bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rare variant pathogenicity triage and inclusion of synonymous variants improves analysis of disease associations
Authors: Dershem Ridge , Metpally Raghu P.R. , Jeffreys Kirk , Krishnamurthy Sarathbabu , Smelser Diane T. , Carey David J. , Hershfinkel Michal , Robishaw Janet D. , Breitwieser Gerda E. 
Published: February 2018

AbstractMany G protein-coupled receptors (GPCRs) lack common variants that lead to reproducible genome-wide disease associations. Here we used rare variant approaches to assess the disease associations of 85 orphan or understudied GPCRs in an unselected cohort of 51,289 individuals. Rare loss-of-function variants, missense variants predicted to be pathogenic or likely pathogenic, and a subset of rare synonymous variants were used as independent data sets for sequence kernel association testing (SKAT). Strong, phenome-wide disease associations shared by two or more variant categories were found for 39% of the GPCRs. Validating the bioinformatics and SKAT analyses, functional characterization of rare missense and synonymous variants of GPR39, a Family A GPCR, showed altered expression and/or Zn2+-mediated signaling for members of both variant classes. Results support the utility of rare variant analyses for identifying disease associations for genes that lack common variants, while also highlighting the functional importance of rare synonymous variants.Author summaryRare variant approaches have emerged as a viable way to identify disease associations for genes without clinically important common variants. Rare synonymous variants are generally considered benign. We demonstrate that rare synonymous variants represent a potentially important dataset for deriving disease associations, here applied to analysis of a set of orphan or understudied GPCRs. Synonymous variants yielded disease associations in common with loss-of-function or missense variants in the same gene. We rationalize their associations with disease by confirming their impact on expression and agonist activation of a representative example, GPR39. This study highlights the importance of rare synonymous variants in human physiology, and argues for their routine inclusion in any comprehensive analysis of genomic variants as potential causes of disease.
Cognitive behaviour therapy for low self-esteem in a person with a learning disability: a case study
Authors: Evans Lauren , Allez Kate 
Published: February 2018

Purpose
Low self-esteem is common in people with learning disabilities. There is limited research examining the effectiveness of cognitive behavioural therapy (CBT) focused on low self-esteem within this client group. The purpose of this paper is to add to the limited evidence by describing the use of CBT focused on low self-esteem for a person with a learning disability in the context of emotion regulation difficulties.

Design/methodology/approach
An individual case study design was used, with repeated quantitative measures to monitor progress during weekly individual psychology sessions.

Findings
There was a reduction in the client’s feelings of anger and an increase in their self-esteem.

Research limitations/implications
Further studies and follow-up would determine longevity of benefits. The inclusion of distress tolerance techniques may have impacted on the findings and limits the conclusions that can be drawn about the impact of CBT focused on low self-esteem.

Originality/value
This case study could make a small contribution to the evidence base for the effectiveness of CBT-based treatments for low self-esteem in people with learning disabilities, which is an under-researched area.
Managing employees with chronic illness
Authors: Singh Maninder , James P.S. , Ganguli Shirshendu 
Published: February 2018

Purpose
The purpose of this paper is to identify future directions for human resource managers to provide work accommodations to chronically ill employees.

Design/methodology/approach
The authors researched empirical studies in management, occupational health journals, and reports on chronically ill employees.

Findings
The paper provides research-based practical insights for human resource practitioners to deal with the growing number of chronically ill employees.

Practical implications
The paper highlights solutions for human resource managers to create an inclusive workplace for employees with chronic illness.

Originality/value
The authors identified effective human resource and health practices for chronically ill employees, which would help to increase their productivity.
Community-based replica management in distributed systems
Authors: Nosrati Masoud , Fazlali Mahmood 
Published: February 2018

Purpose
One of the techniques for improving the performance of distributed systems is data replication, wherein new replicas are created to provide more accessibility, fault tolerance and lower access cost of the data. In this paper, the authors propose a community-based solution for the management of data replication, based on the graph model of communication latency between computing and storage nodes. Communities are the clusters of nodes that the communication latency between the nodes are minimum values. The purpose of this study if to, by using this method, minimize the latency and access cost of the data.

Design/methodology/approach
This paper used the Louvain algorithm for finding the best communities. In the proposed algorithm, by requesting a file according to the nodes of each community, the cost of accessing the file located out of the applicant’s community was calculated and the results were accumulated. On exceeding the accumulated costs from a specified threshold, a new replica of the file was created in the applicant’s community. Besides, the number of replicas of each file should be limited to prevent the system from creating useless and redundant data.

Findings
To evaluate the method, four metrics were introduced and measured, including communication latency, response time, data access cost and data redundancy. The results indicated acceptable improvement in all of them.

Originality/value
So far, this is the first research that aims at managing the replicas via community detection algorithms. It opens many opportunities for further studies in this area.
Minimal implications base for social network analysis
Authors: Raissa Paula , Dias Sérgio , Song Mark , Zárate Luis 
Published: February 2018

PurposeCurrently, social network (SN) analysis is focused on the discovery of activity and social relationship patterns. Usually, these relationships are not easily and completely observed. Therefore, it is relevant to discover substructures and potential behavior patterns in SN. Recently, formal concept analysis (FCA) has been applied for this purpose. FCA is a concept analysis theory that identifies concept structures within a data set. The representation of SN patterns through implication rules based on FCA enables the identification of relevant substructures that cannot be easily identified. The authors’ approach considers a minimum and irreducible set of implication rules (stem base) to represent the complete set of data (activity in the network). Applying this to an SN is of interest because it can represent all the relationships using a reduced form. So, the purpose of this paper is to represent social networks through the steam base.Design/methodology/approachThe authors’ approach permits to analyze two-mode networks by transforming access activities of SN into a formal context. From this context, it can be extracted to a minimal set of implications applying the NextClosure algorithm, which is based on the closed sets theory that provides to extract a complete, minimal and non-redundant set of implications. Based on the minimal set, the authors analyzed the relationships between premises and their respective conclusions to find basic user behaviors.FindingsThe experiments pointed out that implications, represented as a complex network, enable the identification and visualization of minimal substructures, which could not be found in two-mode network representation. The results also indicated that relations among premises and conclusions represent navigation behavior of SN functionalities. This approach enables to analyze the following behaviors: conservative, transitive, main functionalities and access time. The results also demonstrated that the relations between premises and conclusions represented the navigation behavior based on the functionalities of SN. The authors applied their approach for an SN for a relationship to explore the minimal access patterns of navigation.Originality/valueThe authors present an FCA-based approach to obtain the minimal set of implications capable of representing the minimum structure of the users’ behavior in an SN. The paper defines and analyzes three types of rules that form the sets of implications. These types of rules define substructures of the network, the capacity of generation users’ behaviors, transitive behavior and conservative capacity when the temporal aspect is considered.
Implementation and evaluation of an ambient intelligence testbed
Authors: Bylykbashi Kevin , Spaho Evjola , Obukata Ryoichiro , Ozera Kosuke , Liu Yi , Barolli Leonard 
Published: February 2018

Purpose
The purpose of this work is to implement an ambient intelligence (AmI) testbed to improve human sleeping conditions.

Design/methodology/approach
The implemented testbed is composed of the sensor node, sink node and actor node. As sensor node, the authors use a microwave sensor module (MSM) called DC6M4JN3000, which emits microwaves in the direction of a human or animal subject. These microwaves reflect back off the surface of the subject and change slightly in accordance with movements of the subject’s heart and lungs. As sink node, the authors use Raspberry Pi 3 Model B computers. In the sink node, the data are processed and then clustered by the k-means clustering algorithm. Then, the result is sent to the actor node (Reidan Shiki PAD module), which can be used for cooling and heating the bed.

Findings
The authors carried out simulations and experiments. Based on the simulation results, it was found that the room lighting, humidity and temperature have different effects on humans during sleeping. The best performance is shown when LIG parameter is 10 units, HUM parameter is 50 and TEM parameter is 25. Based on experimental results, it was found that the implemented AmI testbed has a good effect on humans during sleeping.

Research limitations/implications
For simulations, three input parameters were considered. However, new parameters that affect human sleeping conditions also need to be investigated. Further, the experiments were carried out for one person. More extensive experiments with multiple people are needed to have a better evaluation.

Originality/value
In this research work, a new fuzzy-based system was implemented to improve human sleeping conditions. The authors presented three new input parameters to evaluate the output (sleeping condition). The authors implemented and evaluated a testbed and showed that the implemented AmI testbed has a good effect on humans during sleeping, thus improving their quality of life (QoL).
A global database and “state of the field” review of research into ecosystem engineering by land animals
Authors: Coggan Nicole V. , Hayward Matthew W. , Gibb Heloise 
Published: February 2018

Abstract

Ecosystem engineers have been widely studied for terrestrial systems, but global trends in research encompassing the range of taxa and functions have not previously been synthesised.

We reviewed contemporary understanding of engineer fauna in terrestrial habitats and assessed the methods used to document patterns and processes, asking: (a) which species act as ecosystem engineers and with whom do they interact? (b) What are the impacts of ecosystem engineers in terrestrial habitats and how are they distributed? (c) What are the primary methods used to examine engineer effects and how have these developed over time? We considered the strengths, weaknesses and gaps in knowledge related to each of these questions and suggested a conceptual framework to delineate “significant impacts” of engineering interactions for all terrestrial animals.

We collected peer‐reviewed publications examining ecosystem engineer impacts and created a database of engineer species to assess experimental approaches and any additional covariates that influenced the magnitude of engineer impacts.

One hundred and twenty‐two species from 28 orders were identified as ecosystem engineers, performing five ecological functions. Burrowing mammals were the most researched group (27%). Half of all studies occurred in dry/arid habitats. Mensurative studies comparing sites with and without engineers (80%) were more common than manipulative studies (20%). These provided a broad framework for predicting engineer impacts upon abundance and species diversity. However, the roles of confounding factors, processes driving these patterns and the consequences of experimentally adjusting variables, such as engineer density, have been neglected. True spatial and temporal replication has also been limited, particularly for emerging studies of engineer reintroductions.

Climate change and habitat modification will challenge the roles that engineers play in regulating ecosystems, and these will become important avenues for future research. We recommend future studies include simulation of engineer effects and experimental manipulation of engineer densities to determine the potential for ecological cascades through trophic and engineering pathways due to functional decline. We also recommend improving knowledge of long‐term engineering effects and replication of engineer reintroductions across landscapes to better understand how large‐scale ecological gradients alter the magnitude of engineering impacts.
2‐Tridecanone impacts surface‐associated bacterial behaviours and hinders plant–bacteria interactions
Authors: López‐Lara Isabel M. , Nogales Joaquina , Pech‐Canul Ángel , Calatrava‐Morales Nieves , Bernabéu‐Roda Lydia M. , Durán Paloma , Cuéllar Virginia , Olivares José , Alvarez Laura , Palenzuela‐Bretones Diana , Romero Manuel , Heeb Stephan , Cámara Miguel , Geiger Otto , Soto María J. 
Published: February 2018

SummarySurface motility and biofilm formation are behaviours which enable bacteria to infect their hosts and are controlled by different chemical signals. In the plant symbiotic alpha‐proteobacterium Sinorhizobium meliloti, the lack of long‐chain fatty acyl‐coenzyme A synthetase activity (FadD) leads to increased surface motility, defects in biofilm development and impaired root colonization. In this study, analyses of lipid extracts and volatiles revealed that a fadD mutant accumulates 2‐tridecanone (2‐TDC), a methylketone (MK) known as a natural insecticide. Application of pure 2‐TDC to the wild‐type strain phenocopies the free‐living and symbiotic behaviours of the fadD mutant. Structural features of the MK determine its ability to promote S. meliloti surface translocation, which is mainly mediated by a flagella‐independent motility. Transcriptomic analyses showed that 2‐TDC induces differential expression of iron uptake, redox and stress‐related genes. Interestingly, this MK also influences surface motility and impairs biofilm formation in plant and animal pathogenic bacteria. Moreover, 2‐TDC not only hampers alfalfa nodulation but also the development of tomato bacterial speck disease. This work assigns a new role to 2‐TDC as an infochemical that affects important bacterial traits and hampers plant–bacteria interactions by interfering with microbial colonization of plant tissues.
Blockholder Exit Threats and Financial Reporting Quality
Authors: Dou Yiwei , Hope Ole‐Kristian , Thomas Wayne B. , Zou Youli 
Published: February 2018

AbstractRecent theoretical and empirical studies suggest that blockholders (shareholders with ownership ≥ 5 percent) exert governance through the threat of exit. Blockholders have strong incentives to gather private information and sell their shares when managers are perceived to underperform. To prevent blockholders from selling their shares and the firm from suffering a stock price decline, managers align their actions with the interests of shareholders. As a result of the greater manager‐shareholder alignment, managers' actions are more likely to be in shareholders' best interest, and consequently there is less need for managers to manipulate earnings. Consistent with these predictions from economic theory, we find evidence that as exit threat increases, firms have higher financial reporting quality. Theory also predicts that the impact of blockholders' exit threat on financial reporting quality (FRQ) should increase as the manager's wealth is tied more closely to the stock price, and this is what we find. Our study contributes to the research on the impact of shareholders on FRQ and to an emerging literature on the impact of blockholders in financial markets. Blockholders play an important role in managers' reporting outcomes through their actions as informed investors.
Identifying women veterans with unhealthy alcohol use using gender‐tailored screening
Authors: Hoggatt Katherine J. , Simpson Tracy , Schweizer Catherine A. , Drexler Karen , Yano Elizabeth M. 
Published: February 2018

Background and ObjectivesTo assess the impact of gender‐tailored alcohol screening criteria.MethodsAmong N = 1,349 women, we calculated the proportion screening positive for unhealthy alcohol use with non‐tailored versus gender‐tailored criteria (a gender‐tailored binge‐drinking item, lower screen‐positive threshold, or both).ResultsThree percent more women screened positive with a modified binge‐drinking question, most reporting risky drinking. Fifteen percent more women screened positive with a lower threshold; most did not report risky drinking.Discussion and ConclusionsGender‐tailored binge‐drinking questions may improve detection of women's unhealthy alcohol use.Scientific SignificanceThese results can inform future efforts to improve alcohol screening for women. (Am J Addict 2018;27:97–100)
Method comparison of two non‐invasive dual‐wavelength spectrophotometric retinal oximeters in healthy young subjects during normoxia
Authors: Told Reinhard , Boltz Agnes , Schmetterer Leopold , Garhöfer Gerhard , Sacu Stefan , Schmidt‐Erfurth Ursula , Pollreisz Andreas 
Published: February 2018

AbstractPurposeSpectrophotometric retinal oximetry is a non‐invasive technology for measuring oxygen saturation in arterioles and venules (SaO2, SvO2). We compared two commercially available systems: the Oxymap T1 (Oxymap ehf., Reykjavik, Iceland) and the Dynamic Vessel Analyzer (DVA, Imedos, Jena, Germany).MethodsTwenty healthy adults were included after giving informed consent. Two measurement cycles 30 min apart, including Oxymap T1, DVA, arterialized capillary blood draw of the earlobe (ScO2) and peripheral oxygen saturation using finger pulse oximetry (SpO2) were scheduled.ResultsSaO2 (p > 0.0004) but not SvO2 (p < 0.05) was statistically significantly different between the retinal oximeters used. Agreement between devices using repeated SO2 measurements resulted in a standard deviation (SD) of differences of 3.5% in retinal arterioles and 4.8% in venules. Bland–Altman plot using the mean of a participant's two measurements from each device showed an average mean difference of 4.4% (95% confidence limits of agreement: −8.6 to 17.4) and −3.3% (95% confidence limits of agreement: −28.8 to 22.2) for SaO2 and SvO2, respectively. Comparison of mean SaO2 and SvO2 with mean ScO2 and SpO2 indicated that SO2 measurements were generally higher in ScO2 and SpO2.ConclusionThis study shows very good repeatability for both devices, which is consistent with the literature. However, it does not show sufficient concordance between SaO2 measurements from both devices, indicating that patients should be followed by one device only. Differences in absorbance wavelengths used and image post‐processing may explain the differences.
Clinician‐rated and self‐reported psychotic‐like experiences in individuals accessing a specialist Youth Mental Health Service
Authors: Hodgekins Jo , Lower Rebecca , Wilson Jon , Cole Hannah , Ugochukwu Uju , Maxwell Sarah , Fowler David 
Published: February 2018

AimThe prevalence of psychotic‐like experiences (PLEs) was explored in a sample of 14‐ to 25‐year‐olds with non‐psychotic mental health difficulties. Associations between PLEs, psychopathology, functioning, trauma history, and pathways to care were examined.MethodsData were collected for 202 young people. Clinicians rated PLEs using the Primary Care Checklist (PCC) and functioning using Global Assessment Scales. Eighty‐three young people completed self‐report assessments of PLEs using the Prodromal Questionnaire (PQ‐16) and measures of social anxiety, depression, trauma history, and pathways to care.ResultsThere was a high prevalence of PLEs in the sample. The prevalence of PLEs was higher when young people self‐rated their experiences. Endorsement frequencies for PLEs ranged from 3.5 to 24% on the PCC and 22 to 70% on the PQ‐16. Higher scores on the PQ‐16 were associated with more pathways into care and greater exposure to traumatic life events.ConclusionsPLEs are common in young people with non‐psychotic mental health difficulties and may reflect increased severity and complexity of mental health difficulties. Routine screening and further assessment of PLEs are important in understanding and responding to such experiences. Screening should include self‐rating of PLEs as well as clinician‐rated scales.Practitioner Points

Clinical Implications

Psychotic‐like experiences are common in young people with severe non‐psychotic mental health problems and should be routinely screened in mental health services.

Psychotic‐like experiences were found to be more prevalent when using a self‐report screening tool compared to a clinician‐rated measure.

The presence of psychotic‐like experiences may reflect more severe and complex mental health problems and may also cause delays in young people accessing the right kind of support.

;Limitations

This study only assessed the presence or absence of psychotic‐like experiences. Further studies should use more detailed assessments to understand more about the nature of such experiences and how they are appraised and responded to.

This study is cross‐sectional, and therefore, the direction of the relationships between psychotic‐like experiences and depression, anxiety, functioning, and trauma cannot be specified.

Longitudinal studies are needed to examine the impact of psychotic‐like experiences on long‐term outcomes.