bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing Resident Safety Culture in Six Nursing Homes in Belgium
Authors: Desmedt Melissa , Petrovic Mirko , Beuckelaere Petra , Vandijck Dominique
Published: March 2018

Objectives

The primary aim was to measure resident safety culture in six nursing homes in northern Belgium (Flanders). In addition, differences in safety culture perceptions between professions were also examined. Finally, results of the present study were compared with the Nursing Home Comparative Database from the Agency for Healthcare Research and Quality (USA).

Methods

A cross-sectional study was conducted by administering the Nursing Home Survey on Patient Safety Culture in six nursing homes in Belgium (Flanders). Each nursing home has 92 to 170 licensed nursing home beds. Data collection occurred between December 2016 and January 2017.

Results

Highest mean scores were found for “feedback and communication about incidents” (mean [SD] = 4.20 [0.58]), “overall perceptions of resident safety” (mean [SD] = 4.07 [0.52]), and “supervisor expectations and actions promoting resident safety” (mean [SD] = 4.04 [0.70]). The lowest mean score was found for “staffing” (mean [SD] = 2.99 [0.61]). In addition, managers/supervisors scored significantly higher on all resident safety dimensions, with the exception of the dimensions “teamwork” and “supervisor expectations and actions promoting resident safety.” Finally, the present study scored higher on the dimensions “teamwork,” “nonpunitive response to mistakes,” “handoffs,” “feedback and communication about incidents,” and “communication openness” than the benchmarking data from the Nursing Home Comparative Database.

Conclusions

More work is necessary to improve the safety of resident care in nursing homes, especially regarding staffing issues and turnover rates. The present research findings serve to shine a light on an often-overlooked patient population and emphasize the need to develop improvement strategies for preventing resident safety incidents in nursing homes.
Neisseria gonorrhoeae vaccine development: hope on the horizon?
Authors: Edwards Jennifer L. , Jennings Michael P. , Seib Kate L.
Published: March 2018

Purpose of review

Neisseria gonorrhoeae is one of the most common causes of sexually transmitted infections, with an estimated more than 100 million cases of gonorrhea each year worldwide. N. gonorrhoeae has gained recent increasing attention because of the alarming rise in incidence and the widespread emergence of multidrug-resistant gonococcal strains. Vaccine development is one area of renewed interest. Herein, we review the recent advances in this area.

Recent findings

Vaccine development for N. gonorrhoeae has been problematic, but recent progress in the field has provided new hope that a gonococcal vaccine may be feasible. Several new vaccine antigens have been characterized in various models of infection. Furthermore, the first potential vaccine-induced protection against gonorrhea in humans has been reported, with decreased rates of gonorrhea described among individuals vaccinated with the Neisseria meningitidis serogroup B vaccine, MeNZB.

As antibiotic resistance continues to increase, vaccine development for N. gonorrhoeae becomes more urgent. The MeNZB vaccine is shown to have efficacy, albeit relatively low, against N. gonorrhoeae. This finding has the potential to reinvigorate research in the field of gonococcal vaccine development and will guide future studies of the antigens and mechanism(s) required for protection against gonococcal infection.
Human adenovirus infections: update and consideration of mechanisms of viral persistence
Authors: Radke Jay R. , Cook James L.
Published: March 2018

Purpose of review

To provide an update on recent studies of human adenoviral (HAdV) infections and to explore the mechanisms of viral persistence and the role of persistent infection in disseminated disease in immunocompromised patients.

Recent findings

Human adenoviruses continue to be a problem in ophthalmology clinics and to cause periodic, limited, global outbreaks of respiratory disease. Ad14p1 remains in worldwide circulation and continues to result in miniepidemics of severe respiratory infections. New variants of Ad4 and Ad7 have emerged in both the United States and Asia. The severity of Ad4 infections in outbreaks appears to depend more on preexisting conditions in patients than on genetically determined, viral virulence factors, in contrast to limited evidence of Ad7 mutations that may convey increased viral pathogenesis. Reactivation of persistent adenovirus infection appears to be the primary source of disseminated infections in immunocompromised patients. New studies suggest that establishment of persistent infection and reactivation are related to variations in interferon-mediated control of viral replication.

Innate immune responses can create a state of adenoviral persistence, and repression of these host defenses can result in reactivation and dissemination of infection. A better definition of the molecular mechanisms of immune-mediated control of viral replication might lead to new strategies for treatment of HAdV reactivation and dissemination.
Group A Streptococcus infections in children: from virulence to clinical management
Authors: Botteaux Anne , Budnik Isolda , Smeesters Pierre R.
Published: March 2018

Purpose of review

Recent findings have open new perspectives on group A Streptococcus (GAS) virulence understanding with special focus on the carrier stage and new hopes for an efficient vaccine against this important pathogen.

Recent findings

Understanding of carriage state, transmission and role of virulence factors in invasive infections have been recently active research fields questioning the link between carriage and infections and highlighting the potential to prevent invasive diseases. New roles for already well known virulence factors, such as Streptolysin O, M protein or NAD(+)-glycohydrolase have been discovered. Immunological studies have also shown diversity in both clinical and immunological responses toward various GAS antigens raising questions, and hopes, for the development of an efficient global vaccine candidate.

A greater understanding of GAS virulence strategies, and their associated clinical manifestations, may be obtained by shifting our research scope toward virulence determinant interactions and cooperation rather than focusing on individual virulence factor or specific strain characterization only.
An Assessment of Organizational Health Literacy Practices at an Academic Health Center
Authors: Prince Latrina Y. , Schmidtke Carsten , Beck Jules K. , Hadden Kristie B.
Published: March 2018

Background:

Organizational health literacy is the degree to which an organization considers and promotes the health literacy of patients. Addressing health literacy at an organizational level has the potential to have a greater impact on more health consumers in a health system than individual-level approaches.

Objective:

The purpose of this study was to assess health care practices at an academic health center using the 10 attributes of a health-literate health care organization.

Methods:

Using a survey research design, the Health Literate Healthcare Organization 10-Item Questionnaire was administered online using total population sampling. Employees (N = 10 300) rated the extent that their organization's health care practices consider and promote patients' health literacy. Differences in responses were assessed using factorial analysis of variance.

Results:

The mean response was 4.7 on a 7-point Likert scale. Employee training and communication about costs received the lowest ratings. Univariate analyses revealed that there were no statistically significant differences (P = .05) by employees' health profession, years of service, or level of patient contact. There were statistically significant differences by highest education obtained with lowest ratings from employees with college degrees.

Conclusions:

Survey responses indicate a need for improvements in health care practices to better assist patients with inadequate health literacy.
Health Literacy Demands of Patient-Reported Evaluation Tools in Orthopedics: A Mixed-Methods Case Study
Authors: Hadden Kristie , Prince Latrina Y. , Barnes C. Lowry
Published: March 2018

Background:

In response to an assessment of organizational health literacy practices at a major academic health center, this case study evaluated the health literacy demands of patient-reported outcome measures commonly used in orthopedic surgery practices to identify areas for improvement.

Methods:

A mixed-methods approach was used to analyze the readability and patient feedback of orthopedic patient-reported outcome materials. Qualitative results were derived from focus group notes, observations, recordings, and consensus documents. Results were combined to formulate recommendations for quality improvement.

Results:

Readability results indicated that narrative portions of sample patient outcome tools were written within or below the recommended eighth-grade reading level (= 5.9). However, document literacy results were higher than the recommended reading level (= 9.8). Focus group results revealed that participants had consensus on 8 of 12 plain language best practices, including use of bullet lists and jargon or technical words in both instruments.

Conclusions:

Although the typical readability of both instruments was not exceedingly high, appropriate readability formula and assessment methods gave a more comprehensive assessment of true readability. In addition, participant feedback revealed the need to reduce jargon and improve formatting to lessen the health literacy demands on patients. As clinicians turn more toward patient-reported measures to assess health care quality, it is important to consider the health literacy demands that are inherent in the instruments they are given in our health systems.
A Stewardship Program to Optimize the Use of Inhaled Nitric Oxide in Pediatric Critical Care
Authors: Di Genova Tanya , Sperling Christina , Gionfriddo Ashley , Da Silva Zelia , Davidson Leanne , Macartney Jason , Finelli Michael , Jankov Robert P. , Laussen Peter C.
Published: March 2018

Purpose:

Inhaled nitric oxide (iNO) is a pulmonary vasodilator that is approved for use in term and near-term neonates with hypoxic respiratory failure associated with evidence of pulmonary hypertension. However, it is commonly used in infants and children to treat a variety of other cardiopulmonary diseases associated with pulmonary hypertension and hypoxic respiratory failure. In critically ill children, iNO therapy may be continued for a prolonged period, and this increases the risk for adverse consequences including toxicity and unnecessary costs. We implemented an iNO Stewardship Program with the aim of improving adherence to guidelines and reducing unnecessary iNO utilization.

Methods:

Between April 1, 2011, and March 31, 2015, a before and after cohort study was conducted at The Hospital for Sick Children. Prospective iNO usage and outcome variables in the poststewardship period were examined.

Results:

Patient characteristics and outcomes were similar before and after stewardship implementation. The number of iNO therapy courses were also similar in the before and after period. Inhaled nitric oxide utilization in the pediatric intensive care unit and the cardiac critical care unit decreased from 15 765 hours in the prestewardship period (April 2011 to March 2013) to 10 342 hours in the poststewardship period (April 2013 to March 2015), with significant improvement in adherence to the iNO guideline and a small decrease in expenditure (3%).

Conclusion:

Implementation of the iNO Stewardship was successful at reducing overall iNO utilization. This quality improvement initiative helped us optimize practice and subsequently expand the methodology to inform the clinical indication for iNO.
A Consensus Position Paper From REAL-PANLAR Group About the Methodological Approach for the Accreditation Process of Centers of Excellence in Rheumatoid Arthritis in Latin America
Authors: Santos-Moreno Pedro , Caballero-Uribe Carlo V. , Cardiel Mario H. , Galarza-Maldonado Claudio , Massardo Loreto , Pineda Carlos , Soriano Enrique , Castro Carlos Alberto , Villarreal Laura , Buitrago Diana
Published: March 2018

Background

By 2015, the World Health Organization reported that 1% of the world population suffered from rheumatoid arthritis (RA) and in Latin America (LA) between 0.5% and 1%. Previously, in May 2014, a consensus meeting was held in Barranquilla, Colombia, where the Project for Implementation and Accreditation of Centers of Excellence (CoE) in RA in LA was established, which then became an official special group of the Pan American League of Associations for Rheumatology (PANLAR).

Objective

The aim of this study was to define the methodological approach for the accreditation process of CoE in RA in LA.

Methods

A meeting was held in April 2015 with participation of the members of the REAL-PANLAR Steering Committee, and representatives of several LA countries, with the support of 2 experts in accreditation processes and models in Colombia. Then, in November 2015 in San Francisco and in November 2016 in Washington, the REAL-PANLAR Steering Committee met to discuss some final aspects of the project.

Results

The following steps for accreditation were defined: application for accreditation, issuance of the concept of assessment of the entity, accreditation decision, and monitoring accreditation.

Conclusions

This is the second REAL-PANLAR consensus paper with the purpose to define the parameters for the accreditation process for future CoE in RA in LA.
A Single-Center Retrospective Validation Study of the American College of Radiology Thyroid Imaging Reporting and Data System
Authors: Zheng Yi , Xu Shangyan , Kang Huili , Zhan Weiwei
Published: March 2018

Objective

This study aimed to evaluate a new risk stratification system, the American College of Radiology (ACR) Thyroid Imaging Reporting and Data System (TI-RADS), published in 2017.

Materials and Methods

From January 2015 to December 2016, 1033 thyroid nodules in 1013 patients who had undergone sonography and thyroid surgery or fine-needle aspiration (FNA) in our hospital were included. The sonographic features were described in a standard manner and analyzed according to the white paper of the ACR TI-RADS Committee. Nodules were assigned points for each feature, and the points were totaled to determine the final TI-RADS levels.

Results

Of the 1033 nodules, 725 were benign and 308 were malignant proven by operation or FNA. The malignant risk was associated with the composition, echogenicity, shape, margins, and echogenic foci of the nodules (P < 0.001). The calculated risk of malignancy was higher in nodules with macrocalcifications than those with peripheral calcifications, which is different from the ACR TI-RADS. The calculated malignancy rates of nodules with TR5, TR4, TR3, and TR2 were 67.1%, 13.0%, 1.1%, and 0%, respectively, which showed a higher malignant risk than the suggested threshold of TR5 in the ACR TI-RADS. Six nodules with TR4 recommended for no follow-up and 55 nodules with TR5 recommended for follow-up were malignant with cervical lymph node metastasis.

Conclusions

The ACR TI-RADS provides effective malignancy risk stratification for thyroid nodules and was useful for the decision for FNA. However, the points assigned for echogenic foci, the set of the TI-RADS risk thresholds, and FNA thresholds may need more consideration and prospective validation.
Superb Microvascular Imaging of Palatine Tonsils in Healthy Children
Authors: Caliskan Emine , Ozturk Mehmet , Bayramoglu Zuhal , Adaletli Ibrahim
Published: March 2018

In healthy children, the normal vascularity index (VI) values were defined for palatine tonsils using the superb microvascular imaging (SMI), and the relationship with potential factors affecting these values was assessed. This prospective study evaluated 74 children (age range = 3–17 years, median = 13 years, SD = 6.4 years). The cases were divided into 3 subgroups based on age as 3 to 6 years (preschool), 7 to 12 years (school age), and 13 to 17 years (adolescent). Demographic data such as sex, age, and body mass index (BMI) were recorded. The VI values of tonsils were measured with SMI and power Doppler (PD), and the correlation with descriptive data was researched. The Student t test, Mann-Whitney U test, and Spearman ρ correlation coefficient were used. The mean VI values on the right tonsil were calculated as 7.5% and 2.6% and on the left tonsil were 6.5% and 2.3% according to SMI and PD, respectively. On SMI, the vascularity was similar in the preschool and school-age groups, with a significant reduction between the school-age and adolescent groups. As BMI increased, tonsil vascularity reduced on SMI and PD. There was no significant difference in tonsil vascularity between the sexes. The VI values were identified to be higher on SMI compared with PD (P = 0.001). In healthy children, the normal VI values for both tonsils were determined with SMI and PD. On SMI, tonsil vascularity reduced significantly in the transition from school age to adolescence. Tonsil vascularity was affected by variations in BMI.
A Narrative Review on Contrast-Enhanced Ultrasound in Aortic Endograft Endoleak Surveillance
Authors: Gummadi Sriharsha , Eisenbrey John R. , Lyshchik Andrej
Published: March 2018

Endovascular repair of abdominal aortic aneurysms have been performed successfully since 1991. However, 20% to 50% of these patients may develop an endoleak or continued aneurysmal sac expansion or perfusion despite stent graft coverage. Current recommendations suggest lifelong surveillance with computed tomographic angiography (CTA) at least 1 month after intervention and yearly after that. In select patients with a stable aneurysm sac on computed tomography performed 1 year after treatment, future screening could be performed with ultrasonography. However, color Doppler ultrasound can fail to detect as many as 31% of endoleaks. Contrast-enhanced ultrasound (CEUS) provides an alternative approach to excluded aneurysm sac follow-up imaging. The Society for Vascular Surgery notes a need for further research on the role of CEUS in endovascular aortic repair surveillance. The European Federation of Societies for Ultrasound in Medicine and Biology suggests that early results are promising. Meta-analyses report pooled sensitivities and specificities of CEUS compared with CTA for the detection of endoleak between 89% and 98% and 86% and 88%, respectively. Owing to the dynamic flow information it provides, CEUS may actually be more sensitive than CTA at detection and characterization in select circumstances. Challenges with adoption, patient selection, and operator dependency remain, but current and future research suggests a role for CEUS in endoleak surveillance.
Healthcare Transition in Pediatrics and Young Adults With Inflammatory Bowel Disease
Authors: Rohatinsky Noelle , Risling Tracie , Kumaran Maha , Hellsten Laurie-ann M. , Thorp-Froslie Nancy
Published: March 2018

The incidence of inflammatory bowel disease has steadily increased in children within the last decade. As young adults transition into the adult healthcare system, lack of support can lead to disease exacerbations and disease-related complications. The purpose of this scoping review was to examine the current healthcare transition literature in pediatrics and young adults with inflammatory bowel disease, with a particular focus on assessment or screening tools to evaluate healthcare transition readiness. Five most relevant databases were searched. Of these, 22 articles met the inclusion criteria and key findings from these are summarized. The majority of articles focused on adolescents or young adults with inflammatory bowel disease and were primarily published in the United States. Since 2008, there has been a growing trend in publications of inflammatory bowel disease healthcare transition literature. Articles were often described as healthcare transition readiness assessment tools, patient outcomes following transition, or transition experiences and barriers. An understanding of the current literature on the readiness assessment and support strategies is required to promote an improved quality of life for pediatric and young adult patients living with inflammatory bowel disease.
Survival in Locally Advanced Pancreatic Cancer After Neoadjuvant Therapy and Surgical Resection
Authors: Gemenetzis Georgios , Groot Vincent P. , Blair Alex B. , Laheru Daniel A. , Zheng Lei , Narang Amol K. , Fishman Elliot K. , Hruban Ralph H. , Yu Jun , Burkhart Richard A. , Cameron John L. , Weiss Matthew J. , Wolfgang Christopher L. , He Jin
Published: March 2018

Objective:

The aim of the study was to identify the survival of patients with locally advanced pancreatic cancer (LAPC) and assess the effect of surgical resection after neoadjuvant therapy on patient outcomes.

Background:

An increasing number of LAPC patients who respond favorably to neoadjuvant therapy undergo surgical resection. The impact of surgery on patient survival is largely unknown.

Materials and Methods:

All LAPC patients who presented to the institutional pancreatic multidisciplinary clinic (PMDC) from January 2013 to September 2017 were included in the study. Demographics and clinical data on neoadjuvant treatment and surgical resection were documented. Primary tumor resection rates after neoadjuvant therapy and overall survival (OS) were the primary study endpoints.

Results:

A total of 415 LAPC patients were included in the study. Stratification of neoadjuvant therapy in FOLFIRINOX-based, gemcitabine-based, and combination of the two, and subsequent outcome comparison did not demonstrate significant differences in OS of 331 non-resected LAPC patients (P = 0.134). Eighty-four patients underwent resection of the primary tumor (20%), after a median duration of 5 months of neoadjuvant therapy. FOLFIRINOX-based therapy and stereotactic body radiation therapy correlated with increased probability of resection (P = 0.006). Resected patients had better performance status, smaller median tumor size (P = 0.029), and lower median CA19-9 values (P < 0.001) at PMDC. Patients who underwent surgical resection had significant higher median OS compared with those who did not (35.3 vs 16.3 mo, P < 0.001). The difference remained significant when non-resected patients were matched for time of neoadjuvant therapy (19.9 mo, P < 0.001).

Conclusions:

Surgical resection of LAPC after neoadjuvant therapy is feasible in a highly selected cohort of patients (20%) and is associated with significantly longer median overall survival.
Noninvasive neuromodulation in migraine and cluster headache
Authors: Starling Amaal
Published: March 2018

Purpose of review

The purpose of this narrative review is to provide an overview of the currently available noninvasive neuromodulation devices for the treatment of migraine and cluster headache.

Recent findings

Over the last decade, several noninvasive devices have undergone development and clinical trials to evaluate efficacy and safety. Based on this body of work, single-pulse transcranial magnetic stimulation, transcutaneous supraorbital neurostimulation, and noninvasive vagal nerve stimulation devices have been cleared by the United States Food and Drug Administration and are available for clinical use for the treatment of primary headache disorders.

Overall, these novel noninvasive devices appear to be safe, well tolerated, and have demonstrated promising results in clinical trials in both migraine and cluster headache. This narrative review will provide a summary and update of the proposed mechanisms of action, evidence, safety, and future directions of various currently available modalities of noninvasive neuromodulation for the treatment of migraine and cluster headache.
Representation of Borders and Swimming Kinematics in the Brain of Freely-Navigating Fish
Authors: Vinepinsky Ehud , Cohen Lear , Perchik Shay , Ben-Shahar Ohad , Donchin Opher , Segev Ronen
Published: March 2018

Like most animals, the survival of fish depends crucially on navigation in space. This capacity has been documented in numerous behavioral studies that have revealed navigation strategies and the sensory modalities used for navigation. However, virtually nothing is known about how freely swimming fish represent space and locomotion in the brain to enable successful navigation. Using a novel wireless neural recording system, we measured the activity of single neurons in the goldfish lateral pallium, a brain region known to be involved in spatial memory and navigation, while the fish swam freely in a two-dimensional water tank. Four cell types were identified: border cells, head direction cells, speed cells and conjunction head direction with speed. Border cells were active when the fish was near the boundary of the environment. Head direction cells were shown to encode head direction. Speed cells only encoded the absolute speed independent of direction suggestive of an odometry signal. Finally, the conjunction of head direction with speed cells represented the velocity of the fish. This study thus sheds light on how information related to navigation is represented in the brain of swimming fish, and addresses the fundamental question of the neural basis of navigation in this diverse group of vertebrates. The similarities between our observations in fish and earlier findings in mammals may indicate that the networks controlling navigation in vertebrate originate from an ancient circuit common across vertebrates.

Navigation is a fundamental behavioral capacity facilitating survival in many animal species. Fish is one lineage where navigation has been explored behaviorally, but it remains unclear how freely swimming fish represent space and locomotion in the brain. This is a key open question in our understanding of navigation in fish and more generally in understanding the evolutionary origin of the brain’s navigation system. To address this issue, we recorded neuronal signals from the brain of freely swimming goldfish and successfully identified representations of border and swimming kinematics in a brain region known to be associated with navigation. Our findings thus provide a glimpse into the building blocks of the neural representation underlying fish navigation. The similarity of the representation in fish with that of mammals may be key evidence supporting a preserved ancient mechanism across brain evolution.
The lysine demethylase dKDM2 is non-essential for viability, but regulates circadian rhythms in Drosophila
Authors: Zheng Yani , Xue Yongbo , Ren Xingjie , Xie Xiao-Jun , Liu Mengmeng , Jia Yu , Li Xiao , Niu Ye , Ni Jian-Quan , Zhang Yong , Ji Jun-Yuan
Published: March 2018

Post-translational modification of histones, such as histone methylation controlled by specific methyltransferases and demethylases, play critical roles in modulating chromatin dynamics and transcription in eukaryotes. Misregulation of histone methylation can lead to aberrant gene expression, thereby contributing to abnormal development and diseases such as cancer. As such, the mammalian lysine-specific demethylase 2 (KDM2) homologs, KDM2A and KDM2B, are either oncogenic or tumor suppressive, depending on specific pathological contexts. However, the role of KDM2 proteins during development in the whole organisms remains poorly understood. Unlike vertebrates, Drosophila has only one KDM2 homolog (dKDM2), but its functions in vivo remain elusive due to the complexities of the existing mutant alleles. To address this problem, we have generated two dKdm2 null alleles using the CRISPR/Cas9 technique. These dKdm2 homozygous mutants are fully viable and fertile, with no developmental defects observed under laboratory conditions. However, the dKdm2 null mutant adults display defects in circadian rhythms. Most of the dKdm2 mutants become arrhythmic under constant darkness, while the circadian period of the rhythmic mutant flies is approximately one hour shorter than the control. Interestingly, opposite defects are observed when dKDM2 is overexpressed in circadian pacemaker neurons. Taken together, these results demonstrate that dKdm2 is not essential for viability; instead, dKDM2 protein plays important roles in regulating circadian rhythms in Drosophila. Further analyses of the molecular mechanisms of how dKDM2 and its orthologs in vertebrates regulate circadian rhythms will advance our understanding of the epigenetic regulations of circadian clocks.
Entropic Forces Drive Clustering and Spatial Localization of Influenza A M2 During Viral Budding
Authors: Madsen Jesper J. , Grime John M. A. , Rossman Jeremy S. , Voth Gregory A.
Published: March 2018

The influenza A matrix 2 (M2) transmembrane protein facilitates virion release from the infected host cell. In particular, M2 plays a role in the induction of membrane curvature and/or in the scission process whereby the envelope is cut upon virion release. Here we show using coarse-grained computer simulations that various M2 assembly geometries emerge due to an entropic driving force, resulting in compact clusters or linearly extended aggregates as a direct consequence of the lateral membrane stresses. Conditions under which these protein assemblies will cause the lipid membrane to curve are explored and we predict that a critical cluster size is required for this to happen. We go on to demonstrate that under the stress conditions taking place in the cellular membrane as it undergoes large-scale membrane remodeling, the M2 protein will in principle be able to both contribute to curvature induction and sense curvature in order to line up in manifolds where local membrane line tension is high. M2 is found to exhibit linactant behavior in liquid-disordered/liquid-ordered phase-separated lipid mixtures and to be excluded from the liquid-ordered phase, in near-quantitative agreement with experimental observations. Our findings support a role for M2 in membrane remodeling during influenza viral budding both as an inducer and a sensor of membrane curvature, and they suggest a mechanism by which localization of M2 can occur as the virion assembles and releases from the host cell, independent of how the membrane curvature is produced.

SIGNIFICANCE STATEMENT

For influenza virus to release from the infected host cell, controlled viral budding must finalize with membrane scission of the viral envelope. Curiously, influenza carries its own protein, M2, which can sever the membrane of the constricted budding neck. Here we elucidate the physical mechanism of clustering and spatial localization of the M2 scission proteins through a combined computational and experimental approach. Our results provide fundamental insights into how M2 clustering and localization interplays with membrane curvature, membrane lateral stresses, and lipid bilayer phase behavior during viral budding in order to contribute to virion release.
Pisces: An Accurate and Versatile Variant Caller for Somatic and Germline Next-Generation Sequencing Data
Authors: Dunn Tamsen , Berry Gwenn , Emig-Agius Dorothea , Jiang Yu , Lei Serena , Iyer Anita , Udar Nitin , Chuang Han-Yu , Hegarty Jeff , Dickover Michael , Klotzle Brandy , Robbins Justin , Bibikova Marina , Peeters Marc , Strömberg Michael
Published: March 2018

Motivation

Next-Generation Sequencing (NGS) technology is transitioning quickly from research labs to clinical settings. The diagnosis and treatment selection for many acquired and autosomal conditions necessitate a method for accurately detecting somatic and germline variants, suitable for the clinic.

Results

We have developed Pisces, a rapid, versatile and accurate small variant calling suite designed for somatic and germline amplicon sequencing applications. Pisces accuracy is achieved by four distinct modules, the Pisces Read Stitcher, Pisces Variant Caller, the Pisces Variant Quality Recalibrator, and the Pisces Variant Phaser. Each module incorporates a number of novel algorithmic strategies aimed at reducing noise or increasing the likelihood of detecting a true variant.

Availability

Pisces is distributed under an open source license and can be downloaded from https://github.com/Illumina/Pisces. Pisces is available on the BaseSpace™ SequenceHub as part of the TruSeq Amplicon workflow and the Illumina Ampliseq Workflow. Pisces is distributed on Illumina sequencing platforms such as the MiSeq™, and is included in the Praxis™ Extended RAS Panel test which was recently approved by the FDA for the detection of multiple RAS gene mutations.

Contact

pisces@illumina.com

Supplementary information

Supplementary data are available online.
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences
Authors: Barbera Pierre , Kozlov Alexey M. , Czech Lucas , Morel Benoit , Darriba Diego , Flouri Tomáš , Stamatakis Alexandros
Published: March 2018

Next Generation Sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse microbial environments. To achieve this, phylogenetic placement methods determine how these sequences fit into an evolutionary context. Previous implementations of phylogenetic placement algorithms, such as the Evolutionary Placement Algorithm (EPA) included in RAxML, or pplacer, are being increasingly used for this purpose. However, due to the steady progress in NGS technologies, the current implementations face substantial scalability limitations. Here we present EPA-ng, a complete reimplementation of the EPA that is substantially faster, offers a distributed memory parallelization, and integrates concepts from both, RAxML-EPA, and pplacer. EPA-ng can be executed on standard shared memory, as well as on distributed memory systems (e.g., computing clusters). To demonstrate the scalability of EPA-ng we placed 1 billion metagenetic reads from the Tara Oceans Project onto a reference tree with 3,748 taxa in just under 7 hours, using 2,048 cores. Our performance assessment shows that EPA-ng outperforms RAxML-EPA and pplacer by up to a factor of 30 in sequential execution mode, while attaining comparable parallel efficiency on shared memory systems. We further show that the distributed memory parallelization of EPA-ng scales well up to 3,520 cores. EPA-ng is available under the AGPLv3 license: https://github.com/Pbdas/epa-ng
A structural mechano-chemical model for dynamic instability of microtubule
Authors: Stewman Shannon F. , Ma Ao
Published: March 2018

Microtubules are a major component of the cytoskeleton and vital to numerous cellular processes. The central dogma of microtubules is that all their functions are driven by dynamic instability; understanding its key phenomena (i.e. catastrophe, rescue, pause, differential behaviors at the plus and minus ends) distilled from a myriad of experiments under a consistent and unified scheme, however, has been unattainable. Here, we present a novel statistical-physics-based model uniquely constructed from conformational states deduced from existing tubulin structures, with transitions between them controlled by steric constraints and mechanical energy of the microtubule lattice. This mechano-chemical model allows, for the first time, all the key phenomena of dynamic instability to be coherently reproduced by the corresponding kinetic simulations. Long-puzzling phenomena, such as aging, small GTP-cap size, fast catastrophe upon dilution and temperature-induced ribbon-to-tube transition of GMPCPP-tubulins, robustly emerge and thus can be understood with confidence.
Dosage sensitivity of X-linked genes in human embryonic single cells
Authors: Yang Jian-Rong , Chen Xiaoshu
Published: March 2018

Fifty years ago, Susumu Ohno proposed that the expression levels of X-linked genes have doubled as dosage compensation for autosomal genes due to degeneration of Y-linked homologs during evolution of mammalian sex chromosomes. Recent studies have nevertheless shown that the X to autosome expression ratio equals ~1 in haploid human parthenogenetic embryonic stem (pES) cells and ~0.5 in diploid pES cells, thus refuting Ohno’s hypothesis. Here, by reanalyzing a RNA-seq-based single-cell transcriptome dataset of human embryos (Petropoulos, et al. 2016), we found that from the 8-cell stage until the time-point just prior to implantation, the expression levels of X-linked genes are not two-fold upregulated in male cells and gradually decrease from two-fold in female cells. This observation suggests that the expression levels of X-linked genes are imbalanced, with autosomal genes starting from the early 8-cell stage, and that the dosage conversion is fast, such that the X:AA expression ratio reaches ~0.5 in no more than a week. Additional analyses of gene expression noise further suggest that the dosage sensitivity of X-linked genes is weaker than that of autosomal genes in differentiated female cells, which contradicts a key assumption of Ohno’s hypothesis. Moreover, the dosage-sensitive housekeeping genes are preferentially located on autosomes, implying selection against X-linkage for dosage-sensitive genes. Our results collectively suggest an alternative to Ohno’s hypothesis that X-linked genes are less likely to be dosage sensitive than autosomal genes.
Branch-recombinant Gaussian processes for analysis of perturbations in biological time series
Authors: Penfold Christopher A. , Sybirna Anastasiya , Reid John , Huang Yun , Wernisch Lorenz , Ghahramani Zoubin , Grant Murray , Surani M. Azim
Published: March 2018

Motivation

A common class of behaviour encountered in the biological sciences involves branching and recombination. During branching, a statistical process bifurcates resulting in two or more potentially correlated processes that may under-go further branching; the contrary is true during recombination, where two or more statistical processes converge into one. A key objective is to identify the time of this bifurcation (branch time) from time series measurements e.g., comparing a control time series with a perturbed time series. Whilst statistical treatments for the two branch (control versus treatment) case exists, the ability to infer more complex branching structure from time series data remains open. Gaussian processes (GPs) represents an ideal framework for such analysis, allowing for nonlinear regression that includes a rigorous treatment of uncertainty. Currently, however, GP models only exist for two-branch systems. Here we highlight how arbitrarily complex branching processes can be built using the correct composition of covariance functions within a GP framework, thus outlining a general framework for the treatment of branching and recombination in the form of branch-recombinant Gaussian processes (B-RGPs). We first demonstrate the performance of B-RGPs compared to a variety of existing regression approaches, and demonstrate robustness to model misspecification. B-RGPs are then used to investigate the branching patterns ofArabidopsis thalianagene expression following inoculation with the hemibotrophic bacteria,Pseudomonas syringae DC3000, and a disarmed mutant strain, hrpA. By grouping genes according to the number of branches, we could naturally separate out genes involved in basal immune response from those subverted by the virulent strain, and show enrichment for targets of pathogen protein effectors. Finally, we identify two early branching genes WRKY11 and WRKY17, and showed that groups of genes that branched at similar times to WRKY11/17 were enriched for W-box binding motifs, and overrepresented for genes differentially expressed in WRKY11/17 knockouts, suggesting that branch time could be used for identifying direct and indirect binding targets of key transcription factors.Software is available from:https://github.com/cap76/BranchingGPs.
Chinese learner in a linguistically challenged environment – an exploratory study
Authors: Wong Grace , Dellaportas Steven , Cooper Barry J.
Published: March 2018

Purpose

The purpose of this paper is to explore the implications for student learning when accounting education is delivered in the student’s non-native language. It examines the impact on learning arising from the different components of English language competencies, namely, listening, reading, writing, and speaking.

Design/methodology/approach

The data are drawn from focus group interviews with students from Mainland China undertaking an accounting degree in Australia.

Findings

The findings indicate that students relied primarily on their reading instead of listening to seek understanding, and in turn, writing was considered less important compared to listening and reading. Notably, speaking was overlooked by many students as it was considered the least important skill necessary to achieve success as a student and to be a competent practitioner. Students developed a misconception that the quality of oral communication required of accountants in practice is unimportant.

Practical implications

The findings will assist accounting educators and the accounting profession in designing and implementing appropriate instructional strategies and assessment tasks for international students. One suggestion includes a more balanced weighting between written and oral assessment.

Originality/value

Few studies have specifically explored the impact of English language on learning accounting. While some studies examine specific aspects of language as a unitary concept, little has been reported on the impact of all components of the language skill-set on student learning.
The role of trip purpose and hotel star rating on guests’ satisfaction and WOM
Authors: Rajaguru Rajesh , Hassanli Najmeh
Published: March 2018

Purpose

This paper aims to understand how guests’ trip purpose and hotel star rating influence the effects of the value for money perceived at hotels and service quality on guest satisfaction and word of mouth (WOM) recommendation.

Design/methodology/approach

Using TripAdvisor, 25 Singaporean hotels were randomly selected for the study, which yielded hotel reviews from 2,040 respondents. Hierarchical and logistic regression analysis was conducted to investigate the relationships proposed in the study.

Findings

Results indicate significant differences between leisure and business guests’ perception of value for money and service quality at hotels with various star ratings. While perceived value for money and service quality were found as significant predictors for both leisure and business guests’ satisfaction and WOM, the effects were moderated by the hotel star rating. Despite the significant effect of hotel star rating on guest satisfaction, the study found no significant relationships between hotel star rating and WOM for leisure and business guests.

Practical implications

The findings suggest that managers in the hotel industry should understand the purpose of guests’ trip and offer services based on their expectations. As the star rating of a hotel creates certain expectations for both leisure and business guests, providing an appropriate level of services and assuring value for money in accordance with the hotel rating contributes to guest satisfaction and WOM recommendation.

Originality/value

This study contributes to the hospitality literature by investigating how hotel star rating moderates the relationship of value for money and service quality on leisure and business guests’ satisfaction and WOM recommendation.
Executive chefs’ calling: effect on engagement, work-life balance and life satisfaction
Authors: Cain Lisa , Busser James , Kang Hee Jung (Annette)
Published: March 2018

Purpose

This paper aims to understand the relationships among calling, employee engagement, work-life balance and life satisfaction for executive chefs based on role theory and spillover theory.

Design/methodology/approach

Surveys were completed by members of the American Culinary Federation in North America, the Nevada Restaurant Association and attendees at the ChefConnect Annual Conference. The data were analysed with confirmatory factor analysis and structural equation modelling.

Findings

All relationships in the model were significantly positive except for calling to life satisfaction. Importantly work-life balance was a significant mediator between calling and life satisfaction as well as for employee engagement and life satisfaction.

Research limitations/implications

The research provides a more comprehensive framework for hospitality scholars to understand the outcomes of work as a calling through meaningfulness. The sample of executive chef limits generalizability.

Practical implications

The identification of a calling through in-depth interviews is recommended. Once recognized, managers should further foster chef’s passion through employee engagement facilitated by workplace autonomy and continuing education and work-life balance supported with human resource management practices including time off for critical life events. This will allow calling to flourish, increase life satisfaction and reduce the likelihood of turnover and burnout.

Originality/value

Outcomes reveal the complexity of the relationship between calling and life satisfaction. Contrary to previous findings, the presence of positive work-life balance was critical to attain life satisfaction, even when work was viewed as a calling.
Evaluating hotel guest technologies: does home matter?
Authors: Beldona Srikanth , Schwartz Zvi , Zhang Xian
Published: March 2018

Purpose

With the advent of the smart home, where connectivity is facilitated by the internet of things, the provision of guest technologies in hotel service delivery has acquired greater significance. This ubiquity of technology implies that hotels need to view their technological offerings as facilitating guest’s broader lifestyles, and not just services in isolated spaces. This study aims to examine the role of “home” as a socio-technological unit, and how customers’ ownership of technologies at home affects evaluations of guest technologies at hotels.

Design/methodology/approach

Data are collected from a sample of US lodging consumers using Amazon’s Mechanical Turk. Partial least squares, which is a component-based structural equation modeling technique with SmartPLS 3.2, is used to test the hypotheses and meet the study’s objectives.

Findings

The findings show that hotel guest technologies should be of a higher standard than those at home, for guests to be satisfied with them. This relationship was robust across all hotel types, and both leisure and business visitation. Also, satisfaction with guest technologies has a relatively stronger impact on customer satisfaction in mid-scale and economy hotels compared to that in upscale and luxury hotels.

Research limitations/implications

By empirically validating “home” as a frame of reference in the evaluations of hospitality experiences, it opens up the potential for future research to study how home affects the evaluation of the hospitality experience as a whole.

Practical implications

Hotels need to identify viable technologies that have the potential to become mainstream, and be ahead of customers in the technology adoption curve.

Originality/value

This study is the first to look at home as a conceptual entity that is integral to hospitality using a socio-psychological lens, and evaluates its impact on evaluations of guest technologies at hotels.