by which ATP hydrolysis drives substrate translocation within the classical clade of AAA+ proteins. However, the operating principles of the distantly related HCLR clade, which includes the important quality control protease Lon, remains poorly defined. We determined a cryo-electron microscopy structure ofY. pestisLon trapped in the act of processing substrate. This structure revealed that sequential ATP hydrolysis and hand-over-hand substrate translocation are conserved in this AAA+ protease. However, Lon processes substrates through a distinct molecular mechanism involving structural features unique to the HCLR clade. Our findings define a previously unobserved translocation mechanism that is likely conserved across HCLR proteins and reveal how fundamentally distinct structural configurations of distantly-related AAA+ enzymes can power hand-over-hand substrate translocation.
Information processing by endoplasmic reticulum stress sensors
Authors: Stroberg Wylie , Eilertsen Justin , Schnell Santiago
Published: April 2019

The unfolded protein response (UPR) is a collection of cellular feedback mechanisms that seek to maintain protein folding homeostasis in the endoplasmic reticulum (ER). When the ER is “stressed”, either through high protein folding demand or undersupply of chaperones and foldases, stress sensing proteins in the ER membrane initiate the UPR. Recently, experiments have indicated that these signaling molecules detect stress by being both sequestered by free chaperones and activated by free unfolded proteins. However, it remains unclear what advantage this bidirectional sensor control offers stressed cells. Here, we show that combining positive regulation of sensor activity by unfolded proteins with negative regulation by chaperones allows the sensor to make a more informative measurement of ER stress. The increase in the information capacity of the combined sensing mechanism stems from stretching of the active range of the sensor, at the cost of increased uncertainty due to the integration of multiple signals. These results provide a possible rationale for the evolution of the observed stress sensing mechanism.
Statistical modeling, estimation, and remediation of sample index hopping in multiplexed droplet-based single-cell RNA-seq data
Authors: Farouni Rick , Djambazian Haig , Ragoussis Jiannis , Najafabadi Hamed S.
Published: April 2019

We introduce a probabilistic model for estimation of sample index-hopping rate in multiplexed droplet-based single-cell RNA sequencing data and for inference of the true sample of origin of the hopped reads. Across the datasets we analyzed, we estimate the sample index hopping probability to range between 0.003–0.009, a small number that counter-intuitively gives rise to a large fraction of ‘phantom molecules’ – as high as 85% in a given sample. We demonstrate that our model-based approach can correct for this artifact by accurately purging the majority of phantom molecules from the data. Code and reproducible analysis notebooks are available at https://github.com/csglab/phantom_purge.

Structure

Section 1 provides a concise summary of the paper. Section 2 provides a brief historical and technical overview of the phenomenon of sample index hopping and an explanation of related concepts. The three sections that follow describe the statistical modeling approach and correspond to the following three goals. (1) Building a generative model that probabilistically describes the phenomenon of sample index hopping of multiplexed sample reads (Section 3). (2) Estimating the index hopping rate from empirical experimental data (Section 4). (3) Correcting for the effects of sample index hopping through a principled probabilistic procedure that reassigns reads to their true sample of origin and discards predicted phantom molecules by optimally minimizing the false positive rate (Section 5). Next, Section 6 details the results of the analyses performed on empirical and experimental validation datasets. The Supplementary Notes consists of three sections: (1) Mathematical Derivations, (2) Overview of Computational Workflow, (3) Method’s Limitations.
Intermanual transfer of visuomotor adaptation is related to awareness
Authors: Werner Susen , Strüder Heiko K. , Donchin Opher
Published: April 2019

Previous studies compared the effects of gradual and sudden adaptation on intermanual transfer to find out whether transfer depends on awareness of the perturbation. Results from different groups were contradictory. Since results of our own study suggest that awareness depends on perturbation size, we hypothesize that awareness-related intermanual transfer will only appear after adaptation to a large, sudden perturbation but not after adaptation to a small sudden perturbation or a gradual perturbation, large or small. To confirm this, four groups (S30, G30, S75, G75) of subjects performed out-and-back reaching movements with their right arm. In a baseline block, they received veridical visual feedback of hand position. In the subsequent adaptation block, feedback was rotated by 30 deg (S30, G30) or 75 deg (S75, G75). This rotation was either introduced suddenly (S30, S75) or gradually in steps of 3 deg (G30, G75). After the adaptation block, subjects did an awareness test comprising exclusion and inclusion conditions. The experiment concluded with an intermanual transfer block, in which movements were performed with the left arm under rotated feedback, and a washout block again under veridical feedback. We used a hierarchical Bayesian model to estimate individual movement directions and group averages. The movement directions in different conditions were then used to calculate group and individual indexes of adaptation, awareness, unawareness, transfer and washout. Both awareness and transfer were larger in S75 than in other groups, while unawareness and washout were smaller in S75 than in other groups. Furthermore, the size of awareness indices correlated to intermanual transfer across subjects, even when transfer was normalized to final adaptation level. Thus, we show for the first time that the amount of intermanual transfer directly relates to the extent of awareness of the learned perturbation.
G-protein coupled receptor 88knock-down in the associative striatum reduces the psychiatric symptoms in a translational model of Parkinson’s disease
Authors: Galet Benjamin , Ingallinesi Manuela , Pegon Jonathan , Thi Anh Do , Ravassard Philippe , Biguet Nicole Faucon , Meloni Rolando
Published: April 2019

Beyond the motor disability, Parkinson’s disease (PD) is also characterized by an early appearance of psychiatric symptoms such as apathy, depression, anxiety and cognitive deficits, which can entail dementia and psychosis in later stages. While current treatments may provide some level of symptomatic relief, their use is limited by the development of adverse effects such as impulse-control disorders. There is thus a medical need for targets with novel modes of action to treat these aspects of PD. In this context, we investigated GPR88, an orphan G-protein coupled receptor that is associated with psychiatric disorders and highly enriched in the striatum, where it exerts an inhibitory control over neurotransmitter systems that are compromised in PD. To evaluate the potential of GPR88 as a target for the treatment of the psychiatric symptoms of PD, we knocked-down (KD) its expression in sensorimotor (dorsolateral, DLS) or associative (dorsomedial, DMS) striatal areas in a translational rat model of early PD. Our findings indicate thatGpr88-KD in the DMS, but not DLS, reduced the alterations in mood, motivation and cognition that characterized the model, through modulation of the expression ofregulator of G-protein signaling 4(Rgs4) and of transcription factor ΔFosB. Furthermore, the rat model of PD exhibited allostatic changes in striatal activity markers that may be related to patterns observed in patients, and which were reduced byGpr88-KD. Taken together, these results thus highlight the relevance of GPR88 as a therapeutic target for the psychiatric symptoms of PD.
An enhanced molecular tension sensor based on bioluminescence resonance energy transfer (BRET)
Authors: Aird Eric J. , Tompkins Kassidy J. , Gordon Wendy R.
Published: April 2019

Molecular tension sensors measure piconewton forces experienced by individual proteins in the context of the cellular microenvironment. Current genetically-encoded tension sensors use FRET to report on extension of an elastic peptide encoded in a cellular protein of interest. Here we present the development and characterization of a new type of molecular tension sensor based on bioluminescence resonance energy transfer (BRET) which exhibits more desirable spectral properties and an enhanced dynamic range compared to other molecular tension sensors. Moreover, it avoids many disadvantages of FRET measurements in cells, including heating of the sample, autofluorescence, photobleaching, and corrections of direct acceptor excitation. We benchmark the sensor by inserting it into the canonical mechanosensing focal adhesion protein vinculin, observing highly resolved gradients of tensional changes across focal adhesions. We anticipate that the BRET-TS will expand the toolkit available to study mechanotransduction at a molecular level and allow potential extension to an in vivo context.
Infant Sleep Quality and its’ Several Related Factors: An Indonesian Samples
Authors: Muskananfola Fiona , Wiguna Tjhin , Ismail Raden Irawati , Nugraheni Teresia Putri Widia , Chairunnisa Shafira
Published: April 2019

Objective

This research aimed to identify factors influencing infant sleep quality including mother-infant bonding, infant stress, parity, and maternal depression and anxiety, and to analyze possible associations between these variables.

Method

A cross-sectional design was adopted to analyze data from mothers and their infants (0–36 months of age) using consecutive sampling. Mothers completed two of several questionnaires in the Indonesian language, including the Mother-Infant Bonding Scale, the Brief Infant Sleep Questionnaire, the Symptoms Checklist-90, and an infant stress questionnaire that was specifically designed for this study. The chi-squared test for bivariate analysis and logistic regression were applied to obtain odds ratios for the predictor variables using SPSS version 21 (IBM Corporation, Armonk, NY, USA) for Mac (Apple Inc, Cupertino, CA, USA).

Results

Findings indicated that the proportion of infants with problematic sleep quality was 33.30%. Three predictors were significantly associated with problematic infant sleep quality: mother-infant bonding; infant stress; and parity. However, logistic regression analysis demonstrated that only mother-infant bonding (odds ratio [OR] 1.66 [95% confidence interval (CI) 1.15–6.12]) and infant stress (OR 1.29 [95% CI 1.07–2.68]) predicted a 38.7% risk for problematic infant sleep quality.

Conclusion

Results of the present study indicated that early detection of mother-infant bonding levels and infant stress is very important. It may be valuable to screen sleep habits for better prognosis among infants because good sleep quality is crucial for optimal growth and development. Results of this study will raise awareness of the importance of mother-infant bonding, infant stress, and problematic infant sleep quality.
Selection shapes synonymous stop codon use in mammals
Authors: Seoighe Cathal , Kiniry Stephen J. , Peters Andrew , Baranov Pavel V. , Yang Haixuan
Published: April 2019

Phylogenetic models of the evolution of protein-coding sequences can provide insights into the selection pressures that have shaped them. In the application of these models synonymous nucleotide substitutions, which do not alter the encoded amino acid, are often assumed to have limited functional consequences and used as a proxy for the neutral rate of evolution. The ratio of nonsynonymous to synonymous substitution rates is then used to categorize the selective regime that applies to the protein (e.g. purifying selection, neutral evolution, diversifying selection). Here, we extend these models to explore the extent of purifying selection acting on substitutions between synonymous stop codons. Using a large collection of coding sequence alignments we estimate that a high proportion (approximately 57%) of mammalian genes are affected by selection acting on stop codon preference. This proportion varies substantially by codon, with UGA stop codons far more likely to be conserved. Genes with evidence of selection acting on synonymous stop codons have distinctive characteristics, compared to unconserved genes with the same stop codon, including enrichment for specific functional properties. Notably, genes with conserved stop codons have longer 3’ UTRs and are associated with shorter mRNA half-life than other genes. The coding regions of these genes are also much more likely to be under strong purifying selection pressure. Our results suggest that the preference for UGA stop codons found in many multicellular eukaryotes is selective rather than mutational in origin.
Structural basis for oligomerization of the prokaryotic peptide transporter PepTSo2
Authors: Nagamura Reina , Fukuda Masahiro , Kawamoto Akihiro , Matoba Kyoko , Dohmae Naoshi , Ishitani Ryuichiro , Takagi Junichi , Nureki Osamu
Published: April 2019

Proton-dependent oligopeptide transporters (POTs) belong to the major facilitator superfamily (MFS) and transport dipeptides and tripeptides from the extracellular environment into the target cell. The human POTs PepT1 and PepT2 are also involved in the absorption of various orally ingested drugs. Previously reported structures revealed that the bacterial POTs possess 14 helices, of which H1–H6 and H7–H12 constitute the typical MFS fold and the residual two helices are involved in the cytoplasmic linker. PepTSo2 from Shewanella oneidensis is a unique POT which reportedly assembles as a 200 kDa tetramer. Although the previously reported structures suggested the importance of H12 for tetramer formation, the structural basis for the PepTSo2-specific oligomerization remains unclear owing to the lack of a high-resolution tetrameric structure. In this study, the expression and purification conditions for tetrameric PepTSo2 were optimized. A single-particle cryo-EM analysis revealed the tetrameric structure of PepTSo2 incorporated into Salipro nanoparticles at 4.1 Å resolution. Furthermore, a combination of lipidic cubic phase (LCP) crystallization and an automated data-processing system for multiple microcrystals enabled crystal structures of PepTSo2 to be determined at resolutions of 3.5 and 3.9 Å. The present structures in a lipid bilayer revealed the detailed mechanism for the tetrameric assembly of PepTSo2, in which a characteristic extracellular loop (ECL) interacts with two asparagine residues on H12 which were reported to be important for tetramerization and plays an essential role in oligomeric assembly. This study provides valuable insights into the oligomerization mechanism of this MFS-type transporter, which will further pave the way for understanding other oligomeric membrane proteins.
Noncovalent structure of SENP1 in complex with SUMO2
Authors: Ambaye Nigus D.
Published: April 2019

SUMOylation is a post-translational modification in which a small ubiquitin-like molecule (SUMO) is appended to substrate proteins and is known to influence myriads of biological processes. A delicate interplay between several families of SUMOylation proteins and their substrates ensures the proper level of SUMOylation required for normal cell function. Among the SUMO proteins, SUMO2 is known to form mono-SUMOylated proteins and engage in poly-SUMO chain formation, while sentrin-specific protease 1 (SENP1) is a key enzyme in regulating both events. Determination of the SENP1–SUMO2 interaction is therefore necessary to better understand SUMOylation. In this regard, the current paper reports the noncovalent structure of SENP1 in complex with SUMO2, which was refined to a resolution of 2.62 Å withRandRfreevalues of 22.92% and 27.66%, respectively. The structure shows that SENP1–SUMO2 complex formation is driven largely by polar interactions and limited hydrophobic contacts. The essential C-terminal motif (QQTGG) of SUMO2 is stabilized by a number of specific bonding interactions that enable it to protrude into the catalytic triad of SENP1 and provide the arrangement necessary for maturation of SUMO and deSUMOylation activity. Overall, the structure shows a number of structural details that pinpoint the basis of SENP1–SUMO2 complex formation.
Cryo-EM structure of the Ebola virus nucleoprotein–RNA complex
Authors: Kirchdoerfer Robert N. , Saphire Erica Ollmann , Ward Andrew B.
Published: April 2019

Ebola virus is an emerging virus that is capable of causing a deadly disease in humans. Replication, transcription and packaging of the viral genome are carried out by the viral nucleocapsid. The nucleocapsid is a complex of the viral nucleoprotein, RNA and several other viral proteins. The nucleoprotein forms large, RNA-bound, helical filaments and acts as a scaffold for additional viral proteins. The 3.1 Å resolution single-particle cryo-electron microscopy structure of the nucleoprotein–RNA helical filament presented here resembles previous structures determined at lower resolution, while providing improved molecular details of protein–protein and protein–RNA interactions. The higher resolution of the structure presented here will facilitate the design and characterization of novel and specific Ebola virus therapeutics targeting the nucleocapsid.
Novel T9 loop conformation of filamenting temperature-sensitive mutant Z from Mycobacterium tuberculosis
Authors: Lazo E. O. , Jakoncic J. , RoyChowdhury S. , Awasthi D. , Ojima I.
Published: April 2019

As of 2017, tuberculosis had infected 1.7 billion people (23% of the population of the world) and caused ten million deaths. Mycobacterium tuberculosis (Mtb) is quickly evolving, and new strains are classified as multidrug resistant. Thus, the identification of novel druggable targets is essential to combat the proliferation of these drug-resistant strains. Filamenting temperature-sensitive mutant Z (FtsZ) is a key protein involved in cytokinesis, an important process for Mtb proliferation and viability. FtsZ is required for bacterial cell division because it polymerizes into a structure called the Z-ring, which recruits accessory division proteins to the septum. Here, the crystal structure of the MtbFtsZ protein has been determined to 3.46 Å resolution and is described as a dimer of trimers, with an inter-subunit interface between protomers AB and DE. In this work, a novel conformation of MtbFtsZ is revealed involving the T9 loop and the nucleotide-binding pocket of protomers BC and EF.
Taking Britain from darkness into light
Authors: Van Der Laan Sandra , Moerman Lee , Campbell David
Published: April 2019

Purpose

This paper aims to contribute to an understanding of the process of the construction of the professional businessman in Britain in the early twentieth century.

Design/methodology/approach

Two books authored by the prominent British industrialist Sir Samuel Turner III are analysed as a form of contemporaneous discourse. This allows for examination of the texts as a particular genre of social media within their social, economic and political contexts.

Findings

Sir Samuel Turner III derived the elite status from his family’s standing as a prominent Lancashire, church-going, industrial dynasty. The role of business and the businessman as a professional are recast as the means to restore Britain to its former pre-World War I glory – a position that continues to resonate in a variety of contexts today.

Originality/value

The paper contributes to our understanding of the construction of the social world through discourse. While Turner’s ideology of the relationship between labour, capital, business and society may appear quaint to our twenty-first-century experiences, it is nevertheless an important reminder that the elite voice influences political and social action.
Viewpoint: conveying managerial relevance into service research
Authors: Klaus Philipp Phil
Published: April 2019

Purpose

This paper aims to propose opportunities on how service research scholars can overcome the challenge of designing, delivering and disseminating managerial relevant studies. The proposed tactics will assist researchers and the community in general to resolve the pressing issues of both, the disconnection between theory formulation and verification and the divide between pursuing theoretical advances versus managerial usefulness.

Design/methodology/approach

Building on insights deriving from academic research, managerial publications and managerial feedback, the paper explores how to turn the challenges of developing managerial relevant research into opportunities.

Findings

Using communication research insights, the paper submits that, contrary to common belief, conducting managerial relevant research is not necessarily the main challenge for service researchers. The author identifies the main communications challenges according to three stages, designing, delivering and disseminating research with managerial relevance to the business community, leading to the phenomenon labeled as “lost before, and in translation.”

Research limitations/implications

This paper highlights the developments leading to service research’s lack of managerial relevance perception. Using these insights, the author develops detailed chronological strategies and tactics how to change these perceptions into more favorable ones by designing, delivering and communicating research’s benefits of the research in a better, more efficient and impactful fashion, catered to the managerial audience.

Practical implications

The strategies and tactics outline build a practical “how-to” foundation for researcher to develop managerial relevant research, increase their publication chances and tap into new networks, data collection and funding opportunities.

Originality/value

This is the, to the author’s knowledge, first study to shed new light on the challenge of conducting managerial relevant research by not challenging the notion of relevance, but the way relevance is communicated, disseminated and originated.
The impact of concurrent HIV and type II diabetes on immune maturation, immune regulation and immune activation
Authors: Tingstedt Jeanette Linnea , Hove‐Skovsgaard Malene , Gaardbo Julie , Ullum Henrik , Nielsen Susanne Dam , Gelpi Marco
Published: April 2019

Chronic immune activation and inflammation are constant findings in people living with HIV (PLWH) and contribute to the risk of non‐AIDS‐related morbidities, including cardiovascular diseases (CVD). Type 2 diabetes (T2D) is also characterized by immune activation and inflammation. We aimed to investigate the impact of concurrent HIV infection and T2D on T‐cell subsets. The study included PLWH with T2D (HIV+T2D+, N = 25) and without T2D (HIV+T2D−, N = 25) and HIV‐negative controls with T2D (HIV−T2D+, N = 22) and without T2D (HIV−T2D−, N = 28). All PLWH in the study were receiving combination antiretroviral therapy. We examined T‐cell homeostasis by determining T‐cell subsets (immune maturation, immune regulation and immune activation) using flow cytometry. HIV+T2D− had lower proportion of Tc17 cells and higher proportion of apoptotic cells than HIV−T2D−. When comparing HIV+T2D+ and HIV+T2D− a lower proportion of CD4+ recent thymic emigrants (RTE) was found (p = 0.028). Furthermore, HIV+T2D+ had a higher proportion of non‐suppressive CD4+ Tregs compared to HIV+T2D− (p = 0.010). In conclusion, even in the setting of treated HIV infection, distinct immunological alterations are found. In PLWH with concomitant T2D, most alterations in T‐cell subsets were related to HIV and only few differences were found between PLWH with and without diabetes.
Editorial: effects of vildagliptin on GLP‐1 levels, gastric motor functions and food intake. A authors' reply
Authors: Masuy Imke , Rotondo Alessandra , Verbeure Wout , Biesiekierski Jessica R. , Deloose Eveline , Tack Jan
Published: April 2019

Linked Content

This article is linked to Rotondo et al and Camelleri papers. To view these articles, visit https://doi.org/10.1111/apt.15195 and https://doi.org/10.1111/apt.15206.
A five‐CpG signature of microRNA methylation in non‐G‐CIMP glioblastoma
Authors: Kang En‐Ming , Yin An‐An , He Ya‐Long , Chen Wei‐Jun , Etcheverry Amandine , Aubry Marc , Barnholtz‐Sloan Jill , Mosser Jean , Zhang Wei , Zhang Xiang
Published: April 2019

Aims

DNA methylation has been found to regulate microRNAs (miRNAs) expression, but the prognostic value of miRNA‐related DNA methylation aberration remained largely elusive in cancers including glioblastomas (GBMs). This study aimed to investigate the clinical and biological feature of miRNA methylation in GBMs of non‐glioma‐CpG island methylator phenotype (non‐G‐CIMP).

Methods

Prognostic miRNA methylation loci were analyzed, with TCGA and Rennes cohort as training sets, and independent datasets of GBMs and low‐grade gliomas (LGGs) were obtained as validation sets. Different statistical and bioinformatic analysis and experimental validations were performed to clinically and biologically characterize the signature.

Results

We identified and validated a risk score based on methylation status of five miRNA‐associated CpGs which could predict survival of GBM patients in a series of training and validation sets. This signature was independent of age and O‐6‐methylguanine‐DNA methyltransferase (MGMT) promoter methylation status. The risk subgroup was associated with angiogenesis and accordingly differential responses to bevacizumab‐contained therapy. MiRNA target analysis and in vitro experiments further confirmed the accuracy of this signature.

Conclusion

The five‐CpG signature of miRNA methylation was biologically relevant and was of potential prognostic and predictive value for GBMs. It might be of help for improving individualized treatment.
Drivers of plant functional group richness and beta diversity in fire‐dependent pine savannas
Authors: Freeman Johanna E. , Kobziar Leda N. , Leone Erin H. , Williges Kent
Published: April 2019

Aim

To assess the drivers of plant functional group richness and beta diversity in fire‐maintained North American Coastal Plain (NACP) savannas.

Location

The southern portion of the NACP, a global biodiversity hotspot. This region is characterized by fire‐dependent pine savanna fragments that are isolated within a matrix of agriculture, urban development, non‐pyrogenic plant communities and plantation forestry.

Methods

We used nested quadrats to sample plant species on 30 fire‐maintained savanna preserves in Florida and Georgia, USA. We analysed between‐site Sørenson dissimilarity, a measure of beta diversity, using NMDS and PerMANOVA. We measured nestedness using NODF, and we used Betapart to partition Sørenson dissimilarity into nestedness and turnover components. We used linear and generalized linear mixed models to explore drivers of functional group richness and composition, including fire regime (return interval, number of fires, time since fire and seasonality), vegetation structure (herbaceous cover, woody cover and tree density) and spatial factors (surrounding landscape and geographic distance).

Results

We found turnover‐dominated beta‐diversity patterns in all functional groups. Turnover was explained partly by spatial and environmental gradients, but roughly half of the turnover between sites was unexplained. Species richness was higher on sites where fire and fire surrogates had been used longer and more consistently, and these effects were partly independent of current vegetation structure. Fire regimes containing more growing season fire and more diversity of burn seasons promoted higher species richness. Relationships between small‐scale and large‐scale species richness varied by soil type and functional group.

Main conclusions

Fire‐maintained savannas in the southeastern NACP vary greatly in their plant functional group richness, but high beta diversity resulting primarily from species turnover suggests that even species‐poor sites can harbour less‐common members of the regional plant metacommunity. Prescribed fire regimes that include growing season fire as well as a diversity of burn seasons may best promote species and functional group richness.
Work ethic and organizational commitment as conditions of unethical pro‐organizational behavior: Do engaged workers break the ethical rules?
Authors: Grabowski Damian , Chudzicka‐Czupała Agata , Chrupała‐Pniak Małgorzata , Mello Abby L. , Paruzel‐Czachura Mariola
Published: April 2019

Unethical pro‐organizational behaviors (UPB) are actions that break rules or established standards, but are undertaken for the purposes of helping the organization or coworkers. Although research has already examined the role of work ethic and organizational commitment in shaping employee behaviors, little is known about the reason for and antecedents of employees undertaking UPB. In a sample of 425 working adults from multiple industries, we tested whether work ethic and organizational commitment dimensions predict the readiness to undertake UPB. The time‐lagged study showed that the work ethics dimension “hard work,” and normative and affective organizational commitment, are positive predictors of UPB. The ethics dimensions “morality/ethics,” “delay of gratification,” “centrality of work” and “anti‐leisure attitudes” are negative predictors of UPB.
The influence of political climate on job pursuit intentions and the moderating effect of Machiavellianism
Authors: Djurdjevic Emilija , Rosen Christopher C. , Conroy Samantha A. , Rawski Shannon L. , Sosna Katherine U
Published: April 2019

Job seekers now have access to a number of internet resources (e.g., social media, chat rooms, and message boards) that provide information about potential employers. These resources provide potential job applicants with extensive amounts of third‐party information about organizations, including information about the extent to which a particular organization's climate can be characterized as being political. Unfortunately, owing to a dearth of research on this topic, it is unclear to what extent such information about an organization's political climate might affect the recruiting process. Therefore, drawing from the Attraction‐Selection‐Attrition model, we considered the extent to which potential job applicants are less (more) likely to pursue jobs in organizations that are perceived as more (less) political. We further identified Machiavellianism as a potential moderator of this relationship, given that this trait reflects the extent to which an individual would “fit” into a highly political work environment. Across three studies, our findings provide evidence that job applicants report being less likely to pursue jobs in organizations characterized by high levels of workplace politics. The results further indicated that Machiavellianism attenuates this negative effect. In light of our findings, we discuss implications for how information that is not controlled by the organization (e.g., information provided by social media or other internet‐based sources) affects job pursuit intentions and the organization's applicant pool.
Charge compensation mechanisms in Li‐substituted high‐entropy oxides and influence on Li superionic conductivity
Authors: Osenciat Nicolas , Bérardan David , Dragoe Diana , Léridon Brigitte , Holé Stéphane , Meena Arun K. , Franger Sylvain , Dragoe Nita
Published: April 2019

The charge compensation mechanisms that occur when Li+ substitutes a 2+ element in superionic conductor (MgCoNiCuZn)O high‐entropy oxide have been studied using a combination of thermogravimetric analysis and X‐ray photoemission spectroscopy. Depending on the concentration of Li+ in the compound, the charge compensation involves first partial oxidation of Co2+ into Co3+ for low fraction of Li+, and then a combination of both the oxidation of cobalt and the formation of oxygen vacancies for large fraction of Li+.
Body composition patterns and breast cancer risk in Chinese women with breast diseases: A latent class analysis
Authors: Zhang Jinyu , Wang Jichuan , Zhou Jie , Fang Qiong , Zhang Nan , Yuan Changrong
Published: April 2019

Aims

To identify unobserved body composition patterns among Chinese women with breast diseases using latent class analysis (LCA) and to examine the relationship between body composition patterns and breast cancer (BC) risk.

Design

A descriptive, cross‐sectional study.

Methods

Female patients (N = 1816) with breast diseases were included in the study from April 2016 ‐ March 2017. Body composition measures were done by the bioelectrical impedance analysis. The LCA models were estimated using Mplus 8.1.

Results

Four latent classes were identified based on water, protein, minerals and body fat mass: Class 1 – Low Muscle Mass class; Class 2 – High Body Composition class; Class 3 – High Fat class; and Class 4 – Normal Body Composition Class. Classes 2 and 3 are higher risk classes for developing BC compared with the other two classes (p < 0.05). Overall, age is positively associated with the odds of BC development (p < 0.001). However, age effect depends on the body composition patterns. Age effect on the odds of BC was statistically significant only for women who had least body fat mass (Class 1, OR = 1.110, 95% C.I.: 1.084–1.136) or had normal body composition (Class 4, OR = 1.090, 95% C.I.: 1.036–1.147). The effect of age was not statistically significant if women had higher risk body composition (e.g., in Classes 2 or 3).

Conclusion

Latent Class Analysis is a useful person‐centred analytical approach for identification of unobserved patterns of body composition and it could be used to predict the risk of BC and develop personalized interventions for body composition studies.
Classification of the seeds of traditional and double‐low cultivars of white mustard based on texture features
Authors: Ropelewska Ewa , Jankowski Krzysztof J.
Published: April 2019

The aim of this study was to develop classification models based on the texture features from the images acquired with a flatbed scanner to distinguish between the seeds of traditional (Radena) and double‐low (Warta) cultivars of white mustard. Texture features were calculated in MaZda software. The classification models for RGB, Lab, and XYZ color space and individual color channels for distinguishing between the seeds of traditional and double‐low cultivars of white mustard were built in the WEKA application with the use of selected Decision Trees (J48), Rules (J Rip), Bayes (Naive Bayes), Lazy (IBk), Meta (Multi Class Classifier), and Functions (FLDA) classifiers. The classification accuracy of the evaluated color models ranged from 77% (XYZ, IBk classifier) to 83% (RGB, JRip classifier). In an evaluation of individual color channels, classification accuracy was highest for channels R, L, and X, and it ranged from 85% for color channels L and X when the IBk classifier was used to 93% for the texture features from color channel R when the JRip classifier was used.

Practical applications

The developed models support fast, cheap, nondestructive, and reliable discrimination of the seeds of white mustard. The proposed classification models based on texture features effectively distinguished between the seeds of traditional (Radena) and double‐low (Warta) cultivars of white mustard. Therefore, they can be reliably used to examine the authenticity of seeds and to detect seed adulteration.
Incorporating the impacts of climate change into infrastructure life cycle assessments: A case study of pavement service life performance
Authors: Guest Geoffrey , Zhang Jieying , Maadani Omran , Shirkhani Hamidreza
Published: April 2019

Climate change is expected to impact both the operational and structural performance of infrastructures such as roads, bridges, and buildings. However, most past life cycle assessment (LCA) studies do not consider how the operational/structural performance of infrastructure will be affected by a changing climate. The goal of this research was to develop a framework for integrating climate change impacts into LCA of infrastructure systems. To illustrate this framework, a flexible pavement case study was considered where life‐cycle environmental impacts were compared across a climate change scenario and several time horizons. The Mechanistic‐Empirical Pavement Design Guide (MEPDG) was utilized to capture the structural performance of each pavement performance scenario and performance distresses were used as inputs into a pavement LCA model that considered construction and maintenance/rehabilitation materials and activities, change in relative surface albedo, and impacts due to traffic. The results from the case study suggest that climate change will likely call for adaptive design requirements in the latter half of this century but in the near‐to‐mid term, the international roughness index (IRI) and total rutting degradation profile was very close to the historical climate run. While the inclusion of mechanistic performance models with climate change data as input introduces new uncertainties to infrastructure‐based LCA, sensitivity analyses runs were performed to better understand a comprehensive range of result outcomes. Through further infrastructure cases the framework could be streamlined to better suit specific infrastructures where only the infrastructure components with the greatest sensitivity to climate change are explicitly modeled using mechanistic‐empirical modeling routines.
Strengthening nursing surveillance in general wards: A practice development approach
Authors: Peet Jacqueline , Theobald Karen , Douglas Clint
Published: April 2019

Aims and objectives

To explore the context and culture of nursing surveillance on an acute care ward.

Background

Prevention of patient deterioration is primarily a nursing responsibility in hospital. Registered nurses make judgements and act on emerging threats to patient safety through a process of nursing surveillance. Organisational factors that weaken nursing surveillance capacity on general wards increase the need for patient rescue at the end point of clinical deterioration with poorer outcomes. Yet little is known about cultures that enable and sustain ward nursing surveillance for patient safety.

Design

Workplace observations and semistructured interviews using a critical lens as the first stage of a larger emancipatory practice development project.

Methods

Researcher immersion including 96 hr of nonparticipant observation with 12 semistructured interviews during July–August 2017. This study adhered to the COREQ guidelines.

Results

We offer a metaphor of nursing surveillance as the threads that support the very fabric of acute care nursing work. These hidden threads enable nurses to weave the tapestry of care that keeps patients safe. This tapestry is vulnerable to internal and external forces, which weaken the structure, putting patients and staff at risk.

Conclusion

Understanding local context is essential to supporting practice change. This workplace observation challenges us to find ways to creatively engage nurses with the underlying cultural and systems issues that so often remain hidden from view in the deteriorating patient literature.

Relevance to clinical practice

Building cultural values that strengthen nursing surveillance is a prerequisite for safe and effective hospital care. As such, practice‐based research that empowers frontline nurses and teams to develop person‐centred workplace cultures can hold the key to unlocking sustainable improvements in patient safety.
Young adult cancer patients’ experiences of private social network support during cancer treatment
Authors: Hauken May Aa. , Larsen Torill M. B.
Published: April 2019

Aims and objectives

To explore young adult cancer patients' experiences of support from their private social network during cancer treatment.

Background

Cancer treatment in young adulthood (aged 18–35 years) can be distressing. Social support is crucial for health and well‐being, especially for young people and in times of crisis. Research indicates that young cancer patients experience a lack of social network support, but little is known about the types of private social network support available during cancer treatment.

Design

Qualitative study with interpretive descriptive design.

Methods

Twenty young adult cancer patients with different cancer diagnoses were interviewed retrospectively using a semi‐structured interview guideline. Data were analysed using systematic text condensation. The COREQ checklist for qualitative research was followed.

Results

“From independence to dependence” was identified as a bridging theme, which was elaborated by four sub‐themes: (1) “My partner was my rock—or not”; (2) “My family stood by me—or not”; (3) “My friends supported me—or not”; and (4) “I lacked young adult cancer peers—or not.”

Conclusion

The patients' major sources of private social network support were their partners and close family members. Only a few friends supported them during cancer treatment, and most lacked peer support. The type of social network support they received varied, and not all support was perceived as helpful. Helpful network support was experienced as being unconditional and given with empathy and without prompting. Patients without sufficient support from a partner or family members seem to be especially vulnerable.

Relevance to clinical practice

Nurses play a crucial role in educating young adult cancer patients about the importance of social support and helping them to map their social network and being explicit when requesting support. Nurses should inform patients' networks about both helpful and unhelpful support and should facilitate interaction between patients.
Discussing sexuality in health care: A systematic review
Authors: Fennell Reginald , Grant Blair
Published: April 2019

Aims and objectives

Using the PRISMA guidelines, a systematic literature review was conducted to explore current and relevant evidence regarding factors that influence nurses’ provision of sexual healthcare education to patients.

Background

The World Health Organization and Healthy People 2020 emphasise the importance of sexual health care. Although the nursing profession has the ability to develop a competent level of sexuality education, sexual health care is often ignored in nursing care and education. Many nurses are failing to engage in meaningful conversations about sexual health with patients, and this could lead to negative health events. However, patients would like reliable and nonjudgmental access to education about sexual health.

Design

Electronic databases were searched for articles published between 2012–2017. Studies of nurses providing sexual health education in healthcare settings were included. The Melnyk and Fineout‐Overholt (2015, Evidence‐based practice in nursing & healthcare, Philadelphia, PA: Walters Kluwer) quality assessment framework was used. The researchers independently reviewed 532 studies and agreed upon ten to include in this review.

Results

Findings from this systematic review suggest that nurses’ provision of sexual health education to patients is influenced by four factors: (a) a lack of knowledge about sexual health, (b) nurses’ attitudes and beliefs that sexual health care is private and not a priority, (c) nurses’ comfort discussing sexual health, and (d) perceived barriers related to time, responsibility and organisational support.

Conclusion

The ten articles reviewed were all Level VI descriptive and qualitative studies, as defined by Melnyk and Fineout‐Overholt (2015). It is evident that sexual healthcare information is not being widely addressed. To reduce stigma, the positive aspects of sexual health care must be promoted on multiple levels.

Relevance to clinical practice

Leaders in professional and community‐based organizations should be on the forefront of making recommendations for nurses and practitioners, so they could improve their ability to provide sexual healthcare information to their patients.