bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Rome criteria for the diagnosis of irritable bowel syndrome in primary care: a survey among European countries
Authors: Mujagic Zlatan , Jonkers Daisy M.A.E. , Hungin A. Pali S. , de Wit Niek J. , Wensaas Knut-Arne , Palka Margaret , Leeters Vico , Kruimel Joanna W. , Leue Carsten , Masclee Ad A.M. , Muris Jean W.M. 
Published: January 2017

Background and objectives
The majority of patients with irritable bowel syndrome (IBS) are diagnosed and treated in primary care. The aim of this study was to investigate the implementation of the Rome criteria in daily primary care clinical practice and adherence of general practitioners (GPs) to recommended diagnostic approaches for IBS.

Patients and methods
A survey consisting of 18 questions was distributed across 11 European countries and was used to assess GPs’ diagnostic approach of IBS, the use of Rome criteria in daily practice and GPs’ perspective on the aetiology of the disorder.

Results
Overall, 185 GPs completed the survey. In daily clinical practice, 32% of GPs reported that they usually make a positive diagnosis on the basis of symptoms only, whereas 36% of GPs reported regular use of the Rome criteria to diagnose IBS. Furthermore, 62% of the responders reported that they applied additional diagnostics, such as blood tests, 31% found it necessary to perform endoscopy to make a positive diagnosis of IBS and 29% referred patients with IBS to a specialist. Psychological factors were the most frequently selected potential aetiological factor of IBS (88% of GPs). Overall, 52% of GPs reported systematically including questions on psychological symptoms in the assessment of history of IBS.

Conclusion
Only about one-third of GPs regularly used the Rome criteria to diagnose IBS. In daily primary care practice, IBS largely remains a diagnosis of exclusion. This has implications in terms of GPs’ specialty training and questions the applicability of IBS guidelines in daily care, which advocate an early, positive, symptom-based diagnosis.
Volume-Targeted Ventilation in the Neonate: Benchmarking Ventilators on an Active Lung Model
Authors: Krieger Tobias J. , Wald Martin 
Published: January 2017

Objective:
Mechanically ventilated neonates have been observed to receive substantially different ventilation after switching ventilator models, despite identical ventilator settings. This study aims at establishing the range of output variability among 10 neonatal ventilators under various breathing conditions.

Design:
Relative benchmarking test of 10 neonatal ventilators on an active neonatal lung model.

Setting:
Neonatal ICU.

Subjects:
Ten current neonatal ventilators.

Interventions:
Ventilators were set identically to flow-triggered, synchronized, volume-targeted, pressure-controlled, continuous mandatory ventilation and connected to a neonatal lung model. The latter was configured to simulate three patients (500, 1,500, and 3,500 g) in three breathing modes each (passive breathing, constant active breathing, and variable active breathing).

Measurements and Main Results:
Averaged across all weight conditions, the included ventilators delivered between 86% and 110% of the target tidal volume in the passive mode, between 88% and 126% during constant active breathing, and between 86% and 120% under variable active breathing. The largest relative deviation occurred during the 500 g constant active condition, where the highest output machine produced 147% of the tidal volume of the lowest output machine.

Conclusions:
All machines deviate significantly in volume output and ventilation regulation. These differences depend on ventilation type, respiratory force, and patient behavior, preventing the creation of a simple conversion table between ventilator models. Universal neonatal tidal volume targets for mechanical ventilation cannot be transferred from one ventilator to another without considering necessary adjustments.
Origin of the scaling laws of sediment transport
Authors: Ali Sk Zeeshan , Dey Subhasish 
Published: January 2017

In this paper, we discover the origin of the scaling laws of sediment transport under turbulent flow over a sediment bed, for the first time, from the perspective of the phenomenological theory of turbulence. The results reveal that for the incipient motion of sediment particles, the densimetric Froude number obeys the ‘(1 +
σ
)/4’ scaling law with the relative roughness (ratio of particle diameter to approach flow depth), where
σ
is the spectral exponent of turbulent energy spectrum. However, for the bedforms, the densimetric Froude number obeys a ‘(1 +
σ
)/6’ scaling law with the relative roughness in the enstrophy inertial range and the energy inertial range. For the bedload flux, the bedload transport intensity obeys the ‘3/2’ and ‘(1 +
σ
)/4’ scaling laws with the transport stage parameter and the relative roughness, respectively. For the suspended load flux, the non-dimensional suspended sediment concentration obeys the ‘

−

Z

’ scaling law with the non-dimensional vertical distance within the wall shear layer, where

Z

is the Rouse number. For the scour in contracted streams, the non-dimensional scour depth obeys the ‘4/(3 −
σ
)’, ‘−4/(3 −
σ
)’ and ‘−(1 +
σ
)/(3 −
σ
)’ scaling laws with the densimetric Froude number, the channel contraction ratio (ratio of contracted channel width to approach channel width) and the relative roughness, respectively.
Literature Consistency of Bioinformatics Sequence Databases is Effective for Assessing Record Quality
Authors: Bouadjenek Mohamed Reda , Verspoor Karin , Zobel Justin 
Published: January 2017

AbstractBioinformatics sequence databases such as Genbank or UniProt contain hundreds of millions of records of genomic data. These records are derived from direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centres; their diversity and scale means that they suffer from a range of data quality issues including errors, discrepancies, redundancies, ambiguities, incompleteness, and inconsistencies with the published literature. In this work, we seek to investigate and analyze the data quality of sequence databases from the perspective of a curator, who must detect anomalous and suspicious records.Specifically, we emphasize the detection of inconsistent records with respect to the literature. Focusing on GenBank, we propose a set of 24 quality indicators, which are based on treating a record as a query into the published literature, and then use query quality predictors. We then carry out an analysis that shows that the proposed quality indicators and the quality of the records have a mutual relationship, in which one depends on the other. We propose to represent record-literature consistency as a vector of these quality indicators. By reducing the dimensionality of this representation for visualization purposes using Principal Component Analysis, we show that records which have been reported as inconsistent with the literature fall roughly in the same area, and therefore share similar characteristics. By manually analyzing records not previously known to be erroneous that fall in the same area than records know to be inconsistent, we show that 1 record out of 4 is inconsistent with respect to the literature. This high density of inconsistent record opens the way towards the development of automatic methods for the detection of faulty records. We conclude that literature inconsistency is a meaningful strategy for identifying suspicious records.
An analytic approach for interpretable predictive models in high dimensional data, in the presence of interactions with exposures
Authors: Bhatnagar Sahir Rai , Yang Yi , Khundrakpam Budhachandra , Evans Alan C , Blanchette Mathieu , Bouchard Luigi , Greenwood Celia MT 
Published: January 2017

AbstractPredicting a phenotype and understanding which variables improve that prediction are two very challenging and overlapping problems in analysis of high-dimensional data such as those arising from genomic and brain imaging studies. It is often believed that the number of truly important predictors is small relative to the total number of variables, making computational approaches to variable selection and dimension reduction extremely important. To reduce dimensionality, commonly-used two-step methods first cluster the data in some way, and build models using cluster summaries to predict the phenotype.It is known that important exposure variables can alter correlation patterns between clusters of high-dimensional variables, i.e., alter network properties of the variables. However, it is not well understood whether such altered clustering is informative in prediction. Here, assuming there is a binary exposure with such network-altering effects, we explore whether use of exposure-dependent clustering relationships in dimension reduction can improve predictive modelling in a two-step framework. Hence, we propose a modelling framework called ECLUST to test this hypothesis, and evaluate its performance through extensive simulations.With ECLUST, we found improved prediction and variable selection performance compared to methods that do not consider the environment in the clustering step, or to methods that use the original data as features. We further illustrate this modelling framework through the analysis of three data sets from very different fields, each with high dimensional data, a binary exposure, and a phenotype of interest. Our method is available in theeclustCRAN package.
Infectious Reactivation of Cytomegalovirus Explaining Age- and Sex-Specific Patterns of Seroprevalence
Authors: Boven Michiel van , Kassteele Jan van de , Korndewal Marjolein J. , van Dorp Christiaan H. , Kretzschmar Mirjam , der Klis Fiona van , de Melker Hester E. , Vossen Ann C. , Baarle Debbie van 
Published: January 2017

AbstractHuman cytomegalovirus is a herpes virus with poorly understood transmission dynamics. We here provide quantitative estimates of the transmissibility of primary infection, reactivation, and re-infection using age-and sex-specific antibody response data. The data are optimally described by three distributions of antibody measurements, i.e. uninfected, infected, and infected after reactivation/re-infection. Estimates of seroprevalence increase gradually with age, such that at 80 years 73% (95%CrI: 64%-78%) of females and 62% (95%CrI: 55%-68%) of males is infected, while 57% (95%CrI: 47%-67%) of females and 37% (95%CrI: 28%-46%) of males has experienced a reactivation or re-infection episode. Merging the statistical analyses with transmission models, we find that infectious reactivation is key to provide a good fit fit to the data. Estimated reactivation rates increase from low values in children to 2%-6% per year older women. The results advance a hypothesis in which adult-to-adult transmission after infectious reactivation is the main driver of infection.
The circadian dynamics of small nucleolar RNA
Authors: Aitken Stuart , Semple Colin A. 
Published: January 2017

AbstractThe circadian regulation of gene expression allows plants and animals to anticipate predictable environmental changes. While the influence of the circadian clock has recently been shown to extend to ribosome biogenesis, the dynamics and regulation of the many small nucleolar RNA that are required in pre-ribosomal RNA folding and modification are unknown. Using a novel computational method, we show that 18S and 28S pre-rRNA are subject to circadian regulation in a nuclear RNA sequencing time course. A population of snoRNA with circadian expression is identified that is functionally associated with rRNA modification. More generally, we find the abundance of snoRNA known to modify 18S and 28S to be inversely correlated with the abundance of their target. Cyclic patterns in the expression of a number of snoRNA indicate a coordination with rRNA maturation, potentially through an upregulation in their biogenesis, or their release from mature rRNA at the end of the previous cycle of rRNA maturation, in antiphase with the diurnal peak in pre-rRNA. Few cyclic snoRNA have cyclic host genes, indicating the action of regulatory mechanisms in addition to transcriptional activation of the host gene. For highly-expressed independently transcribed snoRNA, we find a characteristic RNA polymerase II and H3K4me3 signature that correlates with mean snoRNA expression over the day.
Photorelease of Diacylglycerol Increases the Amplitude and Duration of Protein Kinase C-BetaII Relocationin cyto
Authors: Goedhart Joachim , Gadella Theodorus W.J. 
Published: January 2017

ABSTRACTDiacylglycerol (DAG) is a lipid second messenger produced by receptor stimulated phospholipase C and is capable of activating several PKC isoforms. Classical PKC isoforms require simultaneous presence of calcium and DAG for activation and relocation to membranes. The aim of this study was to synthesize a photolabile precursor of DAG and examine the effect of an immediate increase of the signaling lipid on PKC relocation. Caged DAG was synthesized using a photoreleasable 7-diethyl-aminocoumarin (DEACM) group. Photolysis was monitoredin vitroby an increase in coumarin fluorescence from which an uncaging quantum yield of 1.1% was determined. This quantum yield proved ideal for efficient uncaging at high UV power while allowing localization of the fluorescent compound at low UV power. Taking advantage of the coumarin fluorescence, it was demonstrated that DEACM-DiC8 accumulated inside cells. Effects of DAG photorelease on periodic relocations of PKCbetaII, induced by histamine, UTP or EGF, were studied. Photorelease of DAGin cytoimmediately increased the amplitude and duration of relocation events, regardless of the agonist used. Together, the results demonstrate the usefulness of caged DAG for dissecting PKC signaling and suggest that DAG levels are limiting during signaling.
PEAPODlimits developmental plasticity inArabidopsis
Authors: White Derek W. R. 
Published: January 2017

AbstractHigher plants utilise developmental plasticity to adapt to changes in the environment, especially to variations in light. Much of this change in growth and development involves the light-mediated regulation of multiple hormone pathways. However, despite considerable progress towards understanding the molecular processes controlling light signalling and hormone activity, regulatory mechanisms preventing exaggerated plant developmental responses are not well understood. Here I report that thePPDregulatory complex has a crucial role in limiting developmental plasticity inArabidopsis. Reductions inPPDorKIX8/9gene expression resulted in; tolerance to ABA inhibition of seed germination, hypocotyl elongation, increases in stomata on hypocotyls, cambial cell proliferation and seed weight, and delayed flowering. Transcript profiling and analyses of hormone responses and genetic interactions established PPD modulates developmental plasticity, mainly by a combination of transcriptional activation and repression of genes controlling CRY/PHY light signalling and ABA, auxin, brassinosteroid, cytokinin and gibberellin homeostasis.
UK university policy approaches towards the copyright ownership of scholarly works and the future of open access
Authors: Gadd Elizabeth 
Published: January 2017

PurposeThe purpose of this paper is to consider how the open access policy environment has developed since the Rights Metadata for Open Archiving Project’s call in 2003 for universities and academics to assert joint copyright ownership of scholarly works and investigate whether UK universities are moving towards a joint copyright ownership.Design/methodology/approachThe paper analyses 81 UK university copyright policies to understand what proportion make a claim over: IP ownership of all outputs; the copyright in scholarly works; re-using scholarly works in specific ways; and approaches to moral rights. Results are cross-tabulated by policy age and mission group.FindingsUniversities have not asserted their interest in scholarly works through joint ownership, leaving research funders and publishers to set open access policy. The paper finds an increased proportion of universities assert a generic claim to all IP (87 per cent) relative to earlier studies. In total, 74 per cent of policies relinquished rights in scholarly works in favour of academic staff; 20 per cent of policies share ownership of scholarly works through licensing; 28 per cent of policies assert the right to re-use scholarly works in some way; and 32 per cent of policies seek to protect moral rights. Policies that “share” ownership of scholarly works are more recent. The UK Scholarly Communication Licence (UK-SCL) should have an impact on this area. The reliance on individual academics to enforce a copyright policy or not to opt-out of the UK-SCL could be problematic. The paper concludes that open access may still be best served by joint ownership of scholarly works.Originality/valueThis the first large-scale analysis of UK university policy positions towards scholarly works. The paper discovers for the first time a move towards “shared” ownership of scholarly works in copyright policies.
Factors affecting usage of e-resources: scale development and validation
Authors: Garg Ruchi Jain , Kumar Vinod , Vandana  
Published: January 2017

Purpose
The purpose of this paper is to develop and validate a scale involving the factors affecting usage of e-resources.

Design/methodology/approach
The present study identifies five factors affecting the usage of e-resources: training modes, awareness, influencers, utilitarian benefits, and experiential and hedonic benefits. To generate measurement items, two focus group discussions were carried out which resulted in 20 items. To empirically ensure reliability and validity of scale, data were collected from 347 postgraduate students actively using e-resources. To test reliability of scale, internal consistency reliability and construct reliability were examined. The construct validity of scale (which includes convergent validity and discriminant validity) was verified through confirmatory factor analysis using structure equation modeling.

Findings
Findings of the study present a statistically reliable and valid scale consisting of five factors and 18 items.

Originality/value
The present study is one of the distinctive studies on introducing a scale employing factors affecting usage of e-resources.
Tertiary students’ acceptance of a game to teach information literacy
Authors: Guo Yan Ru , Goh Dion Hoe-Lian , Luyt Brendan 
Published: January 2017

Purpose
The purpose of this paper is to investigate tertiary students’ acceptance of digital game-based learning (DGBL). Specifically, it investigated the influence of learning motivation, enjoyment, and perceived usefulness on students’ behavioral intention to play an information literacy (IL) game.

Design/methodology/approach
In total, 150 tertiary students were recruited to play an IL game, and fill in a survey questionnaire. Multiple linear regression was performed.

Findings
Results indicated that attention, satisfaction, affective enjoyment, and perceived usefulness were significant determinants for the behavioral intention to play IL games. However, relevance, confidence, cognitive enjoyment, and behavioral enjoyment were not found to predict their behavioral intention.

Research limitations/implications
The authors did not consider other factors in the hypotheses, such as the mediating effects of enjoyment on behavioral intention, and the influence of students’ individual characters such as learning styles or personalities on their behavioral intention of using DGBL. Further, the IL game used in the study, Library Escape, may reduce generalizability of the results. The study used self-reported attitudinal data from survey questionnaires, while behavioral data were not considered.

Practical implications
The results showed that pedagogical features, enjoyment factors, and perceived usefulness remain critical in the uptake of IL games by students. Further, the study demonstrated that instead of behavioral or cognitive dimensions of enjoyment, players are more concerned with affective enjoyment. Hence, developing DGBL with affective features should be pursued.

Originality/value
By taking into consideration both pedagogical and gameplay characteristics of DGBL to explain students’ acceptance of IL games, this study integrates and extends previous studies in the context of IL games. Additionally, instead of using perceived enjoyment as a single dimensional construct, this study adopted a multifaceted, more nuanced perspective on the perceived enjoyment of DGBL.
Information need as trigger and driver of information seeking: a conceptual analysis
Authors: Savolainen Reijo 
Published: January 2017

Purpose
The purpose of this paper is to elaborate the picture of the motivators for information behaviour by examining the nature of information need as a trigger and driver of information seeking.

Design/methodology/approach
A conceptual analysis was made by focussing on the ways in which researchers have conceptualised information need in models for human information behaviour (HIB). The study draws on conceptual analysis of 26 key studies focussing on the above topic.

Findings
Researchers have employed two main approaches to conceptualise information needs in the HIB models. First, information need is approached as a root factor which motivates people to identify and access information sources. Second, information need is approached as a secondary trigger or driver determined by more fundamental factors, for example, the information requirements of task performance. The former approach conceptualises information need as a trigger providing an initial impetus to information seeking, while the latter approach also depicts information need as a driver that keeps the information-seeking process in motion. The latter approach is particularly characteristic of models depicting information seeking as a cyclic process.

Research limitations/implications
As the study focusses on information need, no attention is devoted to related constructs such as anomalous state of knowledge and uncertainty.

Originality/value
The study pioneers by providing an in-depth analysis of the nature of information need as a trigger and driver of information seeking. The findings refine the picture of motivators for information behaviour.