bluuebunny/crossref_metadata_2025 huggingface dataset:
4. The age of exploration
Authors: Weaver Stewart A.
Published: April 2017

‘The age of exploration ’ considers why textbooks and teachers privilege late-medieval and early-modern Europe when designating “the age of exploration” and not the earlier Greek, Roman, Arab, Norse, Polynesian, or Mongol achievements in terms of exploration and cultural reach. It is for three main reasons. Firstly, because the late-medieval extrusion of European maritime power and the associated record of exploration were global in reach. Secondly, they were unprecedented in scope and daring. Thirdly, the exploration of the world by fifteenth- and sixteenth-century European mariners, such as Christopher Columbus and Vasco da Gama, permanently and decisively altered the lineaments of global power and set human history on the broad common course that it still to this day follows.
DextMP: deep dive into text for predicting moonlighting proteins
Authors: Khan Ishita K , Bhuiyan Mansurul , Kihara Daisuke
Published: April 2017

Motivation

Moonlighting proteins (MPs) are an important class of proteins that perform more than one independent cellular function. MPs are gaining more attention in recent years as they are found to play important roles in various systems including disease developments. MPs also have a significant impact in computational function prediction and annotation in databases. Currently MPs are not labeled as such in biological databases even in cases where multiple distinct functions are known for the proteins. In this work, we propose a novel method named DextMP, which predicts whether a protein is a MP or not based on its textual features extracted from scientific literature and the UniProt database.

Results

DextMP extracts three categories of textual information for a protein: titles, abstracts from literature, and function description in UniProt. Three language models were applied and compared: a state-of-the-art deep unsupervised learning algorithm along with two other language models of different types, Term Frequency-Inverse Document Frequency in the bag-of-words and Latent Dirichlet Allocation in the topic modeling category. Cross-validation results on a dataset of known MPs and non-MPs showed that DextMP successfully predicted MPs with over 91% accuracy with significant improvement over existing MP prediction methods. Lastly, we ran DextMP with the best performing language models and text-based feature combinations on three genomes, human, yeast and Xenopus laevis, and found that about 2.5–35% of the proteomes are potential MPs.

Availability and Implementation

Code available at http://kiharalab.org/DextMP.
Abundance estimation and differential testing on strain level in metagenomics data
Authors: Fischer Martina , Strauch Benjamin , Renard Bernhard Y
Published: April 2017

Motivation

Current metagenomics approaches allow analyzing the composition of microbial communities at high resolution. Important changes to the composition are known to even occur on strain level and to go hand in hand with changes in disease or ecological state. However, specific challenges arise for strain level analysis due to highly similar genome sequences present. Only a limited number of tools approach taxa abundance estimation beyond species level and there is a strong need for dedicated tools for strain resolution and differential abundance testing.

Methods

We present DiTASiC (Differential Taxa Abundance including Similarity Correction) as a novel approach for quantification and differential assessment of individual taxa in metagenomics samples. We introduce a generalized linear model for the resolution of shared read counts which cause a significant bias on strain level. Further, we capture abundance estimation uncertainties, which play a crucial role in differential abundance analysis. A novel statistical framework is built, which integrates the abundance variance and infers abundance distributions for differential testing sensitive to strain level.

Results

As a result, we obtain highly accurate abundance estimates down to sub-strain level and enable fine-grained resolution of strain clusters. We demonstrate the relevance of read ambiguity resolution and integration of abundance uncertainties for differential analysis. Accurate detections of even small changes are achieved and false-positives are significantly reduced. Superior performance is shown on latest benchmark sets of various complexities and in comparison to existing methods.

Availability and Implementation

DiTASiC code is freely available from https://rki_bioinformatics.gitlab.io/ditasic.

Supplementary information

Supplementary data are available at Bioinformatics online.
Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes
Authors: Nakatani Yoichiro , McLysaght Aoife
Published: April 2017

Motivation

It has been argued that whole-genome duplication (WGD) exerted a profound influence on the course of evolution. For the purpose of fully understanding the impact of WGD, several formal algorithms have been developed for reconstructing pre-WGD gene order in yeast and plant. However, to the best of our knowledge, those algorithms have never been successfully applied to WGD events in teleost and vertebrate, impeded by extensive gene shuffling and gene losses.

Results

Here, we present a probabilistic model of macrosynteny (i.e. conserved linkage or chromosome-scale distribution of orthologs), develop a variational Bayes algorithm for inferring the structure of pre-WGD genomes, and study estimation accuracy by simulation. Then, by applying the method to the teleost WGD, we demonstrate effectiveness of the algorithm in a situation where gene-order reconstruction algorithms perform relatively poorly due to a high rate of rearrangement and extensive gene losses. Our high-resolution reconstruction reveals previously overlooked small-scale rearrangements, necessitating a revision to previous views on genome structure evolution in teleost and vertebrate.

Conclusions

We have reconstructed the structure of a pre-WGD genome by employing a variational Bayes approach that was originally developed for inferring topics from millions of text documents. Interestingly, comparison of the macrosynteny and topic model algorithms suggests that macrosynteny can be regarded as documents on ancestral genome structure. From this perspective, the present study would seem to provide a textbook example of the prevalent metaphor that genomes are documents of evolutionary history.

Availability and implementation

The analysis data are available for download at http://www.gen.tcd.ie/molevol/supp_data/MacrosyntenyTGD.zip, and the software written in Java is available upon request.

Supplementary information

Supplementary data are available at Bioinformatics online.
CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions
Authors: Hallen Mark A , Donald Bruce R
Published: April 2017

Motivation

When proteins mutate or bind to ligands, their backbones often move significantly, especially in loop regions. Computational protein design algorithms must model these motions in order to accurately optimize protein stability and binding affinity. However, methods for backbone conformational search in design have been much more limited than for sidechain conformational search. This is especially true for combinatorial protein design algorithms, which aim to search a large sequence space efficiently and thus cannot rely on temporal simulation of each candidate sequence.

Results

We alleviate this difficulty with a new parameterization of backbone conformational space, which represents all degrees of freedom of a specified segment of protein chain that maintain valid bonding geometry (by maintaining the original bond lengths and angles and ω dihedrals). In order to search this space, we present an efficient algorithm, CATS, for computing atomic coordinates as a function of our new continuous backbone internal coordinates. CATS generalizes the iMinDEE and EPIC protein design algorithms, which model continuous flexibility in sidechain dihedrals, to model continuous, appropriately localized flexibility in the backbone dihedrals ϕ and ψ as well. We show using 81 test cases based on 29 different protein structures that CATS finds sequences and conformations that are significantly lower in energy than methods with less or no backbone flexibility do. In particular, we show that CATS can model the viability of an antibody mutation known experimentally to increase affinity, but that appears sterically infeasible when modeled with less or no backbone flexibility.

Availability and implementation

Our code is available as free software at https://github.com/donaldlab/OSPREY_refactor.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Relationship Between Specialty Certification of Individual Nurses and Outcomes
Authors: Kitto Simon , Grant Rachel , Chappell Kathy , Lundmark Vicki
Published: April 2017

Specialty certification is an important method to demonstrate that RNs possess advanced training, knowledge, and competencies required to provide safe, high-quality care for specific populations.
Pheniqs: Fast and flexible quality-aware sequence demultiplexing
Authors: Galanti Lior , Shasha Dennis , C. Gunsalus Kristin
Published: April 2017

1

Motivation

Output from high throughput sequencing instruments often exceeds what is necessary to assay a single sample. To better utilize this capacity, multiple samples are independently tagged with a unique “barcode” sequence and are then pooled, or “multiplexed”, and sequenced together. Classifying, or “demultiplexing”, the reads involves decoding the barcode sequence. Although instruments estimate the probability of incorrectly calling each nucleobase, available demultiplexers do not consult those estimates or report classification error probabilities.

Results

We present Pheniqs, a fast and flexible sequence demultiplexer and quality analyzer. In addition to providing an efficient implementation of the widespread minimum distance decoder, Pheniqs introduces a novel Phred-adjusted maximum likelihood decoder that consults base calling quality scores and estimates the probability of a barcode decoding error. Setting an upper bound on the permissible error provides an intuitive way to control demultiplexing confidence and directly influence precision and recall. Pheniqs supports FASTQ and multiple Sequence Alignment/Map formats and uses auxiliary SAM tags to report both library classification and demultiplexing error probability. Evaluation on both real and semi-synthetic data indicates that Pheniqs is faster than existing demultiplexers, substantially when demultiplexing longer reads, and achieves greater accuracy by correctly reflecting quality measurements.

Availability and Implementation

Implemented in multithreaded C++ and available under the terms of the AGPL-3.0 license agreement at http://github.com/biosails/pheniqs. Manual and examples are available at http://biosails.github.io/pheniqs.
Cell-intrinsic activation of Orai1 regulates human T cell motility
Authors: Dong Tobias X. , Greenberg Milton L. , Leverrier Sabrina , Yu Ying , Parker Ian , Dynes Joseph L. , Cahalan Michael D.
Published: April 2017

Ca2+signaling through the store-operated Ca2+channel, Orai1, is crucial for T cell function, but a role in regulating T cell motility in lymph nodes has not been previously reported. Tracking human T cells in immunodeficient mouse lymph nodes and in microfabricated PDMS channels, we show that inhibition of Orai1 channel activity with a dominant-negative Orai1-E106A construct increases average T cell velocities by reducing the frequency of pauses in motile T cells. Orai1-dependent motility arrest occurs spontaneously during confined motilityin vitro, even in the absence of extrinsic cell contacts or antigen recognition. Utilizing a novel ratiometric genetically encoded cytosolic Ca2+indicator, Salsa6f, we show these spontaneous pauses during T cell motilityin vitrocoincide with episodes of spontaneous cytosolic Ca2+signaling. Our results demonstrate that Orai1, activated in a cell-intrinsic manner, regulates T cell motility patterns that accompany immune surveillance.
Athlete satisfaction with a major multi-sport event: the importance of social and cultural aspects
Authors: MacIntosh Eric , Parent Milena
Published: April 2017

Purpose

In a major multi-sport event, the athlete is both a benefactor and producer of organizational activities. Athletes’ centrality makes understanding their satisfaction with the event an important management activity. The purpose of this paper is to examine the lived athletes experience (during the event), so as to provide insight into the important Games facets contributing to their satisfaction and to explore the controllable aspects of the event from an organizer’s perspective that athletes felt made the Games special and memorable.

Design/methodology/approach

A multi-dimensional instrument (i.e. Athlete Experience Questionnaire) was designed and tested at previous iterations of a major multi-sport event and was employed during Games-time. In total, 813 athletes completed the questionnaire during the 2014 Glasgow Commonwealth Games.

Findings

The findings demonstrated an overall high level of satisfaction with the event. Several important facets contributed to athlete satisfaction including social-, service- and communication-related aspects. Further, athletes reported on the importance of cultural opportunities within their Games experience.

Research limitations/implications

The paper denotes the importance of the social and cultural interactions and opportunities which lie outside the athletes’ actual competition experience and increase their specialness of the event. Theoretical and practical implications are drawn from the findings relative to the service-dominant logic and service-quality literature within a major multi-sport event Games for the athlete stakeholder.

Originality/value

This paper explores how athletes experience the major international multi-sport event environment. Moreover, this paper offers a significant contribution from a hard-to-reach population (i.e. elite-level international athletes), adopts their perspective of the Games environment and determines what contributes to their satisfaction. As the authors highlight, the paper denotes the importance of the planned social and cultural interactions and opportunities, which lie outside the athlete’s actual competition event experience, to increase athlete satisfaction; in contrast, basic sport competition needs seem to be a “basic” expectation.
Perceived value of advanced mobile messaging services
Authors: Hernandez-Ortega Blanca , Aldas-Manzano Joaquin , Ruiz-Mafe Carla , Sanz-Blas Silvia
Published: April 2017

Purpose

The purpose of this paper is to analyse the role of perceived value on post-acceptance behaviour for users of advanced mobile messaging services (AMMS). The paper also compares differences in the influence of perceived value on satisfaction and of satisfaction on loyalty to AMMS in Spain and Greece, to test the moderating effect of culture.

Design/methodology/approach

Partial least squares path modelling is used to test the model. Perceived value is modelled as a multidimensional reflective construct with four dimensions. Culture is studied at a national level. Differences between countries are tested using the multigroup analysis approach proposed by Henseleret al.(2009).

Findings

Perceived value contributes significantly to satisfaction. Satisfaction also has a significant effect on loyalty. Regarding the moderating effect of culture, the influence of perceived value on satisfaction is higher in Greece than in Spain. The authors report similar findings for the effect of satisfaction on loyalty, demonstrating the relevant moderating role of cultures with different degrees of masculinity, uncertainty avoidance and collectivism.

Practical implications

This cross-cultural comparison enables mobile phone companies to understand how to provide the greatest value with AMMS in each country in order to increase user satisfaction and loyalty to the service.

Originality/value

This is one of the first studies that develops cross-cultural research to analyse the post-acceptance of mobile services. It analyses the effect of perceived value and satisfaction, making an original comparison of two countries generally considered too similar to be compared.
Personality, immune response and reproductive success: an appraisal of the pace‐of‐life syndrome hypothesis
Authors: Monceau Karine , Dechaume‐Moncharmont François‐Xavier , Moreau Jérôme , Lucas Camille , Capoduro Rémi , Motreuil Sébastien , Moret Yannick
Published: April 2017

The pace‐of‐life syndrome (POLS) hypothesis is an extended concept of the life‐history theory that includes behavioural traits. The studies challenging the POLS hypothesis often focus on the relationships between a single personality trait and a physiological and/or life‐history trait. While pathogens represent a major selective pressure, few studies have been interested in testing relationships between behavioural syndrome, and several fitness components including immunity.

The aim of this study was to address this question in the mealworm beetle, Tenebrio molitor, a model species in immunity studies. The personality score was estimated from a multidimensional syndrome based of four repeatable behavioural traits.

In a first experiment, we investigated its relationship with two measures of fitness (reproduction and survival) and three components of the innate immunity (haemocyte concentration, and levels of activity of the phenoloxidase including the total proenzyme and the naturally activated one) to challenge the POLS hypothesis in T. molitor. Overall, we found a relationship between behavioural syndrome and reproductive success in this species, thus supporting the POLS hypothesis. We also showed a sex‐specific relationship between behavioural syndrome and basal immune parameters.

In a second experiment, we tested whether this observed relationship with innate immunity could be confirmed in term of differential survival after challenging by entomopathogenic bacteria, Bacillus thuringiensis. In this case, no significant relationship was evidenced.

We recommend that future researchers on the POLS should control for differences in evolutionary trajectory between sexes and to pay attention to the choice of the proxy used, especially when looking at immune traits.
Engaging conceptions of identity in a context of medical pluralism: explaining treatment choices for everyday illness in Niger
Authors: Sams Kelley
Published: April 2017

This article uses ethnographic research to reflect upon how the treatment of ‘everyday’ illnesses in Niger engages concepts of social identity. Inspired by Bourdieu's concept of social distinction, as well as Appadurai's edited volume on the ‘social lives’ of ‘things’, I present an analysis of how medications are understood by their users in terms of social and ideological meaning in one rural Hausa village. Decisions about medication choice were framed by three main themes: belonging to the ‘modern’ world, ‘traditional’ Hausa culture, and religious identity. This article does not argue that these notions of identity fully explain medication use, nor necessarily predict treatment choices. The purpose of this paper is to reflect on the dynamic meanings given to treatment decisions after they have been made, attributed to the medications themselves and negotiated through their circulation in a context where multiple medical systems are drawn from to manage illness. Producers and sellers of medication also engage these meaning‐centred concepts, which have theoretical and practical interest for the social sciences and public health.

A virtual abstract for this paper can be viewed at: https://www.youtube.com/channel/UC_979cmCmR9rLrKuD7z0ycA
Molecularisation and metaphor
Authors: Armstrong David
Published: April 2017

This article explores the molecularisation of medicine thesis by investigating reports on genetics and molecular medicine in the New England Journal of Medicine. While there has indeed been a large increase in the number of references to molecules in the context of genetics over the last few decades these are mostly embedded in a framework of explanatory metaphors, namely (gene) expressivity, penetrance, regulation and pathways. As most of these metaphors are drawn from the social world it would appear that the molecularisation thesis – that social life is becoming dominated by the molecular – needs to be tempered by the ways in which understanding of that molecular world is itself a reflection of social life.
A Comparative Study of Natural Antimicrobial Delivery Systems for Microbial Safety and Quality of Fresh‐Cut Lettuce
Authors: Hill Laura E. , Oliveira Daniela A. , Hills Katherine , Giacobassi Cassie , Johnson Jecori , Summerlin Harvey , Taylor T. Matthew , Gomes Carmen L.
Published: April 2017

Nanoencapsulation can provide a means to effectively deliver antimicrobial compounds and enhance the safety of fresh produce. However, to date there are no studies which directly compares how different nanoencapsulation systems affect fresh produce safety and quality. This study compared the effects on quality and safety of fresh‐cut lettuce treated with free and nanoencapsulated natural antimicrobial, cinnamon bark extract (CBE). A challenge study compared antimicrobial efficacy of 3 different nanoencapsulated CBE systems. The most effective antimicrobial treatment against Listeria monocytogenes was chitosan‐co‐poly‐N‐isopropylacrylamide (chitosan‐PNIPAAM) encapsulated CBE, with a reduction on bacterial load up to 2 log10 CFU/g (P < 0.05) compared to the other encapsulation systems when fresh‐cut lettuce was stored at 5 °C and 10 °C for 15 d. Subsequently, chitosan‐PNIPAAM‐CBE nanoparticles (20, 40, and 80 mg/mL) were compared to a control and free CBE (400, 800, and 1600 μg/mL) for its effects on fresh‐cut lettuce quality over 15 d at 5 °C. By the 10th day, the most effective antimicrobial concentration was 80 mg/mL for chitosan‐PNIPAAM‐CBE, up to 2 log10 CFU/g reduction (P < 0.05), compared with the other treatments. There was no significant difference between control and treated samples up to day 10 for the quality attributes evaluated. Chitosan‐PNIPAAM‐CBE nanoparticles effectively inhibited spoilage microorganisms’ growth and extended fresh‐cut lettuce shelf‐life. Overall, nanoencapsulation provided a method to effectively deliver essential oil and enhanced produce safety, while creating little to no detrimental quality changes on the fresh‐cut lettuce.
Oral Health Programmes in Indigenous Communities Worldwide—Lessons learned from the field: A qualitative systematic review
Authors: Tsai Carrie , Blinkhorn Anthony , Irving Michelle
Published: April 2017

Objectives

This systematic review examines the evidence on the effectiveness of programmes that aim to improve the oral health of Indigenous populations worldwide, as well as presents a qualitative analysis to explore the design and implementation of these initiatives.

Methods

MEDLINE and EMBASE were searched. Studies were included if they described an oral health programme for an Indigenous population in any country worldwide. A thematic synthesis of the qualitative findings was undertaken for each study's results and discussion sections.

Results

Nineteen studies were included. Sixteen studies reported positive results, twelve of which reported statistically significant findings. Three themes regarding design and implementation emerged from the qualitative analysis: (i) elements of successful programmes, (ii) challenges and barriers to successful interventions and (iii) suggestions for improvements.

Conclusions

Successful programmes considered cultural appropriateness in their design—including extensive community engagement before, during and after implementation to enhance ownership of, and thus participation in the programme. Collaborative approaches were seen as an advantage, not only with Indigenous communities, but also with local health providers and organizations, with particular emphasis on incorporation into existing services. Challenges included low community participation, unstable funding and staffing issues. In addition, future programmes should also incorporate advocacy and community development, focus on changes to public policy, utilize evidence‐based interventions that include traditional models of health, attempt to secure a stable funding base, target strategies to ensure staff retention and develop interventions that target the multilevel causes of general and oral health. This review provides an evidence base that can aid in the successful design, implementation and sustainability of oral health programmes for Indigenous people in the future.
High diagnostic yield of clinically unidentifiable syndromic growth disorders by targeted exome sequencing
Authors: Kim Yoo‐Mi , Lee Yun‐Jin , Park Jae Hong , Lee Hyoung‐Doo , Cheon Chong Kun , Kim Su‐Young , Hwang Jae‐Yeon , Jang Ja‐Hyun , Yoo Han‐Wook
Published: April 2017

Background

As syndromic short stature and overgrowth are heterogeneous and the list of causative genes is rapidly expanding, there is an unmet need for identifying genetic causes based on conventional gene testing or karyotyping. Early diagnosis leads to the proper management of the patient and providing genetic counseling for family members at risk in a timely manner.

Materials and Methods

We conducted targeted exome sequencing to identify the genetic causes of undiagnosed syndromic short stature or overgrowth in 15 pediatric patients from 13 families in Korea. We applied targeted exome sequencing using the Next Seq platform and a TruSight One panel.

Results

Among the 13 families, 6 different disorders in 8 patients with short stature or overgrowth were identified, and the diagnostic yield was 46.2%. One boy with overgrowth had a
TGFB3
gene mutation. In the short stature group, Coffin‐Lowry syndrome (CLS), trichorhinophalangeal syndrome, DYRK1A haploinsufficiency syndrome, short stature with optic atrophy and Pelger‐Huët anomaly syndrome with recurrent hepatitis, and type 4 Meier‐Gorlin syndrome were identified. One CLS patient had a co‐existing monogenic disease, congenital glaucoma, caused by the compound heterozygote mutations of the
CYP1B1
gene.

Conclusion

Targeted exome sequencing is a powerful method for diagnosing syndromic growth disorders. It enables us to understand molecular pathophysiology and investigate new treatments for growth disorders.
Feasibility of colorectal endoscopic submucosal dissection (ESD) carried out by endoscopists with no or little experience in gastric ESD
Authors: Shiga Hisashi , Ohba Reina , Matsuhashi Tamotsu , Jin Mario , Kuroha Masatake , Endo Katsuya , Moroi Rintaro , Kayaba Shoichi , Iijima Katsunori
Published: April 2017

Background and Aim

Colorectal endoscopic submucosal dissection (ESD) is recommended to be carried out only by endoscopists with sufficient experience in gastric ESD. However, early gastric carcinoma is less common in Western countries than in Japan, and endoscopic maneuverability differs between the stomach and colorectum. We assessed the feasibility of colorectal ESD carried out by endoscopists with no or little experience in gastric ESD.

Methods

We analyzed en bloc resection, R0 resection and perforation rates in 180 consecutive colorectal ESD carried out by three endoscopists who had no or <5 cases of experience in gastric ESD. We also identified factors associated with R0 resection failure.

Results

Overall en bloc and R0 resection rates were 93.3% (168/180) and 82.2% (148/180), respectively. All 11 cases with perforation were treated endoscopically. Dividing 180 cases into three learning phases (early, middle, or late phases), the en bloc and R0 resection rates increased from 88.3% and 75.0% in the early phase to 98.3% and 88.3% in the late phase, respectively. Perforation rate also improved from 10.0% to 3.3%. Factors associated with R0 resection failure were location at junctions (odds ratio: 6.8, 95% CI: 1.9–27.5), preoperative factors reflecting fibrosis (5.8, 1.9–19.0), and late phase (0.2, 0.1–0.7).

Conclusion

Endoscopists without experience in gastric ESD carried out colorectal ESD safely. In the early and middle phases (≤40 cases), they should treat mainly rectal lesions but may also resect lesions in the colon avoiding flexures. Lesions located at junctions and those with preoperative factors reflecting fibrosis should be resected after completing 40 procedures.
Untangling the assembly of littoral macroinvertebrate communities through measures of functional and phylogenetic alpha diversity
Authors: Heino Jani , Tolonen Kimmo T.
Published: April 2017

Recent studies have shown that species, functional and phylogenetic diversity are related to different environmental drivers, suggesting that different aspects of alpha diversity may be complementary and may provide different information about community assembly. Such multi‐facet community assembly studies are, however, rare in the freshwater realm.

We examined the responses of species richness, functional alpha diversity and phylogenetic alpha diversity of littoral macroinvertebrates to environmental gradients in near‐pristine boreal lakes. We also examined community assembly mechanisms using null models of functional or phylogenetic clustering, overdispersion and randomness as indications of different assembly mechanisms.

We found that the alpha diversity indices examined responded differently to the underlying environmental gradients. Also, phylogenetic and functional alpha diversity indices showed different levels of overdispersion, clustering and randomness, which also varied slightly between the analyses based on abundance and presence–absence data. These results suggested that different alpha diversity indices may provide different information about overdispersion (e.g. caused by biotic interactions) and clustering (e.g. caused by environmental filtering), and emphasised the fact that most individual lakes were inhabited by species that were merely random draws from the functional or phylogenetic species pools available in the study region.

Our findings suggested that some individual lakes are assembled by deterministic mechanisms, including environmental filtering and biotic interactions, whereas most individual lake macroinvertebrate communities constitute random draws from the regional species pool or are affected by the antagonistic effects of different assembly processes. Our results may stem from site‐specific context dependency in the assembly mechanisms, which might also be a reason why statistical models in aquatic community studies typically explain only a small part of variation in community composition and local diversity.
An Overview of the Patient‐Reported Outcomes Measurement Information System (PROMIS) for Assessing Chronic Low Back Pain Patients
Authors: Licciardone John , Worzer Whitney E. , Hartzell Meredith M. , Kishino Nancy , Gatchel Robert J.
Published: April 2017

This study aimed to demonstrate the relevance of the Patient‐Reported Outcomes Measurement Information System (PROMIS) measures to the assessment of chronic low back pain. A literature search was conducted to find all relevant articles regarding the PROMIS domains of pain impact, behavior, interference, quality, and intensity, as well as the other PROMIS domains of sleep disturbance, fatigue, satisfaction with social roles, anxiety, depression, and physical function. Findings were compiled. Although few measures assessed low back pain specifically, all were found reliable and valid, and useful for a wide variety of other populations. The PROMIS has several advantages over other “legacy” measures, including generalizability, comparability, ease of access and use, having a wide range of methodologies to utilize in assessment, and free availability to the public. Having the PROMIS available at no additional cost will help further research by making it more accessible.
Predictors of Native American children's perceived status of health and physical shape
Authors: Kulinna Pamela H. , Ramirez Ernesto R. , Jahn Julie A. , Cothran Donetta J. , Burns Ryan D. , Kloeppel Tiffany
Published: April 2017

To increase our understanding of predictors of healthy behavior patterns in Native American children. Children from the Southwest (N = 145) United States were administered a questionnaire with predictors of healthy living behaviors (i.e., perceived health status and perceived physical shape [fitness]). Using structural equation modeling, significant path estimates were present for self‐efficacy in predicting beliefs, for (removing) barriers, and for adult/peer support. Further, belief, barriers, and peer social support significantly predicted goals/intentions to be physically active. For children's perceived physical shape (fitness), similar results were found except with no significant relationship between self‐efficacy and (removing) barriers. Efforts focusing on increasing support systems and improving experiences (leading to positive efficacy/beliefs) can lead to significantly greater goals/intentions and perhaps the adoption of healthy behavior patterns by children.
Dispersal modality determines the relative partitioning of beta diversity in spider assemblages on subtropical land‐bridge islands
Authors: Wu Lingbing , Si Xingfeng , Didham Raphael K. , Ge Dapeng , Ding Ping
Published: April 2017

Aim

To identify geographical drivers determining the relative partitioning of species replacement and richness difference or nestedness‐resultant components of beta diversity in spider groups with differing dispersal modalities.

Location

Thousand Island Lake, China.

Methods

We sampled spider assemblages on 31 land‐bridge islands for two years. Each species was classified into a dispersal group based on ballooning propensity (frequent, occasional or non‐ballooners). Two frameworks were used to separate beta diversity (βcc or βjac) of each group into either species replacement (β‐3) and richness difference (βrich) components, or turnover (βjtu) and nestedness‐resultant (βjne) components. Mantel and partial Mantel tests were performed to determine correlations between pairwise dissimilarities and difference in island area, difference in distance to mainland and inter‐island distance for each group.

Results

The multiple‐island dissimilarity of spiders was primarily driven by turnover. Beta diversity (βcc or βjac) was positively associated with difference in island area in frequent ballooners, and negatively associated with difference in island area in occasional ballooners. Difference in island area had positive effects on βjne for all groups, but negative effects on β‐3 and βjtu for occasional or non‐ballooners. βrich was positively associated with difference in island area in frequent and non‐ballooners. We did not find any significant isolation effects for these three measures of dissimilarity.

Main conclusions

The dominant process of extinction resulted in a high contribution of turnover to the multiple‐island dissimilarity of spiders. Specifically, frequent ballooners contributed less turnover to multiple‐island dissimilarity than occasional and non‐ballooners. The most likely explanation for this is that frequent ballooners were potentially able to colonize all islands, whereas occasional and non‐ballooners were constrained by water barriers and were unable to occupy most islands. Contrasting dissimilarities among dispersal groups of spiders demonstrates the importance of beta diversity partitioning, and the mechanistic insight gained on trait‐dependence in community assembly.
Unexpected scenarios from Mediterranean refugial areas: disentangling complex demographic dynamics along the Apennine distribution of silver fir
Authors: Piotti Andrea , Leonarduzzi Cristina , Postolache Dragos , Bagnoli Francesca , Spanu Ilaria , Brousseau Louise , Urbinati Carlo , Leonardi Stefano , Vendramin Giovanni Giuseppe
Published: April 2017

Aim

Mediterranean refugial areas are generally underrepresented in large‐scale genetic surveys of forest trees. In the case of silver fir (Abies alba Mill.), this has led to divergent hypotheses about the exact location of glacial refugia and the trajectory of recolonization routes. Based on the comprehensive sampling of Apennine populations, we aimed to reconcile discrepancies about the number and location of refugia for silver fir in the Apennines and test alternative demographic scenarios developed from palaeobotanical and genetic data.

Location

Mediterranean Basin; the Apennines and surrounding areas.

Methods

1167 individuals from 16 Apennine populations, extensively covering the species’ distribution along the Italian Peninsula, and eight populations from the Alps and Eastern Europe were genotyped at 16 nuclear and three chloroplast microsatellite markers. The geographical distribution of genetic variation was explored using Bayesian clustering and multivariate methods. Based on the inferred genetic structure, the demographic history of A. alba was assessed by the approximate Bayesian computation (ABC) analysis.

Results

Two unexpected characteristics of genetic structure emerged: a sharp genetic boundary in the central Apennines and a tight genetic connection between southern Apennine and Eastern European gene pools. Two Apennine areas, corresponding precisely with refugial areas hypothesized in most recent palaeobotanical syntheses, have high genetic diversity on a par with Eastern European populations. ABC analysis showed an ancient separation between Apennine and Eastern European gene pools followed by an admixture event that, mainly through directional gene flow via pollen, might have established the genetic similarity between southern Apennine and Eastern European populations. In addition, there was evidence that the central Apennines acted as a small‐scale, isolated refugium during the Last Glacial Maximum.

Main conclusions

Silver fir rear edge populations have experienced a complex demographic history across several glacial‐interglacial cycles, leading to unexpected genetic structure. Our study provides new insights into forest tree dynamics in the Mediterranean, showing the putative presence of multiple refugia for silver fir in the Apennines and a trans‐Adriatic connection between silver fir populations in the southern Italy and the Balkans.
Response of parasitoid egg load to host dynamics and implications for egg load evolution
Authors: Phillips C. B. , Kean J. M.
Published: April 2017

A theoretical debate about whether parasitoids should be time or egg limited now recognizes both as feasible, and interest has turned to determining the circumstances under which each might arise in the field, and their implications for parasitoid behaviour and evolution. Egg loads of parasitoids sampled from the field are predicted to show a negative response to host availability, but empirical support for this relationship is scarce. We measured how a parasitoid's egg load responded to seasonal fluctuations in host population density and recorded the predicted correlation. In early summer, parasitoids were at high risk of time limitation due to low host availability, and in late summer, their offspring were at greater risk of egg limitation due to high host availability. Despite clear seasonal changes in selection pressures on egg load and lifespan, the parasitoid showed no evidence of seasonal variation in its reproductive strategy. We made minor modifications to a previously published model to explore the effects of seasonal variation in host availability on optimal investments in eggs and lifespan and obtained several new results. In particular, under circumstances analogous to some of those observed in our field study, temporal stochasticity in reproductive opportunities can cause investments in eggs to increase, rather than decrease as previously predicted. Our model results helped to explain the parasitoid's lack of a seasonally varying reproductive strategy. Understanding the evolution of parasitoid egg load would benefit from a shift of research emphasis from purely stochastic variation in parasitoid reproductive opportunities to greater consideration of host dynamics.
Delivering dignified care: A realist synthesis of evidence that promotes effective listening to and learning from older people's feedback in acute care settings
Authors: Dickson Megan , Riddell Helen , Gilmour Fiona , McCormack Brendan
Published: April 2017

Aims and objectives

To explore effective mechanisms for listening to and learning from feedback from older people in the context of acute care.

Background

Maintaining the dignity of older people in acute care has become an issue of international concern. In the United Kingdom, recommendations for care improvement have led to the formation of an implementation group, the “Listening and Learning Hospitals Pilot Project.” This literature review forms phase 1 of the project.

Design

Realist synthesis was used to explore and synthesise wide‐ranging evidence.

Methods

Using 12 databases, literature was scoped to propose four principles that underpin the context, mechanism and outcomes (CMO) of effective relation‐based interventions with older people and their care partners in the acute care setting. A search was carried out in order to synthesise data to refute or support each principle. A total of 137 studies and 11 sources of grey literature were appraised and included. A final synthesis of evidence across all principles identified key mechanisms for effective relation‐based interventions.

Results

Eight essential mechanisms support effective care interventions.

Conclusions

This review adds depth and breadth to current nursing knowledge in this field through the process of realist synthesis. Acute care organisations need to make a commitment to supporting relational care at organisation and unit levels. Additionally, they need to value and support the well‐being of the nurses delivering it so that interventions to improve care for older people can succeed.

Relevance to clinical practice

Essential mechanisms synthesised from the review, together with other suggested interventions for improving dignified care of older people in acute care by listening to them and learning from their feedback, may contribute towards practice development in acute care.
Unlocking the limitations: Living with chronic obstructive pulmonary disease and receiving care through telemedicine—A phenomenological study
Authors: Barken Tina Lien , Thygesen Elin , Söderhamn Ulrika
Published: April 2017

Aims and objectives

To describe the lived experiences of quality of life among a group of patients living with chronic obstructive pulmonary disease who were included in a telemedical intervention after hospitalisation for disease exacerbation.

Background

Patients with chronic obstructive pulmonary disease have high symptom burden, poor control of symptoms and a need for greater requirements in care. Telemedicine can provide benefits for patients with chronic obstructive pulmonary disease by improving self‐management.

Design

Descriptive phenomenological approach.

Methods

Ten in‐depth interviews were conducted with chronic obstructive pulmonary disease patients participating in a telemedical intervention. The collected data were analysed using a descriptive phenomenological research method.

Results

Living with chronic obstructive pulmonary disease was experienced as creating physical and mental limitations of the diseased body and an increasing identity as a patient, which led to impaired quality of life. Being included in the telemedicine intervention increased accessibility to healthcare services and support from telemedicine nurses. Self‐measurement of health data increased participants’ clinical insight and created a mutual clinical language in dialogue with telemedicine nurses, which led to increased quality of life. However, receiving care through telemedicine was also experienced as a dual chore.

Conclusions

Telemedicine can reduce the perceived limitations imposed by chronic obstructive pulmonary disease through four key elements: (i) improving accessibility to healthcare services, (ii) increasing support from health professionals, (iii) strengthening clinical insight and (iv) developing a mutual clinical language, thus increasing quality of life. The transparency facilitated through telemedicine in this healthcare context encourages open decision‐making, where the participants can increase their knowledge and improve acknowledgement of and collaboration with telemedicine nurses.

Relevance to clinical practice

Telemedicine can be beneficial when rethinking care for chronic obstructive pulmonary disease by providing knowledge on how living with chronic obstructive pulmonary disease can affect the experience of receiving care through telemedicine and further determine for whom telemedicine is useful.
Exploring the concept of “caring cultures”
Authors: Gillin Nicola , Taylor Ruth , Walker Susan
Published: April 2017

Aims and objectives

To critically examine the conceptual, methodological and validity issues with the “caring cultures” construct.

Background

Post the Francis Report, “caring cultures” and alternative terminology such as “culture/s of care/caring/compassionate care” have gained prominence in the literature, especially within a UK policy context. However, in order to understand the value these “caring cultures” hold in terms of clinical practice, the concept itself first needs to be understood.

Design

A discussion and critical examination of the concept of “caring cultures” and associated terminology.

Methods

Grey literature, database, library and reference list searches were conducted.

Results

It is implied that “caring cultures” influence patient care. However, evidence which verifies this assertion is limited. In this article, the concept of “caring cultures” is deconstructed and its validity explored. An alternative to “caring cultures” is proposed in terms of research, whereby the concept of culture is instead explored in detail, on a microsystem level, using appropriate methodology.

Conclusion

The concept of “caring cultures”, although attractive in terms of its apparent simplicity, is not considered the most useful nor appropriate phrases in terms of advancing research. Instead, research which examines the established concept of “culture” in relation to outcomes such as patient care, doing so with an appropriate methodology, is viewed as a more suitable alternative.

Relevance to clinical practice

Clarifying concepts and terminology relating to “caring cultures” is essential for research to progress and the impact of culture on clinical practice to be better understood.