bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying palliative care needs in people with dementia
Authors: Lloyd-Williams Mari , Mogan Caroline , Dening Karen Harrison
Published: September 2017

Purpose of review

Dementia is now recognized as a progressive life-limiting illness where many patients can benefit from access to palliative care.

Recent findings

The present review has focused on three areas namely, advanced care planning in supporting palliative care for dementia, hospice provision for people with dementia and provision of care within family home. In advanced care planning, there is little research on systematically developed and implemented advance care planning interventions or whether they achieve desired outcomes for end-of-life care. There is limited research on hospice-based care for patients with dementia and most studies are U.S. based. Equally studies exploring how family carers can be supported and facilitated to care at home for the person with dementia to the end of life are exploratory rather than determining what factors may be important.

There are relatively few studies, especially quantitative studies or intervention studies being carried out to determine most effective means of providing palliative care for people with dementia, particularly with respect to advanced care planning, the provision of hospice-based care and support at home. Despite increased public awareness of dementia as a terminal illness, more research is required to support patients with dementia and their families at the end of life.
Understanding and mitigating some limitations of Illumina© MiSeq for environmental sequencing of Fungi
Authors: Thomas Dan , Vandegrift Roo , Bailes Graham , Roy Bitty
Published: September 2017

ITS-amplicon metabarcode studies using the illumina MiSeq sequencing platform are the current standard tool for fungal ecology studies. Here we report on some of the particular challenges experienced while creating and using a ribosomal RNA gene (rDNA) amplicon library for an ecological study. Two significant complications were encountered. First, artificial differences in read abundances among OTUs were observed, apparently resulting from bias at two stages: PCR amplification of genomic DNA with ITS-region Illumina-sequence-adapted-primers, and during Illumina sequencing. These differential read abundances were only partially corrected by a common variance-stabilization method. Second, tag-switching (or the shifting of amplicons to incorrect sample indices) occurred at high levels in positive mock-community controls. An example of a bioinformatic method to estimate the rate of tag switching is shown, some recommendations on the use of positive controls and primer choice are given, and one approach to reducing potential false positives resulting from these technological biases is presented.
When a rose is not a rose: Pyramidal neurons respond differently in healthy and epileptic human neocortex
Authors: Joseph Kevin , Ravi Vidhya M. , Argiti Katerina , Feuerstein Thomas J. , Zentner Josef , Migliore Rosanna , Migliore Michele , Hofmann Ulrich G.
Published: September 2017

Epilepsy affects a huge number of patients by severe disruption of brain functions and is characterised by recurrent seizures, sometimes hard to be treated by medications. Seizure induced cellular consequences in ionic gradient and homeostasis are expected to result in electrophysiological differences between epileptic and non-epileptic neurons.

In the following work we demonstrate these differences in layer III cortical pyramidal neurons sourced from epileptic and non-epileptic human patient tissue. Although visually indistinguishable and featuring similar membrane potentials and latency to first spikes upon whole cell patch stimulation, epileptic pyramidal neurons display a larger rheobase and a smaller membrane resistance, responding less efficiently to electrical stimulation than their peri-tumorous equivalents. This decreased excitability contradicts results in comparable animal models of epilepsy and was further corroborated by detailed analysis of spiking characteristics and phase plot analysis of these events. Both point to an overexpression of K+ channels trying to compensate for the hyperexcited, epileptic network state. A computational model of a pyramidal neuron was utilized to give an estimate of the needful relative changes in K+ and Na+ conductances.
Expect to neglect: Cross-modal resource allocation in anticipation of visual load
Authors: Bangel Katrin A. , Slagter Heleen A. , Mazaheri Ali
Published: September 2017

Human information processing is limited in capacity. To prevent sensory overload, expectation of upcoming events has been suggested to allocate processing resources to task-relevant regions (e.g., visual system), at the expense of processing in task-irrelevant regions (e.g., auditory system). In support of this, for tasks involving a high visual perceptual load (e.g. visual target search within physically similar distractors), auditory evoked responses were found to be attenuated1. This EEG study aimed to further elucidate the neural mechanisms by which the brain prepares for sensory overload. We investigated how expectancy about visual load modulated neural activity, prior to the onset of visual stimuli. Visual load in a letter search task was manipulated by varying the target letter’s similarity to the remaining letters and the letter set size from which flankers were randomly drawn. Importantly, audio-visual cues signaled the likely visual load of the upcoming stimulus-array, manipulating expectancy about visual task load. Cues signaling high visual load elicited attenuated auditory-evoked responses and increased alpha activity over task-irrelevant (auditory) regions, suggesting a functional inhibition of those regions already prior to the arrival of the visual array to suppress auditory cue processing. We also observed a sustained posterior positivity in the ERPs after high perceptual load cues, whose amplitude correlated with reaction times, suggestive of resource allocation for the upcoming visual targets. Expectation about visual load may thus prepare the attentional system both by facilitating target processing and task execution and inhibiting irrelevant sensory processing, thus providing efficient means to overcome attentional limits in situations with complex visual input.
Instantiation of incentive value and movement invigoration by distinct midbrain dopamine circuits
Authors: Saunders Benjamin T. , Richard Jocelyn M. , Margolis Elyssa B. , Janak Patricia H.
Published: September 2017

Environmental cues, through Pavlovian learning, become conditioned stimuli that guide animals towards the acquisition of “rewards” (i.e., food) that are necessary for survival. Here, we test the fundamental role of midbrain dopamine neurons in conferring predictive or motivational properties to cues, independent of external rewards. We demonstrate that phasic optogenetic excitation of dopamine neurons throughout the midbrain, when presented in temporal association with discrete sensory cues, is sufficient to instantiate those cues as conditioned stimuli that subsequently both evoke dopamine neuron activity on their own, and elicit cue-locked conditioned behaviors. Critically, we identify highly parcellated behavioral functions for dopamine neuron subpopulations projecting to discrete regions of striatum, revealing dissociable mesostriatal systems for the generation of incentive value and movement invigoration. These results show that dopamine neurons orchestrate Pavlovian conditioning via functionally heterogeneous, circuit-specific motivational signals to shape cue-controlled behavior.
The widespread misconception about the Japanese major biogeographic boundary, the Watase line (Tokara gap), revealed by bibliographic and beta diversity analyses
Authors: Komaki Shohei , Igawa Takeshi
Published: September 2017

The biota of the Japanese Archipelago is divided into the Palearctic and Oriental realms by the Watase line (Tokara gap), a major biogeographic boundary of Japan. This boundary is generally placed between Akusekijima and Kodakarajima Islands of the Tokara Archipelago, and has been the subject of many biogeographic debates. However, despite being widely accepted, the position of the boundary is doubtful because of a lack of clear evidence. Here, to verify the definition and existence of the biogeographic boundary, we performed a documentary search and beta diversity analysis of multiple taxa. Our documentary search suggested that the Watase line (Tokara gap) should be put between Yakushima/Tanegashima and Amamioshima Islands, but recent references to it clearly deviate from its original definition, and that the placement of the boundary line between Akusekijima and Kodakarajima Islands is based on limited and biased evidence. Our beta diversity analyses found no common biogeographic boundary dividing the Tokara Archipelago into two realms, and showed that the beta diversity pattern of this region is explained by the areas and geographic distances of the islands in agreement with the general principles of island biogeography. The widespread misunderstanding of biogeography in this region could have been perpetuated by preconception and the citation of references without verification. Our study proposes that revision of the biogeography in the Tokara Archipelago, a gap region between the Palearctic and Oriental realms, is necessary and demonstrates the negative influence of preconception in biogeographic debate.
IPCAPS: an R package for iterative pruning to capture population structure
Authors: Chaichoompu Kridsadakorn , Yazew Fentaw Abegaz , Tongsima Sissades , Shaw Philip James , Sakuntabhai Anavaj , Pereira Luísa , Van Steen Kristel
Published: September 2017

Background

Resolving population genetic structure is challenging, especially when dealing with closely related or geographically confined populations. Although Principal Component Analysis (PCA)-based methods and genomic variation with single nucleotide polymorphisms (SNPs) are widely used to describe shared genetic ancestry, improvements can be made especially when fine-scale population structure is the target.

Results

This work presents an R package called IPCAPS, which uses SNP information for resolving possibly fine-scale population structure. The IPCAPS routines are built on the iterative pruning Principal Component Analysis (ipPCA) framework that systematically assigns individuals to genetically similar subgroups. In each iteration, our tool is able to detect and eliminate outliers, hereby avoiding severe misclassification errors.

Conclusions

IPCAPS supports different measurement scales for variables used to identify substructure. Hence, panels of gene expression and methylation data can be accommodated as well. The tool can also be applied in patient sub-phenotyping contexts. IPCAPS is developed in R and is freely available frombio3.giga.ulg.ac.be/ipcaps
Rapid seasonal evolution in innate immunity of wildDrosophila melanogaster
Authors: Behrman Emily L. , Howick Virginia M. , Kapun Martin , Staubach Fabian , Bergland Alan O. , Petrov Dmitri A. , Lazzaro Brian P. , Schmidt Paul S.
Published: September 2017

Understanding the rate of evolutionary change and the genetic architecture that facilitates rapid adaptation is a current challenge in evolutionary biology. Comparative studies show that genes with immune function are among the most rapidly evolving genes in a range of taxa. Here, we use immune defense in natural populations ofD. melanogasterto understand the rate of evolution in natural populations and the genetics underlying the rapid change. We probed the immune system using the natural pathogensEnterococcus faecalisandProvidencia rettgerito measure post-infection survival and bacterial load of wildD. melanogasterpopulations collected across seasonal time along a latitudinal transect on the eastern North America (Massachusetts, Pennsylvania, and Virginia). There are pronounced and repeatable changes in the immune response over approximately 10 generations between the spring and fall populations with a significant but less distinct difference among geographic locations. Genes with known immune function are not enriched among alleles that cycle with seasonal time, but the immune function of a subset of seasonally cycling alleles in immune genes was tested using reconstructed outbred populations. We find that flies containing seasonal alleles inThioester-containing protein 3 (Tep3)have different functional responses to infection and that epistatic interactions among seasonalTep3andDrosomycin-like 6 (Dro6)alleles produce the immune phenotypes observed in natural populations. This rapid, cyclic response to seasonal environmental pressure broadens our understanding of the complex ecological and genetic interactions determining the evolution of immune defense in natural populations.
A minimalist approach to protein identification
Authors: Sampath G.
Published: September 2017

Computations on proteome sequence databases show that most proteins can be identified from a protein’s isoelectric point (IEP) and digitized linear sequence volume (equal to the total volume of its residues). This is illustrated with four proteomes:H. pylori(1553 proteins),E. coli(4306 proteins),S. cerevisiae(6721 proteins), andH. sapiens(20207 proteins); the identification rate exceeds 90% in all four cases for appropriate parameter values. IEP can be obtained with 1-d gel electrophoresis (GE), whose accuracy is better than 0.01. Linear protein sequence volumes of unbroken proteins can be obtained with a sub-nanometer diameter nanopore that can measure residue volume with a resolution of 0.07-0.1 nm3(Kennedy et al.,Nature Nanotech., 2016,11, 968-976; Dong et al.,ACS Nano, 2017, doi: 10.1021/acsnano.6b08452); the blockade current due to a translocating protein is roughly proportional to the volume it excludes in the pore. There is no need to identify any of the residues. More than 90% of all the proteins have estimated translocation times higher than 1 μs, which is within the time resolution of available detectors. This is a minimalist proteolysis-free GE-and nanopore-based single-molecule approach requires very small samples, is non-destructive (the sample can be recovered for reuse), and can be translated with currently available technology into a portable device for possible use in the field, an academic lab, or a pre-screening step preceding conventional mass spectrometry.
Researcher vs advocate: ethnographic-ethical dilemmas in feminist scholarship
Authors: Jain Tania
Published: September 2017

Purpose

The purpose of this paper is to explore the nature of dilemmas that emerge at the theoretical and practical interfaces of ethnographic fieldwork and feminist advocacy. This is done by examining the researcher’s role in the field and the complex relationships between the researcher and the researched.

Design/methodology/approach

Critical self-reflections and autoethnographic analyses of fieldwork experiences in the author’s home country in South Asia are used to explore these dilemmas.

Findings

Using situated examples from a typical organisational setting involving both the oppressive and the oppressed, the researcher’s participant observation is found to be conflicted between critical participation and critical observation. Conscious and/or unconscious critical participation through enactment of feminist ethics by combining researcher and advocacy roles allows a route to assuage these conflicts. Practical strategies used to accomplish this are also discussed.

Research limitations/implications

Although the practical strategies discussed in this paper are culturally and organisationally specific and hence limited by them, it is hoped that suitable variants will emerge for readers from their discussion. Further research is needed to investigate the variety of ways in which the researcher-advocate positionality proposed in this paper can be strategically adopted conditional on cultural and organisational contexts, feminist research questions, and researchers’ abilities and constraints.

Practical implications

This paper seeks to shed light on the dilemmas of feminist ethics faced by critical feminist researchers conducting ethnographic fieldwork. It also discusses ways to enable researchers to circumvent these dilemmas in both epistemologically productive ways by collecting rich data and in ontologically enriching ways by allowing some enactment of feminist ethics. To this end, a positionality of the feminist researcher-advocate is conceptualised that does not enforce constraints of extreme positionalities of either a conventional ethnographer or an action researcher.

Social implications

Besides illustrating the need to stretch beyond traditional boundaries of participant observation, the researcher-advocate positionality also allows feminist researchers to make small, but directly tangible impact towards gender equality in their field setting. Implications for researchers’ emotional, and cognitive safety are also discussed especially when they identify with one or more minority identities.

Originality/value

This paper contributes to discussions on the theory of methods by highlighting the benefits of enacting feminist ethics as a way of critical participation in research settings.
Meezan Bank: category leader in Islamic banking
Authors: Gul Rashid Amber , Usmani Obaid , Ejaz Lalarukh , Faraz Hasan
Published: September 2017

Subject area

Islamic Banking has been in the limelight since the recession of 2008. Although around for a long time, it is enjoying a renaissance of sorts. This case provides an introduction.

Study level/applicability

EMBA and/or MBA introduction to banking, senior semester undergraduate, specialization in Islamic Banking.

Case overview

This case is written in the form of an interview with Meezan Bank, one of the leading financial institutions in the Islamic banking sector. It is based on primary as well as secondary data obtained via interviews and documentary analysis.

Expected learning outcomes

This is an analytical case and not a decision-making one. The main theme of the case revolves around analysing what Islamic banking is, the challenges that Meezan has faced, the pros and cons of doing business this way and the future issues it can face.

Supplementary materials

Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code

CSS 7: Management Science.
Storytelling and innovative behavior: an empirical study in a Brazilian group
Authors: D’Arrigo Fernanda Pauletto , Robini Eduardo , Larentis Fabiano , Camargo Maria Emilia , Schmiedgen Peter
Published: September 2017

Purpose

The paper aims to identify the relationship between the use of storytelling and innovative work behavior (IWB) in organizations.

Design/methodology/approach

The research took place in a human resource development (HRD) training session for leaders of Alpha Group. In this session, storytelling was adopted to discuss innovation and IWB. Following the training, the leaders completed a questionnaire about the effectiveness of the stories for the construction of knowledge and IWB. Data were collected from 97 leading sectors. Subsequently, data analysis was performed to identify correlations between the aspects.

Findings

The paper provides empirical insights about the use of storytelling, the effectiveness of the stories, as well as their relationship with the innovative behavior of sectors leaders in a Brazilian organization. It has identified the relation between effectiveness of stories and level of innovative behavior.

Research limitations/implications

Owing to the chosen research approach, the research results cannot be generalized. Because it is a study of a single organization, the results concern to the reality experienced in the organization studied. Therefore, researchers are encouraged to test this relationship in other organizations to contribute to the discussion and practice of innovation in HRD.

Practical implications

Stories can contribute to innovative behavior, and innovative behavior contributes to helping understand the stories. HRD practitioners can provide the use of storytelling, combined with other forms of interventions, to enhance IWB to promote collaborative learning culture and work engagement.

Originality/value

Previous papers have identified the role of HRD in the development of IWB in organizations. Theoretically, previous papers have also highlighted that storytelling can be a tool for the development of innovative behavior. The paper empirically has tested these contributions, identifying emerging aspects of this relationship.
Does reflective supervision have a future in English local authority child and family social work?
Authors: Wilkins David
Published: September 2017

Purpose

The purpose of this paper is to discuss the underlying assumption that social workers need reflective supervision specifically, as opposed to managerial or any other form of supervision or support, and to consider whether our focus on the provision of reflective supervision may be preventing us from thinking more broadly and creatively about what support local authority child and family social workers need and how best to provide it.

Design/methodology/approach

The paper provides an argument based on the author’s own research and a selective review of the literature.

Findings

Reflective supervision has no future in local authority child and family social work because: first, there is no clear understanding of what reflective supervision is; second, there is no clear evidence for its effectiveness; and third, sizeable proportion of local authority child and family social workers in England do not receive reflective supervision and many never have.

Originality/value

The paper challenges the received wisdom about the value of reflective supervision and advocates exploring alternative models for supporting best practice in child and family social work.
Does past failure inhibit future entrepreneurial intent? Evidence from Ghana
Authors: Acheampong George , Tweneboah-Koduah Ernest Yaw
Published: September 2017

Purpose

The purpose of this paper is to examine the relationship between past entrepreneurial failure and future entrepreneurial intentions. It also considers the moderating role of past entrepreneurial failure on the relationship between attitude, subjective norms and perceived behavioural control (PBC) and entrepreneurial intentions.

Design/methodology/approach

Data from the Ghana Global Entrepreneurship Monitor Adult Population Survey (2013) are used to test the hypotheses developed after an extensive literature review. The empirical specification was estimated with a probit of standard form and marginal derivatives estimated for the purposes of interpretation.

Findings

The mean future entrepreneurial intent is 63.2 per cent of the sample with 75 per cent having failed in the past and 60 per cent never failed before. Also, only 20.9 per cent of the interviewed entrepreneurs have failed at a past entrepreneurial activity. Past entrepreneurial failure has a positive effect on future entrepreneurial intentions. The interaction between attitude and failure yields a positive effect on future entrepreneurial intentions. The same effects can be reported for the interactions between subjective norms and failure as well as PBC and failure.

Originality/value

In this study, the authors are able to show that the mean moderational effects are important but they can be deceptive. Rather, a decomposition helps the authors to disaggregate these effects to better understand the underlying mechanisms.
Novel insights on population and range edge dynamics using an unparalleled spatiotemporal record of species invasion
Authors: Grayson Kristine L. , Johnson Derek M.
Published: September 2017

Quantifying the complex spatial dynamics taking place at range edges is critical for understanding future distributions of species, yet very few systems have sufficient data or the spatial resolution to empirically test these dynamics. This paper reviews how data from a large‐scale pest management programme have provided important contributions to the fields of population dynamics and invasion biology.

The invasion of gypsy moth (Lymantria dispar) is well‐documented from its introduction near Boston, MassachusettsUSAin 1869 to its current extent of over 900,000 km2in Eastern North America. Over the past two decades, theUSDAForest Service Slow the Spread (STS) programme for managing the future spread of gypsy moth has produced unrivalled spatiotemporal data across the invasion front.

TheSTSprogramme annually deploys a grid of 60,000–100,000 pheromone‐baited traps, currently extending from Minnesota to North Carolina. The data from this programme have provided the foundation for investigations of complex population dynamics and the ability to examine ecological hypotheses previously untestable outside of theoretical venues, particularly regarding invasive spread and Allee effects.

This system provides empirical data on the importance of long‐distance dispersal and time‐lags on population establishment and spatial spread. Studies showing high rates of spatiotemporal variation of the range edge, from rapid spread to border stasis and even retraction, highlight future opportunities to test mechanisms that influence both invasive and native species ranges.

TheSTStrap data have also created a unique opportunity to study low‐density population dynamics and quantify Allee effects with empirical data. Notable contributions include evidence for spatiotemporal variation in Allee effects, demonstrating empirical links between Allee effects and spatial spread, and testing mechanisms of population persistence and growth rates at range edges.

There remain several outstanding questions in spatial ecology and population biology that can be tested within this system, such as the scaling of local ecological processes to large‐scale dynamics across landscapes. The gypsy moth is an ideal model of how important ecological questions can be answered by thinking more broadly about monitoring data.
Fundamental niche prediction of the pathogenic yeasts Cryptococcus neoformans and Cryptococcus gattii in Europe
Authors: Cogliati Massimo , Puccianti Erika , Montagna Maria T. , De Donno Antonella , Susever Serdar , Ergin Cagri , Velegraki Aristea , Ellabib Mohamed S. , Nardoni Simona , Macci Cristina , Trovato Laura , Dipineto Ludovico , Rickerts Volker , Akcaglar Sevim , Mlinaric‐Missoni Emilija , Bertout Sebastien , Vencà Ana C.F. , Sampaio Ana C. , Criseo Giuseppe , Ranque Stéphane , Çerikçioğlu Nilgün , Marchese Anna , Vezzulli Luigi , Ilkit Macit , Desnos‐Ollivier Marie , Pasquale Vincenzo , Polacheck Itzhack , Scopa Antonio , Meyer Wieland , Ferreira‐Paim Kennio , Hagen Ferry , Boekhout Teun , Dromer Françoise , Varma Ashok , Kwon‐Chung Kyung J. , Inácio Joäo , Colom Maria F.
Published: September 2017

Fundamental niche prediction of Cryptococcus neoformans and Cryptococcus gattii in Europe is an important tool to understand where these pathogenic yeasts have a high probability to survive in the environment and therefore to identify the areas with high risk of infection. In this study, occurrence data for C. neoformans and C. gattii were compared by MaxEnt software with several bioclimatic conditions as well as with soil characteristics and land use. The results showed that C. gattii distribution can be predicted with high probability along the Mediterranean coast. The analysis of variables showed that its distribution is limited by low temperatures during the coldest season, and by heavy precipitations in the driest season. C. neoformans var. grubii is able to colonize the same areas of C. gattii but is more tolerant to cold winter temperatures and summer precipitations. In contrast, the C. neoformans var. neoformans map was completely different. The best conditions for its survival were displayed in sub‐continental areas and not along the Mediterranean coasts. In conclusion, we produced for the first time detailed prediction maps of the species and varieties of the C. neoformans and C. gattii species complex in Europe and Mediterranean area.
Dissemination and loss of a biofilm‐related genomic island in marine Pseudoalteromonas mediated by integrative and conjugative elements
Authors: Wang Pengxia , Zeng Zhenshun , Wang Weiquan , Wen Zhongling , Li Jie , Wang Xiaoxue
Published: September 2017

Acquisition of genomic islands (GIs) plays a central role in the diversification and adaptation of bacteria. Some GIs can be mobilized in trans by integrative and conjugative elements (ICEs) or conjugative plasmids if the GIs carry specific transfer‐related sequences. However, the transfer mechanism of GIs lacking such elements remains largely unexplored. Here, we investigated the transmissibility of a GI found in a coral‐associated marine bacterium. This GI does not carry genes with transfer functions, but it carries four genes required for robust biofilm formation. Notably, this GI is inserted in the integration site for SXT/R391 ICEs. We demonstrated that acquisition of an SXT/R391 ICE results in either a tandem GI/ICE arrangement or the complete displacement of the GI. The GI displacement by the ICE greatly reduces biofilm formation. In contrast, the tandem integration of the ICE with the GI in cis allows the GI to hijack the transfer machinery of the ICE to excise, transfer and re‐integrate into a new host. Collectively, our findings reveal that the integration of an ICE into a GI integration site enables rapid genome dynamics and a new mechanism by which SXT/R391 ICEs can augment genome plasticity.
Host‐microbe interaction in the gastrointestinal tract
Authors: Parker Aimée , Lawson Melissa A. E. , Vaux Laura , Pin Carmen
Published: September 2017

The gastrointestinal tract is a highly complex organ in which multiple dynamic physiological processes are tightly coordinated while interacting with a dense and extremely diverse microbial population. From establishment in early life, through to host‐microbe symbiosis in adulthood, the gut microbiota plays a vital role in our development and health. The effect of the microbiota on gut development and physiology is highlighted by anatomical and functional changes in germ‐free mice, affecting the gut epithelium, immune system and enteric nervous system. Microbial colonisation promotes competent innate and acquired mucosal immune systems, epithelial renewal, barrier integrity, and mucosal vascularisation and innervation. Interacting or shared signalling pathways across different physiological systems of the gut could explain how all these changes are coordinated during postnatal colonisation, or after the introduction of microbiota into germ‐free models. The application of cell‐based in‐vitro experimental systems and mathematical modelling can shed light on the molecular and signalling pathways which regulate the development and maintenance of homeostasis in the gut and beyond.
Genome‐wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens
Authors: Cheng Xu , Etalo Desalegn W. , van de Mortel Judith E. , Dekkers Ester , Nguyen Linh , Medema Marnix H. , Raaijmakers Jos M.
Published: September 2017

Pseudomonas fluorescens strain SS101 (Pf.SS101) promotes growth of Arabidopsis thaliana, enhances greening and lateral root formation, and induces systemic resistance (ISR) against the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Here, targeted and untargeted approaches were adopted to identify bacterial determinants and underlying mechanisms involved in plant growth promotion and ISR by Pf.SS101. Based on targeted analyses, no evidence was found for volatiles, lipopeptides and siderophores in plant growth promotion by Pf.SS101. Untargeted, genome‐wide analyses of 7488 random transposon mutants of Pf.SS101 led to the identification of 21 mutants defective in both plant growth promotion and ISR. Many of these mutants, however, were auxotrophic and impaired in root colonization. Genetic analysis of three mutants followed by site‐directed mutagenesis, genetic complementation and plant bioassays revealed the involvement of the phosphogluconate dehydratase gene edd, the response regulator gene colR and the adenylsulfate reductase gene cysH in both plant growth promotion and ISR. Subsequent comparative plant transcriptomics analyses strongly suggest that modulation of sulfur assimilation, auxin biosynthesis and transport, steroid biosynthesis and carbohydrate metabolism in Arabidopsis are key mechanisms linked to growth promotion and ISR by Pf.SS101.
Genomes of rumen bacteria encode atypical pathways for fermenting hexoses to short‐chain fatty acids
Authors: Hackmann Timothy J. , Ngugi David Kamanda , Firkins Jeffrey L. , Tao Junyi
Published: September 2017

Bacteria have been thought to follow only a few well‐recognized biochemical pathways when fermenting glucose or other hexoses. These pathways have been chiseled in the stone of textbooks for decades, with most sources rendering them as they appear in the classic 1986 text by Gottschalk. Still, it is unclear how broadly these pathways apply, given that they were established and delineated biochemically with only a few model organisms. Here, we show that well‐recognized pathways often cannot explain fermentation products formed by bacteria. In the most extensive analysis of its kind, we reconstructed pathways for glucose fermentation from genomes of 48 species and subspecies of bacteria from one environment (the rumen). In total, 44% of these bacteria had atypical pathways, including several that are completely unprecedented for bacteria or any organism. In detail, 8% of bacteria had an atypical pathway for acetate formation; 21% of bacteria had an atypical pathway for propionate or succinate formation; 6% of bacteria had an atypical pathway for butyrate formation and 33% of bacteria had an atypical or incomplete Embden–Meyerhof–Parnas pathway. This study shows that reconstruction of metabolic pathways – a common goal of omics studies – could be incorrect if well‐recognized pathways are used for reference. Furthermore, it calls for renewed efforts to delineate fermentation pathways biochemically.
Swimming or Drowning in the Depths of Partnership
Authors: Sturup Sophie
Published: September 2017

This exploratory research paper seeks to consider the problems that may arise in the process of creating deep and lasting partnerships in public‐private partnerships (PPPs). It does this by contrasting two case studies of very different PPPs, Copenhagen's metro project and Melbourne City Link. The paper puts forward the case for the author's concern that a deep partnership could lead either to mercantile government or quasi‐governmental private parties and thus lead to a diminution of the benefits of PPPs. The paper concludes that these concerns are relevant and need to be considered and guarded against no matter the contract conditions.
Interaction effects between local flower richness and distance to natural woodland on pest and beneficial insects in apple orchards
Authors: Saunders Manu E. , Luck Gary W.
Published: September 2017

Local and landscape factors interact to influence animal populations and, ultimately, crop yields in agroecosystems. Yet few studies have considered interactions and trade‐offs between these factors within a single agroecosystem.

We sampled insect communities (fruit‐damaging pests and Diptera and Hymenoptera pollinator and natural enemy taxa) associated with focal apple trees in south‐eastern Australian orchards across a single growing season. We also measured marketable fruit yields on netted (preventing access to vertebrates) and open branches on each focal tree. We focused on relationships with local (ground cover attributes) and landscape (proximity to natural woodland) factors.

Importantly, we found that local flower richness in orchard understoreys may buffer the negative effects that isolation from natural woodland has on wild bee and natural enemy communities and the ecosystem services they provide.

The results of the present study suggest that floral diversity may be more effective in supporting beneficial insects in crop interiors, rather than at edges near natural vegetation.

More studies are needed that identify how local and landscape vegetation structure interact to influence communities of pest and beneficial taxa, and relevant ecosystem functions, in agroecosystems.
Performance of the Minto model for the target‐controlled infusion of remifentanil during cardiopulmonary bypass
Authors: Cho Y. J. , Jo W. Y. , Oh H. , Koo C.‐H. , Oh J. , Cho J.‐Y. , Yu K.‐S. , Jeon Y. , Kim T. K.
Published: September 2017

We studied the predictive performance of the Minto pharmacokinetic model during cardiopulmonary bypass in patients undergoing cardiac surgery. Patients received remifentanil target‐controlled infusion using the Minto model during total intravenous anaesthesia with propofol. From 56 patients, 275 arterial blood samples were drawn before, during and after bypass to determine the plasma concentration of remifentanil, and the predicted concentrations were recorded at each time. For pooled data, the median prediction error and median absolute prediction error were 21.3% and 21.8%, respectively, and 22.1% and 22.3% during bypass. Both were 148.4% during hypothermic circulatory arrest and measured concentrations were more than three times greater than predicted (26.9 (17.0) vs. 7.1 (1.6) ng.ml−1). The Minto model showed considerable bias but overall acceptable precision during bypass. The target concentration of remifentanil should be reduced when using the Minto model during hypothermic circulatory arrest.
Systematic review with meta‐analysis: breastfeeding and the risk of Crohn's disease and ulcerative colitis
Authors: Xu L. , Lochhead P. , Ko Y. , Claggett B. , Leong R. W. , Ananthakrishnan A. N.
Published: September 2017

Background

Breastfeeding is a modifiable factor that may influence development of inflammatory bowel diseases. However, literature on this has been inconsistent and not accounted for heterogeneity in populations and exposure.

Aim

To conduct a meta‐analysis to examine the association between breastfeeding in infancy and risk of Crohn's disease (CD) and ulcerative colitis (UC).

Methods

A systematic search of Medline/PubMed and Embase was performed for full text, English‐language literature through November 2016. Studies were included if they described breastfeeding in infancy in patients with CD or UC, and healthy controls. Data were pooled using a random effects model for analysis.

Results

A total of 35 studies were included in the final analysis, comprising 7536 individuals with CD, 7353 with UC and 330 222 controls. Ever being breastfed was associated with a lower risk of CD (OR 0.71, 95% CI 0.59‐0.85) and UC (OR 0.78, 95% CI 0.67‐0.91). While this inverse association was observed in all ethnicity groups, the magnitude of protection was significantly greater among Asians (OR 0.31, 95% CI 0.20‐0.48) compared to Caucasians (OR 0.78, 95% CI 0.66‐0.93; P = .0001) in CD. Breastfeeding duration showed a dose‐dependent association, with strongest decrease in risk when breastfed for at least 12 months for CD (OR 0.20, 95% CI 0.08‐0.50) and UC (OR 0.21, 95% CI 0.10‐0.43) as compared to 3 or 6 months.

Conclusion

Breastfeeding in infancy protects against the development of CD and ulcerative colitis.
Systematic review with meta‐analysis: the global recurrence rate of Helicobacter pylori
Authors: Hu Y. , Wan J.‐H. , Li X.‐Y. , Zhu Y. , Graham D. Y. , Lu N.‐H.
Published: September 2017

Background

Up‐to‐date information regarding the recurrence rate of Helicobacter pylori (H. pylori) after eradication therapy is not available.

Aim

To evaluate the global recurrence rate following H. pylori eradication therapy and confirm its association with socioeconomic and sanitary conditions.

Methods

A systematic search of PubMed, EMBASE and the Cochrane library was performed to identify potentially relevant publications using the following keywords: “Helicobacter pylori” or “H. pylori” or “Hp” and “recurrence” or “recrudescence” or “reinfection” or “recurrent” or “recurred” or “re‐infect*” or “relapse*.”

Results

A total of 132 studies (53 934 patient‐years) were analysed. Each study was weighted according to the duration of patient‐years. The global annual recurrence, reinfection and recrudescence rate of H. pylori were 4.3% (95% CI, 4‐5), 3.1% (95% CI, 2‐5) and 2.2% (95% CI, 1‐3), respectively. The H. pylori recurrence rate was inversely related to the human development index (HDI) (ie, 3.1% [95% CI, 2‐4], 6.2% [95% CI, 4‐8] and 10.9% [95% CI, 6‐18] in countries with a very high, high and medium or low HDI) (P <.01) and directly related to H. pylori prevalence (10.9% [95% CI, 7‐16], 3.7% [95% CI, 3‐5], 3.4% [95% CI, 2‐5] and 1.6% [95% CI, 0.5‐3] in countries with a very high, high, medium or low local H. pylori prevalence) (P <.01). Global recurrence rates remained relatively stable between 1990s, 2000s and 2010s but varied across different regions (P <.05).

Conclusions

H. pylori recurrence remains a problem closely associated with socioeconomic and sanitary conditions. Methods to reduce recurrence in developing countries are needed.
‘Where there is a will, there is a way’: Belief in school meritocracy and the social‐class achievement gap
Authors: Darnon Céline , Wiederkehr Virginie , Dompnier Benoît , Martinot Delphine
Published: September 2017

Meritocratic ideology can promote system justification and the perpetuation of inequalities. The present research tests whether priming merit in the school context enhances the effect of socioeconomic status (SES) on school achievement. French fifth graders read a text priming either school merit or a neutral content, reported their French and mathematics self‐efficacy as well as their belief in school meritocracy (BSM), and then took French and mathematics tests. Compared to the neutral condition, the merit prime condition increased the SES achievement gap. Self‐efficacy and BSM were tested as two potential mediators of the effect. The results support a mediated moderation model in which belief in school meritocracy is the mechanism through which the merit prime increased the SES achievement gap.
Short‐term results of self‐expanding metal stents for acute malignant large bowel obstruction
Authors: Kobborg M. , Broholm M. , Frostberg E. , Jeppesen M. , Gögenür I.
Published: September 2017

Aim

Self‐expanding metal stents (SEMSs) can be used as a palliative treatment or to initially decompress colon prior to definitive surgery (as a so‐called ‘bridge to surgery’). The purpose of this study was to investigate the efficacy and safety of SEMS used as palliation and bridge to surgery for malignant large bowel obstruction.

Method

A multicentre retrospective study was conducted from January 2010 to December 2013 to identify patients undergoing stent placement for acute large bowel obstruction. Patients were included from four Danish colorectal centres. Outcomes identified included clinical success, 30‐day mortality, stent related complications and surgery related complications. Furthermore, we analysed for predictive factors for successful stenting. Clinical success was defined as relief of obstructive symptoms, without the need of other additional surgical interventions during the hospital stay.

Results

SEMSs were inserted in 239 patients for whom the indication was as a bridge to surgery in 112 patients (47%) and as palliation in 127 (53%) patients. Clinical success was achieved in 90 patients (80.4%) in the bridge to surgery group and in 105 patients (82.8%) in the palliation group. The 30‐day mortality rates in the two groups were 5.4% and 11.8% for bridge to surgery and palliation respectively. A total of 17.8% of the patients in the bridge to surgery group had a stent related complication and in the palliation group it was 20.4%. Multivariate analysis demonstrated that clinical failure is a predictive factor of 30‐day mortality (OR 11.1, 95% CI: 4.1–30.0).

Conclusion

The use of a SEMS to relieve a malignant large bowel obstruction is generally an effective and safe method, but complications are seen in about 20% of patients. Further investigations are required to determine the role of SEMSs in the treatment of acute, malignant, large bowel obstruction.
A Pilot Dose‐Finding Study of Etanercept in Rheumatoid Arthritis
Authors: Breedveld Ferdinand C. , Jones Heather E. , Peifer Kim , Korth‐Bradley Joan
Published: September 2017

A randomized, parallel‐dose study assessed the pharmacokinetics (PK) and pharmacodynamics (PD) of etanercept in 61 patients with rheumatoid arthritis (RA) who received doses from 10 mg once‐weekly to 50 mg twice‐weekly for 4 weeks. Empiric application of a maximal‐effect (Emax) model to pooled steady‐state concentrations (Css) and PD markers provided half‐maximal‐effect concentration estimates of 567, 573, 465, 87, and 159 ng/mL for change from baseline in number of swollen joints, number of painful joints, erythrocyte sedimentation rate, interleukin‐6, and matrix metalloproteinase‐3, respectively. Css >∼2,000 ng/mL did not appear to offer additional benefit. It was concluded that the middle doses, 10 mg twice‐weekly, 50 mg every 2 weeks, and 50 mg once‐weekly, would provide Css in the target range of 500–2,000 ng/mL. The revised US Food and Drug Administration guideline for development of medicines for treatment of RA encourages a study design incorporating PK/PD assessment to inform later studies.
Histopathologic features of cutaneous leishmaniasis and use of CD1a staining for amastigotes in Old World and New World leishmaniasis
Authors: Sundharkrishnan Lohini , North Jeffrey P.
Published: September 2017

Background

Positive CD1a staining of Leishmania has been reported in Old World leishmaniasis, but the sensitivity of such staining for other Leishmania species is unknown.

Methods

A retrospective review was done on skin biopsies of proven cutaneous leishmaniasis based on histology, immunohistochemistry, culture and/or polymerase chain reaction (PCR). We assessed the pattern of inflammation present and assessed for CD1a (MTB1 clone) positivity in amastigotes. Patients without a clearly documented travel history to delineate Old vs New World leishmaniasis and cases without tissue for CD1a staining were excluded.

Results

Various patterns of granulomatous inflammation were observed including sarcoidal (31%), diffuse (25%), suppurative and granulomatous (25%), palisaded (13%) and lichenoid (6%). CD1a staining was positive in amastigotes in 9 of 16 cases (56%). Five of 7 (71%) cases of Old World disease were CD1a positive, while 4 of 9 cases (44%) of New World cases were positive.

Conclusions

Multiple patterns of granulomatous inflammation occur in cutaneous leishmaniasis. Our results confirm CD1a (MTB1 clone) can be a diagnostic adjunct to highlight amastigotes in biopsies of cutaneous leishmaniasis, with variable positivity in both Old World and New World forms of the disease. As 44% of cases were CD1a negative in our cohort, there are significant limitations to this screening approach.