bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of the Contact Lens User Experience: CLUE Scales
Authors: Wirth R. J. , Edwards Michael C. , Henderson Michael , Henderson Terri , Olivares Giovanna , Houts Carrie R. 
Published: July 2016

ABSTRACT

Purpose
The field of optometry has become increasingly interested in patient-reported outcomes, reflecting a common trend occurring across the spectrum of healthcare. This article reviews the development of the Contact Lens User Experience: CLUE system designed to assess patient evaluations of contact lenses. CLUE was built using modern psychometric methods such as factor analysis and item response theory.

Methods
The qualitative process through which relevant domains were identified is outlined as well as the process of creating initial item banks. Psychometric analyses were conducted on the initial item banks and refinements were made to the domains and items. Following this data-driven refinement phase, a second round of data was collected to further refine the items and obtain final item response theory item parameters estimates.

Results
Extensive qualitative work identified three key areas patients consider important when describing their experience with contact lenses. Based on item content and psychometric dimensionality assessments, the developing CLUE instruments were ultimately focused around four domains: comfort, vision, handling, and packaging. Item response theory parameters were estimated for the CLUE item banks (377 items), and the resulting scales were found to provide precise and reliable assignment of scores detailing users’ subjective experiences with contact lenses.

Conclusions
The CLUE family of instruments, as it currently exists, exhibits excellent psychometric properties.
Timely Hemodynamic Resuscitation and Outcomes in Severe Pediatric Traumatic Brain Injury
Authors: Kannan Nithya , Wang Jin , Mink Richard B. , Wainwright Mark S. , Groner Jonathan I. , Bell Michael J. , Giza Christopher C. , Zatzick Douglas F. , Ellenbogen Richard G. , Boyle Linda Ng , Mitchell Pamela H. , Rivara Frederick P. , Rowhani-Rahbar Ali , Vavilala Monica S. 
Published: July 2016

Objectives
Early resuscitation may improve outcomes in pediatric traumatic brain injury (TBI). We examined the association between timely treatment of hypotension and hypoxia during early care (prehospital or emergency department locations) and discharge outcomes in children with severe TBI.

Methods
Hypotension was defined as systolic blood pressure less than 70 + 2 (age in years), and hypoxia was defined as Pao
2 less than 60 mm Hg or oxygen saturation less than 90% in accordance with the 2003 Brain Trauma Foundation guidelines. Timely treatment of hypotension and hypoxia during early care was defined as the treatment within 30 minutes of a documented respective episode. Two hundred thirty-six medical records of children younger than 18 years with severe TBI from 5 regional pediatric trauma centers were examined. Main outcomes were in-hospital mortality and discharge Glasgow Outcome Scale (GOS) score.

Results
Hypotension occurred in 26% (60/234) during early care and was associated with in-hospital mortality (23.3% vs 8.6%; P = 0.01). Timely treatment of hypotension during early care occurred in 92% (55/60) by use of intravenous fluids, blood products, or vasopressors and was associated with reduced in-hospital mortality [adjusted relative risk (aRR), 0.46; 95% confidence interval, 0.24–0.90] and less likelihood of poor discharge GOS (aRR, 0.54; 95% confidence interval, 0.39–0.76) when compared to children with hypotension who were not treated in a timely manner. Early hypoxia occurred in 17% (41/236) and all patients received timely oxygen treatment.

Conclusions
Timely resuscitation during early care was common and associated with lower in-hospital mortality and favorable discharge GOS in severe pediatric TBI.
Multisite Single-Blinded Randomized Control Study of Transfer and Retention of Knowledge and Skill Between Nurses Using Simulation and Online Self-Study Module
Authors: Rutherford-Hemming Tonya , Kelsey Nichole C. , Grenig Deanna L. , Feliciano Michelle , Simko Leslie , Henrich Christina M. 
Published: July 2016

Introduction
Obstetric (OB) nurses must be proficient in performing a basic neurologic examination to assess and detect changes in a patients’ neurologic status. This study aimed to compare knowledge and skill acquisition for a basic neurologic examination between OB nurses who participated in simulation and those who participated in an online self-study module. Short- and long-term knowledge retention and skill transfer between groups were evaluated.

Methods
Nurses were randomized to either simulation or online self-study module and assessed by direct observation and completion of a standardized instrument by the observer at 3 time points: baseline (time 1), within 7 days of baseline in the clinical setting (time 2), and at 2 months (time 3) using a validated12-item Neurologic Knowledge Assessment and a 14-item performance skill checklist.

Results
Among OB nurses, those in the simulation group demonstrated higher levels in both short-term (time 2) [mean (SD), 67.6 (20.2) vs. 29.6 (19.0); P < 0.001] and long-term (time 3) [mean (SD), 46.1 (17.6) vs. 27.5 (15.9); P < 0.001] skill performance compared with nurses in the online self-study module. Nurses in the simulation and online self-study module groups had similar mean levels on Neurologic Knowledge Assessment scores at time 2 (P = 0.86) and time 3 (P = 0.59), but these mean scores were not significant.

Conclusions
The greater transfer of skills by nurses who received simulation education is an important finding because few studies have addressed this level of translation with practicing nurses. There was a lack of differences in short- and long-term knowledge acquisition between nurses in the simulation and online self-study module groups. More research is needed to determine the timing of simulation-based education repetition over time to aid in knowledge and skills retention.
Live Cell Partial Wave Spectroscopic microscopy: Label-free Imaging of the Native, Living Cellular Nano-architecture
Authors: Almassalha L. M. , Bauer G. M. , Chandler J. , Gladstein S. , Cherkezya L. , Stypula-Cyrus Y. , Weinberg S. , Zhang D. , Thusgaard Ruhoff P. , Roy H. , Subramanian H. , Chandel N. , Szleifer I. , Backman V. 
Published: July 2016

AbstractThe organization of chromatin is a regulator of molecular processes including transcription, replication, and DNA repair. The structures within chromatin that regulate these processes span from the nucleosomal (10nm) to the chromosomal (>200nm) levels, with little known about the dynamics of chromatin structure between these scales due to a lack of quantitative imaging technique in live cells. Previous work using Partial Wave Spectroscopic (PWS) microscopy, a quantitative imaging technique with sensitivity to macromolecular organization between 20-200nm, has shown that transformation of chromatin at these length scales is a fundamental event during carcinogenesis. As the dynamics of chromatin likely play a critical regulatory role in cellular function, it is critical to develop live-cell imaging techniques that can probe the real-time temporal behavior of the chromatin nano-architecture. Therefore, we developed a live cell PWS technique which allows high-throughput, label-free study of the causal relationship between nanoscale organization and molecular function in real-time. In this work, we employ live cell PWS to study the change in chromatin structure due to DNA damage and expand on the link between metabolic function and the structure of higher-order chromatin. In particular, we studied the temporal changes to chromatin during UV light exposure, show that live cell DNA binding dyes induce damage to chromatin within seconds, and demonstrate a direct link between higher-order chromatin structure and mitochondrial membrane potential. Since biological function is tightly paired with structure, live cell PWS is a powerful tool to study the nanoscale structure-function relationship in live cells.Significance StatementChromatin is one of the most critical structures within the cell because it houses most genetic information. Its structure is well understood at the nucleosomal (<20nm) and chromosomal (>200nm) levels, however, due to the lack of quantitative imaging modalities to study this organization, little is known about the higher-order structure between these length scales in live cells. We present a label-free technique, live cell Partial Wave Spectroscopic (PWS) microscopy with sensitivity to structures between 20-200nm that can quantify the nano-architecture in live cells. With this technique, we can detect DNA fragmentation and expand on the link between metabolic function and higher-order chromatin structure. Live cell PWS allows high-throughput, label-free study of the causal relationship between nanoscale organization and molecular function in live cells.
Hearing scenes: A neuromagnetic signature of perceived auditory spatial extent
Authors: Teng Santani , Sommer Verena , Pantazis Dimitrios , Oliva Aude 
Published: July 2016

SummaryPerceiving the geometry of surrounding space is a multisensory process, crucial to contextualizing object perception and guiding navigation behavior. Auditory cues are informative about the shape and extent of large-scale environments: humans can make judgments about surrounding spaces from reverberation cues. However, how the scale of auditory space is represented neurally is unknown. Here, by orthogonally varying the spatial extent and sound source content of auditory scenes during magnetoencephalography (MEG) recording, we report a neural signature of auditory space size perception, starting ~145 ms after stimulus onset. Importantly, this neuromagnetic response is readily dissociable in form and time into representations of the source and its reverberant enclosing space: while the source exhibits an early and transient response, the neural signature of space is sustained and independent of the original source that produced it. Further, the space size response is robust to variations in sound source, and vice versa. The MEG decoding signal was distributed primarily across bilateral temporal sensor locations, significantly correlated with behavioral responses in a separate experiment. Together, our results provide the first neuromagnetic evidence for a robust auditory space size representation in the human brain, sensitive to reverberant decay, and reveal the temporal dynamics of how such a code emerges over time from the transformation of complex naturalistic auditory signals.
Immunoecology of species with alternative reproductive tactics and strategies
Authors: Lozano George A. , Ros Albert F. H. 
Published: July 2016

AbstractAlternative reproductive tactics and strategies (ARTS) refer to polymorphic reproductive behaviours in which in addition to the usual two sexes, there are one or more alternative morphs, usually male, that have evolved the ability to circumvent direct intra-sexual competition. Each morph has its own morphological, ecological, developmental, behavioural, life-history, and physiological profile that shifts the balance between reproduction and self-maintenance, one aspect being immunity. Immunoecological work on species with ARTS, which is the topic of this review, is particularly interesting because the alternative morphs make it possible to separate the effects of sex,per se, from other factors that in other species are inextricably linked with sex. We first summarize the evolution, development and maintenance of ARTS. We then review immunoecological hypotheses relevant to species with ARTS, dividing them into physiological, life-history, and ecological hypotheses. In context of these hypotheses, we critically review in detail all immunoecological studies we could find on species with ARTS. Several interesting patterns emerge. Oddly, there is a paucity of studies on insects, despite the many benefits that arise from working with insects: larger sample sizes, simple immune systems, and countless forms of alternative reproductive strategies and tactics. Of all the hypotheses considered, the immunocompetence handicap hypothesis has generated the greatest amount of work, but not necessarily the greatest level of understanding. Unfortunately, it is often used as a general guiding principle rather than a source of explicitly articulated predictions. Other hypotheses are usually considereda posteriori, but it is perhaps time that they take centre stage. Whereas blanket concepts such as “immunocompetence” and “androgens” might useful to develop a rationale, predictions need to be far more explicitly articulated. Integration so far has been a one-way street, with ecologists delving deeper into physiology, seemingly at the cost of ignoring their organisms’ evolutionary history and ecology. One possible useful framework is to divide ecological and evolutionary factors affecting immunity into those that stimulate the immune system, and those that depress it. Finally, the contributions of genomics to ecology are being increasingly recognized, including in species with ARTS, but we must ensure that evolutionary and ecological hypotheses drive the effort, as there is no grandeur in the strict reductionist view of life.
HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
Authors: Kamath Govinda M. , Shomorony Ilan , Xia Fei , Courtade Thomas A. , Tse David N. 
Published: July 2016

ABSTRACTLong-read sequencing technologies have the potential to produce gold-standard de novo genome assemblies, but fully exploiting error-prone reads to resolve repeats remains a challenge. Aggressive approaches to repeat resolution often produce mis-assemblies, and conservative approaches lead to unnecessary fragmentation. We present HINGE, an assembler that seeks to achieve optimal repeat resolution by distinguishing repeats that can be resolved given the data from those that cannot. This is accomplished by adding "hinges" to reads for constructing an overlap graph where only unresolvable repeats are merged. As a result, HINGE combines the error resilience of overlap-based assemblers with repeat-resolution capabilities of de Bruijn graph assemblers. HINGE was evaluated on the long-read bacterial datasets from the NCTC project. HINGE produces more finished assemblies than Miniasm and the manual pipeline of NCTC based on the HGAP assembler and Circlator. HINGE also allows us to identify 40 datasets where unresolvable repeats prevent the reliable construction of a unique finished assembly. In these cases, HINGE outputs a visually interpretable assembly graph that encodes all possible finished assemblies consistent with the reads, while other approaches such as the NCTC pipeline and FALCON either fragment the assembly or resolve the ambiguity arbitrarily.
MINOTAUR: A platform for the analysis and visualization of multivariate results from genome scans with R Shiny
Authors: Verity Robert , Collins Caitlin , Card Daren C. , Schaal Sara M. , Wang Liuyang , Lotterhos Katie E. 
Published: July 2016

AbstractGenome scans are widely used to identify “outliers” in genomic data: loci with different patterns compared with the rest of the genome due to the action of selection or other non-adaptive forces of evolution. These genomic datasets are often high-dimensional, with complex correlation structures among variables, making it a challenge to identify outliers in a robust way. The Mahalanobis distance has been widely used for this purpose, but has the major limitation of assuming that data follow a simple parametric distribution. Here we develop three new metrics that can be used to identify outliers in multivariate space, while making no strong assumptions about the distribution of the data. These metrics are implemented in the R package MINOTAUR, which also includes an interactive web-based application for visualizing outliers in high-dimensional datasets. We illustrate how these metrics can be used to identify outliers from simulated genetic data, and discuss some of the limitations they may face in application.
iDamIDseq and iDEAR: An improved method and a computational pipeline to profile chromatin-binding proteins of developing organisms
Authors: Gutierrez-Triana Jose Arturo , Mateo Juan L. , Ibberson David , Wittbrodt Joachim 
Published: July 2016

AbstractDNA adenine methyltransferase identification (DamID) has emerged as an alternative for profiling protein-DNA interactions, however critical issues in the method limit its applicability. Here we present iDamlDseq, a protocol that improves specificity and robustness making its use compatible with developing organisms. In addition, we present the analysis tool iDEAR (iDamlDseq Enrichment Analysis with R) to determine protein-DNA interactions genome wide. The combination of both allows establishing highly reliable transcription factor profiles, even in transient assays. For tissue specific expression we improved the Dam coding sequence to overcome predominant aberrant splicing of Dam fusions we discovered with the commonly used sequence.
Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments
Authors: Robson Michael I. , de las Heras Jose I. , Czapiewski Rafal , Sivakumar Aishwarya , Kerr Alastair R. W. , Schirmer Eric C. 
Published: July 2016

AbstractThe 3D organization of the genome changes concomitantly with expression changes during hematopoiesis and immune activation. However, studies of this phenomenon have focused either on lamina-associated domains (LADs) or on topologically-associated domains (TADs), defined by preferential local chromatin interactions, and chromosome compartments, defined as higher-order interactions between TADs in functionally similar states. However, few studies have investigated how these affect one another. To address this, we mapped LADs using Lamin B1-DamID during Jurkat T-cell activation, finding significant genome re-organization at the nuclear periphery dominated by release of loci frequently important for T-cell function. To assess how these changes at the nuclear periphery influence wider genome organization, our DamID datasets were contrasted with TAD contact domains and compartments identified with high resolution in the GM12878 lymphoblastoid cell line. Features of specific repositioning events were then tested by fluorescencein situhybridization. First, considerable overlap between TAD contact domains and LADs was observed and we found that the TAD repositioned as a unit during T-cell activation. Second, sub-compartments of the A compartment, termed A1 and A2, are segregated in 3D space through differences in proximity to LADs along chromosomes. Third, genes and a putative enhancer that occurred in LADs that were released from the periphery during T-cell activation tended to become associated particularly with A2 sub-compartments and were thus constrained to the relative proximity of the lamina. Thus, lamina-associations clearly influence internal nuclear organization while changes in LADs during T-cell activation may provide an important additional mode of gene regulation.
Host genetic variation in mucosal immunity pathways influences the upper airway microbiome
Authors: Igartua Catherine , Davenport Emily R , Gilad Yoav , Nicolae Dan , Pinto Jayant , Ober Carole 
Published: July 2016

ABSTRACTThe degree to which host genetic variation can modulate microbial communities in humans remains an open question. Here we performed a genetic mapping study of the microbiome in two accessible upper airway sites, the nasopharynx and the nasal vestibule, during two seasons in 144 adult members of a founder population of European decent. We estimated the relative abundances (RAs) of genus level bacteria from 16S rRNA gene sequences and examined associations with 148,653 genetic variants (linkage disequilibrium [LD] r2< 0.5) selected from among all common variants discovered in genome sequences in this population. We identified 37 microbiome quantitative trait loci (mbQTLs) that showed evidence of association with the RAs of 22 genera (q < 0.05), and were enriched for genes in mucosal immunity pathways. The most significant association was between the RA ofDermacoccus(phylum Actinobacteria) and a variant 8kb upstream ofTINCR(rs117042385; p = 1.61⨯10−8; q = 0.002), a long non-coding RNA that binds to peptidoglycan recognition protein 3 (PGLYRP3) mRNA, a gene encoding a known antimicrobial protein. A second association was between a missense variant inPGLYRP4(rs3006458) and the RA of an unclassified genus of family Micrococcaceae (phylum Actinobacteria) (p = 5.10⨯10−7; q = 0.032). Our findings provide evidence of host genetic influences on upper airway microbial composition in humans, and implicate mucosal immunity genes in this relationship.
Intra-organisational injustice in the construction industry
Authors: Loosemore Martin , Lim Benson Teck-Heng 
Published: July 2016

Purpose
– Increasing workforce casualisation, under representation of women and other minority groups, racial discrimination, corruption and poor safety are just some of the documented examples of intra-organisational injustice in the industry. Typically these issues are problematised separately using different theoretical frameworks, yet at the most fundamental behavioural level they have a common cause which lies in the “unjust” treatment of one person by another. The purpose of this paper is to integrate the conceptual understanding of these hitherto separated but conceptually linked problems.

Design/methodology/approach
– A survey 135 consultants, contractors, subcontractors and suppliers from across the Australian construction supply chain.

Findings
– Surprisingly despite widespread academic concerns about injustice in the construction industry, there are not significant concerns within the industry community. Contrary to much research about the poor culture of the construction industry, the results indicate that the relatively low levels of perceived injustice are institutional rather than cultural. The research also highlights the plight of middle management, which appear to consistently suffer the highest levels of injustice across all its theoretical categories.

Research limitations/implications
– Sample size and Australian focus.

Practical implications
– Informs organisational policies to reduce injustice in the construction industry.

Social implications
– By reducing injustice, this research will improve the fairness of business practices in the construction industry.

Originality/value
– Application of justice theories to conceptualise unfair construction practices.