bluuebunny/crossref_metadata_2025_split huggingface dataset:
Addressing Dual Patient and Staff Safety Through A Team-Based Standardized Patient Simulation for Agitation Management in the Emergency Department
Authors: Wong Ambrose H. , Auerbach Marc A. , Ruppel Halley , Crispino Lauren J. , Rosenberg Alana , Iennaco Joanne D. , Vaca Federico E. 
Published: April 2018

IntroductionEmergency departments (EDs) have seen harm rise for both patients and health workers from an increasing rate of agitation events. Team effectiveness during care of this population is particularly challenging because fear of physical harm leads to competing interests. Simulation is frequently employed to improve teamwork in medical resuscitations but has not yet been reported to address team-based behavioral emergency care. As part of a larger investigation of agitated patient care, we designed this secondary study to examine the impact of an interprofessional standardized patient simulation for ED agitation management.MethodsWe used a mixed-methods approach with emergency medicine resident and attending physicians, Physician Assistants (PAs) and Advanced Practice Registered Nurses (APRNs), ED nurses, technicians, and security officers at two hospital sites. After a simulated agitated patient encounter, we conducted uniprofessional and interprofessional focus groups. We undertook structured thematic analysis using a grounded theory approach. Quantitative data consisted of responses to the KidSIM Questionnaire addressing teamwork and simulation-based learning attitudes before and after each session.ResultsWe reached data saturation with 57 participants. KidSIM scores revealed significant improvements in attitudes toward relevance of simulation, opportunities for interprofessional education, and situation awareness, as well as four of six questions for roles/responsibilities. Two broad themes emerged from the focus groups: (1) a team-based agitated patient simulation addressed dual safety of staff and patients simultaneously and (2) the experience fostered interprofessional discovery and cooperation in agitation management.ConclusionsA team-based simulated agitated patient encounter highlighted the need to consider the dual safety of staff and patients while facilitating interprofessional dialog and learning. Our findings suggest that simulation may be effective to enhance teamwork in behavioral emergency care.
Haplotype-aware genotyping from noisy long reads
Authors: Ebler Jana , Haukness Marina , Pesout Trevor , Marschall Tobias , Paten Benedict 
Published: April 2018

MotivationCurrent genotyping approaches for single nucleotide variations (SNVs) rely on short, relatively accurate reads from second generation sequencing devices. Presently, third generation sequencing platforms able to generate much longer reads are becoming more widespread. These platforms come with the significant drawback of higher sequencing error rates, which makes them ill-suited to current genotyping algorithms. However, the longer reads make more of the genome unambiguously mappable and typically provide linkage information between neighboring variants.ResultsIn this paper we introduce a novel approach for haplotype-aware genotyping from noisy long reads. We do this by considering bipartitions of the sequencing reads, corresponding to the two haplotypes. We formalize the computational problem in terms of a Hidden Markov Model and compute posterior genotype probabilities using the forward-backward algorithm. Genotype predictions can then be made by picking the most likely genotype at each site. Our experiments indicate that longer reads allow significantly more of the genome to potentially be accurately genotyped. Further, we are able to use both Oxford Nanopore and Pacific Biosciences sequencing data to independently validate millions of variants previously identified by short-read technologies in the reference NA12878 sample, including hundreds of thousands of variants that were not previously included in the high-confidence reference set.
An accurate and robust algorithm for solvent-excluded surface computation
Authors: Wang Lincong 
Published: April 2018

AbstractThe solvent-excluded surface (SES1) of a molecule is an important geometrical property relevant to its solvation in aqueous solution and its interactions with other molecules. In this paper we present an accurate and robust analytic algorithm suitable for a large-scale SES analysis. The accuracy and robustness of our algorithm are made possible by an iterative strategy for the treatments of probe-probe intersections, probe-probe overlaps and limited numerical precision. The accuracy and robustness of our algorithm in turn make it possible to analyze on a large-scale the SESs for different types of proteins and various sets of ligand-protein interaction interfaces. The results illustrate the usefulness of SES and SES-defined physical and geometrical properties for the characterization of protein-solvent interaction and ligand-protein interaction where ligand could be either small molecule compound, or membrane lipid, or DNA or protein.
Coarse-Grained Model of the SNARE Complex Shows that Quick Zippering Requires Partial Assembly
Authors: Fortoul N. , Bykhovskaia M. , Jagota A. 
Published: April 2018

ABSTRACTNeuronal transmitters are released from nerve terminals via the fusion of synaptic vesicles with the presynaptic membrane. Vesicles become attached to the membrane via the SNARE complex. The SNARE complex comprises the vesicle associate protein Synaptobrevin (Syb), the membrane associated protein syntaxin (Syx), and the cytosolic protein SNAP25, which together form a four-helical bundle. The full assembly of Syb onto the core SNARE bundle promotes vesicle fusion. We investigated SNARE assembly using a coarse-grained model of the SNARE complex. The model retains chemical specificity, and was calibrated using single molecule experiments and all-atom molecular dynamics simulations. Steered force-control simulations of SNARE unzippering by peeling off Syb were used to set up initial disassembled states of the SNARE complex. From these states, the assembly process was simulated. We found that if Syb is in helical form, then the SNARE complex assembles rapidly, on a sub-microsecond time-scale. We found that assembly times grow exponentially with separation distance between Syb and Syx C-termni. The formation of helical turns is likely to substantially decelerate the assembly, consistent with single molecule force experiments that show SNARE assembly duration on the time-scale of hundreds of ms. Since synaptic vesicle fusion occurs at a sub-millisecond time-scale, our results indicate that for biologically relevant rapid assembly the SNARE complex needs to be partially zippered and its constituent helices brought into proximity, possibly by means of molecular chaperones.
User conceptualizations of derivative relationships in the bibliographic universe
Authors: Tallerås Kim , Dahl Jørn Helge B. , Pharo Nils 
Published: April 2018

Purpose
Considerable effort is devoted to developing new models for organizing bibliographic metadata. However, such models have been repeatedly criticized for their lack of proper user testing. The purpose of this paper is to present a study on how non-experts in bibliographic systems map the bibliographic universe and, in particular, how they conceptualize relationships between independent but strongly related entities.

Design/methodology/approach
The study is based on an open concept-mapping task performed to externalize the conceptualizations of 98 novice students. The conceptualizations of the resulting concept maps are identified and analyzed statistically.

Findings
The study shows that the participants’ conceptualizations have great variety, differing in detail and granularity. These conceptualizations can be categorized into two main groups according to derivative relationships: those that apply a single-entity model directly relating document entities and those (the majority) that apply a multi-entity model relating documents through a high-level collocating node. These high-level nodes seem to be most adequately interpreted either as superwork devices collocating documents belonging to the same bibliographic family or as devices collocating documents belonging to a shared fictional world.

Originality/value
The findings can guide the work to develop bibliographic standards. Based on the diversity of the conceptualizations, the findings also emphasize the need for more user testing of both conceptual models and the bibliographic end-user systems implementing those models.
Lifeworld as “unit of analysis”
Authors: Gorichanaz Tim , Latham Kiersten F. , Wood Elizabeth 
Published: April 2018

Purpose
The authors discuss the lifeworld as a research concept for the field of information behaviour, which serves to problematise the concept of unit of analysis. In so doing, the authors demonstrate how the lifeworld can be adopted as a unit of analysis in information behaviour research, that is, how research can be based in the lifeworld rather than merely looking at the lifeworld. The paper aims to discuss these issues.

Design/methodology/approach
The authors first situate our discussion in the current of information behaviour scholarship. The authors then introduce the concepts of lifeworld and unit of analysis and consider how they intersect. Next, to show the importance of the lifeworld, the authors present two recent studies in which the lifeworld emerged. Finally, the authors discuss how lifeworld-based research can be conducted more conscientiously.

Findings
Though many research approaches deal with lived experience in one way or another, they tend not to fully grasp these experiences. As opposed to units of analysis such as individual, social group, person-in-situation, etc., using lifeworld as a unit of analysis allows phenomena to be researched holistically and without reductionism.

Research limitations/implications
The authors limit the discussion to the concept of the lifeworld as developed by Husserl, the concept’s originator. The lifeworld has been discussed and extended by other authors since, but this work is not considered here. The viewpoint is offered as a supplementary perspective, meant to be enriching to our field of study, rather than divisive.

Originality/value
This is the first time the concept of the lifeworld has been fully explicated in information science. As the authors discuss, two recent information behaviour studies that “discovered” the lifeworld through their analysis. Future studies that attend to the lifeworld from the start have the capacity to build on this work and extend the horizons of information science.
Delays in new product introduction
Authors: Adaku Ebenezer , Amoatey Charles Teye , Nornyibey Israel , Famiyeh Samuel , Asante-Darko Disraeli 
Published: April 2018

Purpose
Speed to the market is becoming a key competitive priority in developing countries’ environments even though lack of technology, poor skilled labour and under-developed infrastructure remain daunting challenges. The purpose of this paper is to examine the causes and relative importance of delay factors in the introduction of food products to the market in the era of time-based competition.

Design/methodology/approach
The study employed a case study approach in understanding the phenomenon in its natural settings and making sense of it through process and participants observations. Again, a two-stage approach (first, interviews and second, questionnaire) was used in collecting data from the respondents who work in a project team for a large food processing firm. The data was analysed using the relative importance index technique.

Findings
The results show that the most important causes of delays in new products introduction, especially in the food processing industry, are: high number of projects running concurrently; lack of project management process; lack of consistent project management structure; high workload on project team and delays caused by external laboratory.

Originality/value
This study sought to identify detailed delay factors in the introduction of new products with respect to the food processing industry and more importantly established the relative importance of these delay factors as a decision support system for managers in the food processing industry.
A planktonic diatom displays genetic structure over small spatial scales
Authors: Sefbom Josefin , Kremp Anke , Rengefors Karin , Jonsson Per R. , Sjöqvist Conny , Godhe Anna 
Published: April 2018

SummaryMarine planktonic microalgae have potentially global dispersal, yet reduced gene flow has been confirmed repeatedly for several species. Over larger distances (>200 km) geographic isolation and restricted oceanographic connectivity have been recognized as instrumental in driving population divergence. Here we investigated whether similar patterns, that is, structured populations governed by geographic isolation and/or oceanographic connectivity, can be observed at smaller (6–152 km) geographic scales. To test this we established 425 clonal cultures of the planktonic diatom Skeletonema marinoi collected from 11 locations in the Archipelago Sea (northern Baltic Sea). The region is characterized by a complex topography, entailing several mixing regions of which four were included in the sampling area. Using eight microsatellite markers and conventional F‐statistics, significant genetic differentiation was observed between several sites. Moreover, Bayesian cluster analysis revealed the co‐occurrence of two genetic groups spread throughout the area. However, geographic isolation and oceanographic connectivity could not explain the genetic patterns observed. Our data reveal hierarchical genetic structuring whereby despite high dispersal potential, significantly diverged populations have developed over small spatial scales. Our results suggest that biological characteristics and historical events may be more important in generating barriers to gene flow than physical barriers at small spatial scales.
Evidence for selective bacterial community structuring on microplastics
Authors: Ogonowski Martin , Motiei Asa , Ininbergs Karolina , Hell Eva , Gerdes Zandra , Udekwu Klas I. , Bacsik Zoltan , Gorokhova Elena 
Published: April 2018

SummaryIn aquatic ecosystems, microplastics are a relatively new anthropogenic substrate that can readily be colonized by biofilm‐forming organisms. To examine the effects of substrate type on microbial community assembly, we exposed ambient Baltic bacterioplankton to plastic substrates commonly found in marine environments (polyethylene, polypropylene and polystyrene) as well as native (cellulose) and inert (glass beads) particles for 2 weeks under controlled conditions. The source microbial communities and those of the biofilms were analyzed by Illumina sequencing of the 16S rRNA gene libraries. All biofilm communities displayed lower diversity and evenness compared with the source community, suggesting substrate‐driven selection. Moreover, the plastics‐associated communities were distinctly different from those on the non‐plastic substrates. Whereas plastics hosted greater than twofold higher abundance of Burkholderiales, the non‐plastic substrates had a significantly higher proportion of Actinobacteria and Cytophagia. Variation in the community structure, but not the cell abundance, across the treatments was strongly linked to the substrate hydrophobicity. Thus, microplastics host distinct bacterial communities, at least during early successional stages.
Functional compartmentalisation of nutrients and phenolics in the tissues of galls induced by Leptocybe invasa (Hymenoptera: Eulophidae) on Eucalyptus camaldulensis (Myrtaceae)
Authors: Isaias Rosy Mary dos Santos , Ferreira Bruno Garcia , Alvarenga Danielle Ramos de , Barbosa Leonardo Rodrigues , Salminen Juha‐Pekka , Steinbauer Martin J 
Published: April 2018

AbstractGalling herbivores induce structural and chemical alterations in their host plant's tissues. These insects have been the focus of little study in the case of Australian taxa. Leptocybe invasa, a native Australian galling hymenopteran associated with Eucalyptus species, causes economic damage to plantation eucalypts in many countries around the world. Leptocybe invasa oviposits in the midribs and petioles of expanding leaves thereby intercepting photosynthates and impairing normal expansion. We analysed the ultrastructural and chemical cellular changes in L. invasa galls on Eucalyptus camaldulensis (probably subspecies camaldulensis) to diagnose how the insect manipulates plant cells and tissues and the significance of these alterations for insect nutrition and protection. Galling stimuli induce the formation of two functionally compartmentalised types of tissue. Phenolic plant secondary metabolites and anthocyanins (plant pigments) accumulate in the outer compartment, while primary metabolites accumulate in the inner compartment. The nutritive cells (inner compartment) accumulate protein and lipids that provide food for the larvae. Total polyphenol concentrations did not differ significantly between outer and inner compartments. Nevertheless, the concentrations of quercetin and kaempferol derivatives were higher in the outer compartment than in the inner compartment. These differences could be related to the protection of plant tissues against ultraviolet rays and the maintenance of redox homeostasis. There were higher ratios of hexahydroxydiphenoyl‐containing hydrolysable tannins rather than galloyl‐containing hydrolysable tannins in the inner compartment. This shift in the oxidative capacity of the polyphenols in the inner compartment could represent a defensive plant response to the larvae.
Immunological and hematological effects of IL‐5(Rα)‐targeted therapy: An overview
Authors: Hassani M. , Koenderman L. 
Published: April 2018

AbstractIL‐5 is an important cytokine for priming and survival of mature eosinophils and for proliferation and maturation of their progenitors. Hence, IL‐5(Rα) targeting will be increasingly used in diseases where eosinophils are the key immune effector cells such as eosinophilic asthma (EA), hypereosinophilic syndrome (HES), eosinophilic esophagitis (EE), and eosinophilic granulomatosis with polyangiitis (EGPA). Therefore, several neutralizing monoclonal antibodies directed against IL‐5 (mepolizumab and reslizumab) and its receptor IL‐5Rα (benralizumab) have found or will find their way to the clinic. While the clinical effect of these drugs has been extensively investigated and reviewed, the understanding of the underlying immunological and hematological mechanisms remains less clear. This review will discuss the translational outcomes of treatment with these monoclonal antibodies in humans to shed light on the mechanisms underlying the main immunological and hematological findings from these clinical trials in humans.
The role of neutrophil‐to‐lymphocyte ratio in men with erectile dysfunction—preliminary findings of a real‐life cross‐sectional study
Authors: Ventimiglia E. , Cazzaniga W. , Pederzoli F. , Frego N. , Chierigo F. , Capogrosso P. , Boeri L. , Dehò F. , Abbate C. , Moretti D. , Piemonti L. , Montorsi F. , Salonia A. 
Published: April 2018

SummaryThe aim of this study was to investigate the role of systemic inflammation by means of the neutrophil‐to‐lymphocyte ratio (NLR) in men with erectile dysfunction (ED). Complete demographic, clinical, and laboratory data from 279 consecutive men with newly diagnosed ED were analyzed. Health‐significant comorbidities were scored with the Charlson Comorbidity Index (CCI). A complete blood count was requested for every man, and the NLR was calculated for every individual. Patients were invited to complete the IIEF questionnaire. Logistic regression models tested the odds (OR, 95% CI) of severe ED (defined as IIEF‐EF <11, according to Cappelleri's criteria) after adjusting for age, BMI, comorbidities (CCI >0), metabolic syndrome, NLR, cigarette smoking, and color duplex Doppler ultrasound parameters. Likewise, LNR values were also dichotomized according to the most informative cutoff predicting severe ED using the minimum p value approach. Median [IQR] age of included men was 51 [40–64] years. Of all, 87 (31%) men had severe ED. Men with severe ED were older (median [IQR] age: 61 [47–67] vs. 49 [39–58] years) and had a higher rate of CCI>0 [46/87 (53%) vs. 44/192 (23%) patients]. Thereof, NLR was dichotomized according to the most informative cutoff (NLR>3); patients with severe ED more frequently had NLR>3 as compared to all other ED patients [namely, 18/87 (21%) vs. 13/192 (7%)]. At multivariable logistic regression analysis, NLR>3.0 emerged as an independent predictor (OR [CI] 2.43 [1.06; 5.63]) of severe ED, after accounting for other clinical variables. A NLR>3 increased the risk of having severe ED in our cohort, boosting the already existing evidence linking systemic inflammation to ED. Moreover, this easily obtainable index can be clinically useful in better risk‐stratifying patients with ED.
Design of Bioartificial Pancreases From the Standpoint of Oxygen Supply
Authors: Iwata Hiroo , Arima Yusuke , Tsutsui Yusuke 
Published: April 2018

AbstractA bioartificial pancreas (BAP), in which islets of Langerhans (islets) are enclosed in a semipermeable membrane, has been developed to realize islet transplantation without the use of immunosuppressive drugs. Although recent progress in induced pluripotent stem (iPS) and embryonic stem (ES) cells has attracted attention owing to the potential applications of these cells as insulin‐releasing cells, concerns about the safety of implantation of these cells remain. The use of the BAP has the advantage of easy removal if insulin‐releasing cells derived from iPS/ES cells undesirably proliferate and form tumors in the BAP. Oxygen supply is a crucial issue for cell survival in BAPs as insufficient oxygen supply causes central necrosis of cell aggregates. In this study, we derived several simple equations considering oxygen supply in BAPs in order to provide insights into the rational design of three different types of BAPs (spherical microcapsules, cylindrical capsules, and planar capsules). The equations give (i) the thickness of a capsule membrane leading to no central necrosis of encapsulated cell aggregates as a function of the original size of the cell aggregate; (ii) the oxygen concentration profiles in BAPs; (iii) the effects of encapsulation of a cell aggregate on insulin release; (iv) the amount of encapsulated cells required to normalize blood glucose levels of a patient; and (v) the total volumes and sizes of BAPs. As an example, we used the equations in order to design three different types of BAPs for subcutaneous implantation.