bluuebunny/crossref_metadata_2025 huggingface dataset:
Reconstructing phylogeny from linkage diffusion
Authors: Pelkey Jamin
Published: November 2015

Linkage models of language diversification (Ross 1988, François 2014) represent the slow differentiation of closely related sister languages via dialect continua. Such historical relationships are said to prevent the reconstruction of branchinternal phylogeny. A newly defined mode of linkage variation challenges this restriction. In cladistic hinge diversification, speakers of a geographically central variety mediate innovations between isolated extremes of a sub-branch, while all three daughter branches maintain evidence of their own exclusive innovations. The resulting pattern blends linkage relations with family relations. Following a contextual review, the paper presents supporting evidence for the distinction from the Phowa languages of southwest China (Ngwi < Burmic < Tibeto-Burman). Data analysis includes sociohistory, dialectometry and genetic linguistic components. The argument affirms both wave and tree models of language change, enabling an enriched understanding of focal, relic and transition areas and their influence on the leveling, development and diffusion of linguistic innovations.
An exceptional career, a lasting legacy
Authors: Bowcher Wendy L.
Published: November 2015

Ruqaiya Hasan passed away on the 24th of June 2015 not long after complications arose following treatment for lung cancer. She had a remarkable career during which she played a major role in directing the trajectory of Systemic Functional Linguistic research.
A corpus-based investigation into key words and key patterns in post-war fiction
Authors: Siepmann Dirk
Published: November 2015

This study is an exploratory investigation into lexico-grammatical items specific to a large corpus of English-language post-war novels, as compared to corpora of conversation, news and academic English. Its overall aim is threefold: first, to show how the subjective impression of ‘literariness’ arising from fictional works is at least partly based on the statistically significant use of highly specific words and lexico-grammatical configurations; second, to attempt a broad classification of key words and patterns; third, to illustrate the fiction-specific patterns formed by three key words. Analysis proceeded in three steps. First, a key word analysis was performed. In the second step, all two-to-five word strings contained in the English corpus were generated. In the third step, multi-word strings, collocations and colligations associated with three English key words (‘thought’, ‘sun’ and ‘jerk’) were analysed. Results indicate that post-war fiction is characterized by the dense use of specific sets of key words and key patterns, such as multi-word strings (must have been), phrase frames (like a + NP,there was a + NP) colligations (PossDetthoughts were onNP), collocations (the strengthening sun) and lexically specific narrative patterns (PossDetthoughts were interrupted when/as + time clause). The patterns in question are shown to be interconnected through a complex web of analogical creations. Implications are discussed for theories of literature, lexicology and translation.
RNA-Enrich: a cut-off free functional enrichment testing method for RNA-seq with improved detection power
Authors: Lee Chee , Patil Snehal , Sartor Maureen A.
Published: November 2015

Summary: Tests for differential gene expression with RNA-seq data have a tendency to identify certain types of transcripts as significant, e.g. longer and highly-expressed transcripts. This tendency has been shown to bias gene set enrichment (GSE) testing, which is used to find over- or under-represented biological functions in the data. Yet, there remains a surprising lack of tools for GSE testing specific for RNA-seq. We present a new GSE method for RNA-seq data, RNA-Enrich, that accounts for the above tendency empirically by adjusting for average read count per gene. RNA-Enrich is a quick, flexible method and web-based tool, with 16 available gene annotation databases. It does not require a P-value cut-off to define differential expression, and works well even with small sample-sized experiments. We show that adjusting for read counts per gene improves both the type I error rate and detection power of the test.

Availability and implementation: RNA-Enrich is available at http://lrpath.ncibi.org or from supplemental material as R code.

Contact:  sartorma@umich.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Simulated diurnal pH fluctuations radically increase variance in—but not the mean of—growth in the barnacle Balanus improvisus
Authors: Eriander L. , Wrange A.-L. , Havenhand J. N.
Published: November 2015

Shallow coastal waters are characterized by substantial diurnal fluctuations in pH, especially in nearshore environments. The biological effects of ocean acidification in combination with these natural fluctuations have received relatively little attention to date. We exposed multiple batches (≈ different genotypes) of newly settled barnacles, Balanus improvisus, to constant pH under “control” (pH = 8.1) or “stable acidified” (pH = 7.7) conditions, as well as a treatment that simulated the maximum diurnal pH fluctuations seen in the nearshore habitats where this barnacle lives (±0.2 pH units), superimposed on the stable acidified treatment (“fluctuating acidified”; 7.5 ≤ pH ≤ 7.9). We found that fluctuating acidification had no effect on mean response in growth and shell mineralogy, but caused an ∼20-fold increase in variance of responses, compared with stable acidification. In contrast to these results, we found no effect of fluctuating acidification on variances of response ratios for barnacle survival and shell strength. Similarly, mean survival did not vary significantly with pH. However, we observed a strong negative effect of stable and fluctuating acidification on mean shell strength. Our finding that barnacles respond differently to fluctuating pH than to stable low pH indicate the importance of including fluctuating acidification treatments when studying species that live in variable environments. Importantly, because phenotypic variance is the raw material for natural selection, and thus lays at the heart of evolutionary responses to environmental variability and change, our findings also highlight the need to study changes in variance of—as well as mean—responses to changing ocean climates.
A data-driven approach for quality assessment of radiologic interpretations
Authors: Hsu William , Han Simon X , Arnold Corey W , Bui Alex AT , Enzmann Dieter R
Published: November 2015

Given the increasing emphasis on delivering high-quality, cost-efficient healthcare, improved methodologies are needed to measure the accuracy and utility of ordered diagnostic examinations in achieving the appropriate diagnosis. Here, we present a data-driven approach for performing automated quality assessment of radiologic interpretations using other clinical information (e.g., pathology) as a reference standard for individual radiologists, subspecialty sections, imaging modalities, and entire departments. Downstream diagnostic conclusions from the electronic medical record are utilized as “truth” to which upstream diagnoses generated by radiology are compared. The described system automatically extracts and compares patient medical data to characterize concordance between clinical sources. Initial results are presented in the context of breast imaging, matching 18 101 radiologic interpretations with 301 pathology diagnoses and achieving a precision and recall of 84% and 92%, respectively. The presented data-driven method highlights the challenges of integrating multiple data sources and the application of information extraction tools to facilitate healthcare quality improvement.
Principles of Partnerships Between Public Health and Primary Care
Authors: Michener J. Lloyd , Castrucci Brian C. , Koo Denise
Published: November 2015

Drawing on the experiences of hundreds of public health and primary care clinicians from across the United States, this book explains why population health is receiving so much attention from policy makers in states and federal agencies, the practical steps that clinicians and public health professionals can take to work together to meet the needs of their community, signs that you are on the right track (or not) and how to sustain successes to the benefit of patients, community members, and the health care and public health teams that care for them.
Stages of Partnerships Between Public Health and Primary Care
Authors: Michener J. Lloyd , Castrucci Brian C.
Published: November 2015

Drawing on the experiences of hundreds of public health and primary care clinicians from across the United States, this book explains why population health is receiving so much attention from policy makers in states and federal agencies, the practical steps that clinicians and public health professionals can take to work together to meet the needs of their community, signs that you are on the right track (or not) and how to sustain successes to the benefit of patients, community members, and the health care and public health teams that care for them.
The Practice of Public Health and How It Is Changing
Authors: Castrucci Brian C. , Tilson Hugh H. , Koo Denise , Leider Jonathon P.
Published: November 2015

Drawing on the experiences of hundreds of public health and primary care clinicians from across the United States, this book explains why population health is receiving so much attention from policy makers in states and federal agencies, the practical steps that clinicians and public health professionals can take to work together to meet the needs of their community, signs that you are on the right track (or not) and how to sustain successes to the benefit of patients, community members, and the health care and public health teams that care for them.
Return on Investment and Economic Evaluation
Authors: Teutsch Steven M. , Koo Denise , Grosse Scott D.
Published: November 2015

Drawing on the experiences of hundreds of public health and primary care clinicians from across the United States, this book explains why population health is receiving so much attention from policy makers in states and federal agencies, the practical steps that clinicians and public health professionals can take to work together to meet the needs of their community, signs that you are on the right track (or not) and how to sustain successes to the benefit of patients, community members, and the health care and public health teams that care for them.
Use of Electronic Health Records for Population Health
Authors: Koo Denise , King Raymond J. , Foldy Seth
Published: November 2015

Drawing on the experiences of hundreds of public health and primary care clinicians from across the United States, this book explains why population health is receiving so much attention from policy makers in states and federal agencies, the practical steps that clinicians and public health professionals can take to work together to meet the needs of their community, signs that you are on the right track (or not) and how to sustain successes to the benefit of patients, community members, and the health care and public health teams that care for them.
Using Geographic Health Information Systems for Population Health
Authors: Tootoo Joshua L. , Castrucci Brian C. , Maxson Pamela , Casper Michele , Miranda Marie Lynn
Published: November 2015

Drawing on the experiences of hundreds of public health and primary care clinicians from across the United States, this book explains why population health is receiving so much attention from policy makers in states and federal agencies, the practical steps that clinicians and public health professionals can take to work together to meet the needs of their community, signs that you are on the right track (or not) and how to sustain successes to the benefit of patients, community members, and the health care and public health teams that care for them.
Data and the Future of Public Health
Authors: Engel Jeffrey
Published: November 2015

Drawing on the experiences of hundreds of public health and primary care clinicians from across the United States, this book explains why population health is receiving so much attention from policy makers in states and federal agencies, the practical steps that clinicians and public health professionals can take to work together to meet the needs of their community, signs that you are on the right track (or not) and how to sustain successes to the benefit of patients, community members, and the health care and public health teams that care for them.
“Top-Down” and “Bottom-Up” Initiatives Create a Comprehensive Prescription Drug Overdose Prevention Program in North Carolina
Authors: Watson Virginia
Published: November 2015

Drawing on the experiences of hundreds of public health and primary care clinicians from across the United States, this book explains why population health is receiving so much attention from policy makers in states and federal agencies, the practical steps that clinicians and public health professionals can take to work together to meet the needs of their community, signs that you are on the right track (or not) and how to sustain successes to the benefit of patients, community members, and the health care and public health teams that care for them.
Essay The Value of Early Wins in Be Well Lake County
Authors: Arnold Christina
Published: November 2015

Drawing on the experiences of hundreds of public health and primary care clinicians from across the United States, this book explains why population health is receiving so much attention from policy makers in states and federal agencies, the practical steps that clinicians and public health professionals can take to work together to meet the needs of their community, signs that you are on the right track (or not) and how to sustain successes to the benefit of patients, community members, and the health care and public health teams that care for them.
Coma
Authors: Fugate Jennifer , Wijdicks Eelco
Published: November 2015

Coma is an ominous sign and has been known since antiquity. Over several decades, a much better understanding of the mechanisms of coma, patterns of brain tissue shift, and its clinical correlates has developed. Methods of the examination and the details of approaching a diagnosis of patients in coma have evolved gradually over this time. In this chapter, the key articles that formed the basis of this evaluation are discussed. These articles offer an understanding of how the current level of sophistication regarding determination of the severity of brain injury, of improvement potential, and of an appropriate level of care was reached.
Dementia
Authors: Burrell James R. , Hodges John R.
Published: November 2015

Cognitive neurology has exploded over the last century, and especially over the last 20 years. From the distinction of dementia as a pathological entity, rather than just ‘normal’ ageing, to more sophisticated sub-classification of dementia syndromes, much has been learned, though great challenges remain. From an incredible array of worthy research studies, ten landmark papers in the field of dementia are presented in this chapter. With regard to Alzheimer’s disease, the following are discussed: the initial description of the disease, both clinically and pathologically; the development of meaningful clinical assessment measures; the early clinical manifestations and genetic causes; the precursors to symptomatic treatment; the use of neuroimaging to identify amyloid pathology in vivo; and the staging of Alzheimer’s pathology. The clinical features and genetic causes of frontotemporal dementia, an important non-Alzheimer’s primary dementia syndrome seen especially in younger patients, are also discussed.
Myology
Authors: Swash Michael
Published: November 2015

Diseases of muscle have become better understood by careful clinical observations, resulting in a clinically useful classification of the different groups of disorders e.g. inherited muscular dystrophies such as Duchenne muscular dystrophy, limb-girdle and metabolic myopathies, and myotonic disorders. A number of scientific approaches have determined the directions taken by this evolving classification. Understanding of the anatomy of the motor unit’s distribution in muscle transformed muscle pathology and muscle electrophysiology, and key to these pathological advances was the use of the histochemical technique for identifying myofibrillar ATPase in muscle fibres. This allowed studies of the distribution of fibre types in muscle in many different disorders. The inflammatory muscle diseases have been better understood since recent advances in immunology have characterized the underlying processes. The limb-girdle and childhood myopathies have proven to be heterogeneous, with many different, apparently causative, underlying genetic mutations.
Seasonal Variation in the Presentation of Infectious Keratitis
Authors: Gorski Matthew , Genis Alina , Yushvayev Sharon , Awwad Ahmed , Lazzaro Douglas R.
Published: November 2015

Introduction:

Infectious keratitis is a common ophthalmic disease with the potential for severe ocular morbidity. Multiple studies have described various risk factors for the development of infectious keratitis. The purpose of this study was to analyze the seasonal variation in the presentation of infectious keratitis, and also seasonal changes in its etiologies and risk factors.

Methods:

A retrospective chart review was performed on consecutive patients presenting to the emergency department at our tertiary care urban hospital center who were diagnosed with infectious keratitis from 2008 to 2013. A chi-square analysis was performed to determine whether a significant seasonal variation existed between the month, season, frequency of presentation of ulcers, and other risk factors.

Results:

A total of 155 patients—53 men and 102 women—with a mean age of 40 (range, 3–97; median, 36) diagnosed with infectious keratitis were included in the analysis. Sixty-nine (44.5%) ulcers presented in the summer, 19 (12.3%) in the fall, 34 (21.9%) in the winter, and 33 (21.3%) in the spring (P<0.0001). Seventeen (11%) patients experienced diabetes mellitus, 60 (39%) were contact lens wearers, 12 (8%) ulcers occurred in the setting of trauma, and 19 (12%) patients underwent previous ocular surgery. A total of 92 ulcers were cultured, of which 53.8% were positive in the summer, 42.9% in the fall, 55.0% in the winter, and 42.1% in the spring. A significant seasonal variation in the frequency of 1 organism, Pseudomonas aeruginosa, was identified (P=<0.0001); up to 47.6% of culture-positive ulcers in the summer were P. aeruginosa positive, whereas cultures in the remaining seasons were 0, 9.1% and 12.5% positive for this organism.

Discussion:

The summer months have a higher frequency of infectious keratitis and P. aeruginosa positivity in this study. Possible factors leading to this increased summer presentation include warmer temperatures, higher humidity, and greater ocular exposure to water. Clinicians should increase their vigilance and education to high-risk patients during these periods and potentially modify empiric treatment regimens.
Spread of the pandemic Zika virus lineage is associated with NS1 codon usage adaptation in humans
Authors: Freire Caio Cesar de Melo , Iamarino Atila , Neto Daniel Ferreira de Lima , Sall Amadou Alpha , Zanotto Paolo Marinho de Andrade
Published: November 2015

Zika virus (ZIKV) infections were more common in the zoonotic cycle until the end of the 20th century with few human cases in Africa and Southeastern Asia. Recently, the Asian lineage of ZIKV is spreading along human-to-human chains of transmission in the Pacific Islands and in South America. To better understand its recent urban expansion, we compared genetic differences among the lineages. Herein we show that the recent Asian lineage spread is associated with significant NS1 codon usage adaptation to human housekeeping genes, which could facilitate viral replication and increase viral titers. These findings were supported by a significant correlation with growth in Malthusian fitness. Furthermore, we predicted several epitopes in the NS1 protein that are shared between ZIKV and Dengue. Our results imply in a significant dependence of the recent human ZIKV spread on NS1 translational selection.
Cell-type and state-dependent synchronization among rodent areas S1BF, V1, perirhinal cortex and hippocampus CA1
Authors: Vinck Martin , Bos Jeroen J. , Van Mourik-Donga Laura A. , Oplaat Krista T. , Klein Gerbrand A. , Jackson Jadin C. , Gentet Luc J. , Pennartz Cyriel M.A.
Published: November 2015

Beta and gamma rhythms have been hypothesized to be involved in global and local coordination of neuronal activity, respectively. Here, we investigated how cells in rodent area S1BF are entrained by rhythmic fluctuations at various frequencies within the local area and in connected areas, and how this depends on behavioral state and cell type. We performed simultaneous extracellular field and unit recordings in four connected areas of the freely moving rat (S1BF, V1M, perirhinal cortex, CA1). S1BF spiking activity was strongly entrained by both beta and gamma S1BF oscillations, which were associated with deactivations and activations, respectively. We identified multiple classes of fast spiking and excitatory cells in S1BF, which showed prominent differences in rhythmic entrainment and in the extent to which phase locking was modulated by behavioral state. Using an additional dataset acquired by whole-cell recordings in head-fixed mice, these cell classes could be compared with identified phenotypes showing gamma rhythmicity in their membrane potential. We next examined how S1BF cells were entrained by rhythmic fluctuations in connected brain areas. Gamma-synchronization was detected in all four areas, however we did not detect significant gamma coherence among these areas. Instead, we only found long-range coherence in the theta-beta range among these areas. In contrast to local S1BF synchronization, we found long-range S1BF-spike to CA1-LFP synchronization to be homogeneous across inhibitory and excitatory cell types. These findings suggest distinct, cell-type contributions of low and high-frequency synchronization to intra- and inter-areal neuronal interactions.
Genome-wide expression profilingDrosophila melanogasterdeficiency heterozygotes reveals diverse genomic responses
Authors: Lee Hangnoh , Cho Dong-Yeon , Whitworth Cale , Eisman Robert , Phelps Melissa , Roote John , Kaufman Thomas , Cook Kevin , Russell Steven , Przytycka Teresa M. , Oliver Brian
Published: November 2015

Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for mapping genes and for genetic pathway discovery via dose-dependent suppressor and enhancer screens. More recently, it has become clear that deviations from normal gene dosage are associated with multiple disorders in a range of species including humans. While we are beginning to understand some of the transcriptional effects brought about by gene dosage changes and the chromosome rearrangement breakpoints associated with them, much of this work relies on isolated examples. We have systematically examined deficiencies on the left arm of chromosome2and characterize gene-by-gene dosage responses that vary from collapsed expression through modest partial dosage compensation to full or even over compensation. We found negligible long-range effects of creating novel chromosome domains at deletion breakpoints, suggesting that cases of changes in gene regulation due to altered nuclear architecture are rare. These rare cases includetransde-repression when deficiencies delete chromatin characterized as repressive in other studies. Generally, effects of breakpoints on expression are promoter proximal (~100 bp) or within the gene body. Genome-wide effects of deficiencies are observed at genes with regulatory relationships to genes within the deleted segments, highlighting the subtle expression network defects in these sensitized genetic backgrounds.

Author summary

Deletions alter gene dose in heterozygotes and bring distant regions of the genome into juxtaposition. We find that the transcriptional dose response is generally varied, gene-specific, and coherently propagates into gene expression regulatory networks. Analysis of deletion heterozygote expression profiles indicates that distinct genetic pathways are weakened in adult flies bearing different deletions even though they show minimal or no overt phenotypes. While there are exceptions, breakpoints have a minimal effect on the expression of flanking genes, despite the fact that different regions of the genome are brought into contact and that important elements such as insulators are deleted. These data suggest that there is little effect of nuclear architecture and long-range enhancer and/or silencer promoter contact on gene expression in the compactDrosophilagenome.
Structural insights into the synthesis of FMN in prokaryotic organisms
Authors: Herguedas Beatriz , Lans Isaias , Sebastián María , Hermoso Juan A. , Martínez-Júlvez Marta , Medina Milagros
Published: November 2015

Riboflavin kinases (RFKs) catalyse the phosphorylation of riboflavin to produce FMN. In most bacteria this activity is catalysed by the C-terminal module of a bifunctional enzyme, FAD synthetase (FADS), which also catalyses the transformation of FMN into FAD through its N-terminal FMN adenylyltransferase (FMNAT) module. The RFK module of FADS is a homologue of eukaryotic monofunctional RFKs, while the FMNAT module lacks homologyto eukaryotic enzymes involved in FAD production. Previously, the crystal structure ofCorynebacterium ammoniagenesFADS (CaFADS) was determined in its apo form. This structure predicted a dimer-of-trimers organization with the catalytic sites of two modules of neighbouring protomers approaching each other, leading to a hypothesis about the possibility of FMN channelling in the oligomeric protein. Here, two crystal structures of the individually expressed RFK module ofCaFADS in complex with the products of the reaction, FMN and ADP, are presented. Structures are complemented with computational simulations, binding studies and kinetic characterization. Binding of ligands triggers dramatic structural changes in the RFK module, which affect large portions of the protein. Substrate inhibition and molecular-dynamics simulations allowed the conformational changes that take place along the RFK catalytic cycle to be established. The influence of these conformational changes in the FMNAT module is also discussed in the context of the full-lengthCaFADS protomer and the quaternary organization.
Hotelvp: swimming with sharks
Authors: Gong Yan , Velamuri Ramakrishna , Zhao Liman , Dong Liang
Published: November 2015

Subject area

This case is written for those people who are interested in entrepreneurship, and to generate discussions on the Lean Start-up methodology, as well as other topics related to entrepreneurship and innovation.

Study level/applicability

It can be used with senior undergraduates, MBAs, EMBAs and senior executives.

Case overview

In August 2011, Mars Ren and Gene Deng created a technology-based venture, Shanghai Tianhailu Network Information Technology Ltd. Filled with passion, they aspired to be the first “factory outlet” in China' hotel booking industry. To achieve this goal, they developed the Hotelvp app for mobile users. After 6:00 p.m. every day, users could book accommodation online in hotels above three-star standard for that same night at significant discounts. Hotels also benefited because they could sell their unsold room nights at the last minute and improve their revenue management. Ren and Deng were convinced that this win-win idea would take off. Unfortunately, it failed to fully satisfy either the users or the hotels. In spite of the founders' passion and energy, it was still acquired by a much more powerful player in the online sector, JD.com, in early 2014. This case is designed to stimulate in-depth discussions based on the question: What are the key obstacles when launching a startup and how to overcome them?

Expected learning outcomes

Through class discussion, it aims at teaching the student how to define and practice a start-up idea successfully by following the “Lean Start-up” methodology and/or take advantage of a practical tool, discovery-driven planning. Specifically, this case intends to teach students how: To identify and define a good start-up idea; To take actions based on the idea/opportunity, iterate and modify it along the way to create new start-ups, and finally lead the new start-ups to grow and succeed; To understand the key concepts, frameworks and theoretical logics of Lean Start-up methodology, and apply it in practice.

Supplementary materials

Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.
Quality of life and human rights conditions in a public psychiatric hospital in Cairo
Authors: Elnemais Fawzy Michael
Published: November 2015

Purpose

– There is no documented evidence on service users’ perceptions of quality of care and observance of human rights in mental health residential facilities in Egypt after the new mental health law passed in 2009. The purpose of this paper is to investigate El-Abbassia Mental Health Hospital in Cairo. Special attention is paid as to the variety of human rights violations which are experienced by the users and the context in which these violations occur.

Design/methodology/approach

– A cross-sectional study was performed relying on 36 depth interviews with patients, 58 staff members and 15 family members, reviews of documents and observations by an independent assessment team consisting of the author, another psychiatrist, a nurse and a family member using the World Health Organization Quality Rights Tool Kit which uses the Convention on the Rights of Persons with Disabilities (CRPD) as its framework.

Findings

– The study reported empirical insights into how the steps taken by the hospital to address several of the themes drawn from the CRPD require either improvement or initiation to comply fully with the convention’s themes.

Research limitations/implications

– Respondents may have failed to disclose their true experiences due to fear of punishment.

Practical implications

– Users admitted to mental hospitals have often been forgotten, thus becoming victims of violence, neglect and other human rights violations.

Social implications

– An opportunity to promote public awareness of the rights of patients.

Originality/value

– The importance of this study came from being the first documented evidence on service users’ perceptions of quality of care and observance of human rights in mental health residential facilities in Egypt after the new mental health law passed in 2009.
Linking transient dynamics and life history to biological invasion success
Authors: Iles David T. , Salguero‐Gómez Roberto , Adler Peter B. , Koons David N.
Published: November 2015

Upon arriving in a novel environment, invading populations are likely to be small and far from a stable stage structure. This unstable stage structure can cause transient (short‐term) population dynamics to differ greatly from asymptotic (long‐term) dynamics. Because the persistence of small populations depends heavily on population growth rate, short‐term dynamics may strongly influence the viability of invading populations.

We used published matrix population models to study the dynamics of small ‘invading’ populations for 105 plant species spanning a range of life histories, including species classified as both invasive and non‐invasive. We simulated the matrix population models to estimate the effect of transient dynamics on population viability (i.e. potential invasiveness) after a hypothetical seed dispersal event into a novel environment. We then evaluated the predictive power of transient and long‐term population growth rates to explain variation in population viability and identified the life‐history correlates of population dynamics that best explained establishment success.

Transient and long‐term population growth rates were positively but independently correlated with population viability across species. Minimum transient density (minimum population density attained en route to a stable stage structure) was the best transient predictor of population viability. This suggests that avoidance of severe short‐term population declines is more important during establishment than either the rate of decline or transient ability to increase in density following a decline.

Despite a negative correlation between transient density and fecundity, species with high fecundity had disproportionately favourable transient dynamics and higher long‐term population growth rates, resulting in higher population viability. Together, these results suggest that highly fecund species are better equipped to overcome the early effects of demographic stochasticity in the establishment phase than less fecund species and help explain the common empirical finding that species invasiveness is correlated with fecundity.

Synthesis. Transient and long‐term population dynamics are independent predictors of demographic performance that influence the viability of invading (i.e. small, unstable) populations subjected to strong effects of demographic stochasticity. Greater long‐term population growth rates and disproportionately favourable transient dynamics may account for the commonly observed invasiveness of highly fecund species. Given the strong dependence of population viability on population growth and the wide range of transient responses among species, transient analysis may provide critical insights into the demographic correlates of biological invasion potential.
Housing in a Federation: From Wicked Problem to Complexity Cascade?
Authors: Walter James , Holbrook Carolyn
Published: November 2015

The Commonwealth's periodic attempts at housing and urban policy reform since the 1940s have been made in the face of a federal structure that allocates responsibility for such matters to the states. This paper explores the experience of federal governments since the 1940s, considering the various styles of political leadership, varying ways in which the problem has been framed, and differing policy settings that have been employed in resolving policy challenges. The historical narrative clarifies phases of active engagement and reaction, linking these to fiscal asymmetry and distribution of federal–state responsibilities, historical ‘gateway’ events, and transitions in policy paradigms. We argue that housing is a perpetual concern (both a basic need and an aspirational objective) and is so integrally related to other policy domains—in which decisions may have unintended consequences for housing—that it is never conclusively resolved. The complexity (and uncertainty) consequent upon these inter‐relationships ensures that housing remains a wicked problem. The visual metaphor of a complexity cascade, however, may assist a more nuanced appreciation of the direction of policy travel.
Can prehospital Modified Early Warning Score identify non‐trauma patients requiring life‐saving intervention in the emergency department?
Authors: Leung Siu Chung , Leung Ling Pong , Fan Kit Ling , Yip Wai Lam
Published: November 2015

Objective

We aim to investigate whether prehospital Modified Early Warning Score (MEWS) can identify non‐trauma patients requiring life‐saving intervention (LSI) within 4 h of presentation to the ED.

Methods

It was a prospective study of non‐trauma ED patients by ambulance who were 16 years or older from 1 to 27 November 2013. Prehospital MEWS was calculated according to vital signs measured by the ambulance crew. Data on patients' demographics, triage category, LSI within 4 h of ED presentation and 24 h mortality were retrieved. LSI was defined as emergency interventions to airway, breathing and circulation, emergency procedures and medications administered. The performance of prehospital MEWS was analysed with sensitivity, specificity, predictive values (PV), likelihood ratios (LR) and the receiver operating characteristic curve.

Results

Recruited during the study period were 1493 patients. The median age was 78 years. Of the patients, 49.9% belonged to critical, emergent or urgent triage categories. LSI was required in 321 patients (21.5%). Thirteen died within 24 h of ED presentation. The area under the receiver operating characteristic curve of prehospital MEWS relating to LSI was 0.72 (95% confidence interval 0.69 to 0.75). The sensitivity, specificity, positive PV, negative PV, positive LR and negative LR were 0.57, 0.76, 0.40, 0.87, 2.43 and 0.56, respectively, when prehospital MEWS  ≥3 was chosen as the cut‐off value.

Conclusions

Prehospital MEWS is useful in identifying non‐trauma patients requiring LSI within 4 h of ED presentation. This may in turn enhance the triage accuracy in the ED in addition to clinical assessment.
What Determines Efficiency in Local Government? A DEA Analysis of NSW Local Government
Authors: Drew Joseph , Kortt Michael , Dollery Brian
Published: November 2015

Data envelopment analysis (DEA) has the potential to make strong contributions to the formulation of public policy. In particular, DEA can be used to identify the determinants of efficiency and this information can be used to inform debate around municipal boundary reform and other matters. However, there is a dearth of empirical literature on the accurate and correct specification of DEA. We use conceptual considerations to posit an ideal specification for Australian municipal DEA before estimating a number of models to demonstrate the effect of specification on the identification of determinants. Our evidence suggests that incorrect specification may well produce spurious associations and lead to poor public policymaking.
Efficacy and safety of the combination of paclitaxel and platinum in advanced thymic carcinoma
Authors: Xu Jian‐ping , Hao Xue‐zhi , Zhang Xiang‐ru , Yang Sheng , Shi Yuan‐kai
Published: November 2015

This study aimed to assess the efficacy and safety of a combination of paclitaxel and cisplatin/carboplatin for the treatment of advanced thymic carcinoma. Thirty‐seven patients (23 men and 14 women, median age 47 years, performance status score ≤2) with pathologically or cytologically diagnosed advanced thymic carcinoma were recruited. Patients received 175 mg/m2 paclitaxel on day 1 and 75 mg/m2 cisplatin or 300 mg/m2 carboplatin on day 2 of a 21 day cycle for at least two cycles to evaluate efficacy and adverse events. No complete response (CR) was observed; 11 patients had a partial response (PR), 16 patients had no change (NC), and 10 had progressive disease, resulting in an overall response rate of 29.7%, a stable rate of 43.2%, and a disease control rate (CR + PR + NC) of 72.9%. Grade I/II and III/IV neutropenia were observed in 21 (56.7%) and 13 (35.1%) patients, respectively. Four (10.8%) patients developed grade I/II thrombocytopenia. Grade I/II and III/IV nausea and vomiting were observed in 19 (51.2%) and five (13.5%) patients, respectively. Grade I/II liver dysfunction was observed in seven (18.9%) patients. Two patients with grade III liver dysfunction recovered after hepatoprotective treatment. The combination of paclitaxel and platinum was effective and well tolerated in patients with advanced thymic carcinoma.
piecewiseSEM: Piecewise structural equation modelling inr for ecology, evolution, and systematics
Authors: Lefcheck Jonathan S.
Published: November 2015

Ecologists and evolutionary biologists rely on an increasingly sophisticated set of statistical tools to describe complex natural systems. One such tool that has gained significant traction in the biological sciences is structural equation models (SEM), a form of path analysis that resolves complex multivariate relationships among a suite of interrelated variables.

Evaluation ofSEMs has historically relied on covariances among variables, rather than the values of the data points themselves. While this approach permits a wide variety of model forms, it limits the incorporation of detailed specifications. Recent developments have allowed for the simultaneous implementation of non‐normal distributions, random effects and different correlation structures using local estimation, but this process is not yet automated and consequently, evaluation can be prohibitive with complex models.

Here, I present a fully documented, open‐source packagepiecewiseSEM, a practical implementation of confirmatory path analysis for therprogramming language. The package extends this method to all current (generalized) linear, (phylogenetic) least‐square, and mixed effects models, relying on familiarrsyntax. I also provide two worked examples: one involving random effects and temporal autocorrelation, and a second involving phylogenetically independent contrasts.

My goal is to provide a user‐friendly and tractable implementation ofSEMthat also reflects the ecological and methodological processes generating data.
boral – Bayesian Ordination and Regression Analysis of Multivariate Abundance Data in r
Authors: Hui Francis K.C.
Published: November 2015

Model‐based methods have emerged as a powerful approach for analysing multivariate abundance data in community ecology. Key applications include model‐based ordination, modelling the various sources of correlations across species, and making inferences while accounting for these between species correlations.

boral (version 0.9.1, licence GPL‐2) is an r package available on cran for model‐based analysis of multivariate abundance data, with estimation performed using Bayesian Markov chain Monte Carlo methods. A key feature of the boral package is the ability to incorporate latent variables as a parsimonious method of modelling between species correlation.

Pure latent variable models offer a model‐based approach to unconstrained ordination, for visualizing sites and the indicator species characterizing them on a low‐dimensional plot.

Correlated response models consist of fitting generalized linear models to each species, while including latent variables to account for residual correlation between species, for example, due to unmeasured covariates.
Neurophysiological effects of needle trauma and intraneural injection in a porcine model: a pilot study
Authors: Kirchmair L. , Ströhle M. , Löscher W. N. , Kreutziger J. , Voelckel W. G. , Lirk P.
Published: November 2015

Background

Neurophysiological data are lacking in the research of nerve injury during regional anaesthesia. The aim of this pilot study was to establish a large animal model in order to test the hypothesis that needle trauma alone or in combination with intraneural injection would result in measurable nerve injury.

Methods

The experimental set‐up was elaborated in four pre‐test animals. In the remaining animals (n = 11), 22 sciatic nerves were randomly assigned to one of four groups: needle trauma (n = 5) generated by ultrasound‐guided forced needle advancement; intraneural injection of 2.5 ml saline (n = 6); intraneural injection of 5 ml saline (n = 6); extraneural injection of 5 ml saline (n = 5) as control group. Compound muscle action potential (CMAP) amplitudes as well as latencies were taken as outcome parameter and monitored over 180 min. Sonographic assessments were performed simultaneously.

Results

Following needle trauma and intraneural injection, CMAP amplitudes declined significantly over 180 min (P < 0.001). The control group showed no electrophysiological alterations. At 60 min, decreases in amplitude were significant after needle trauma (P = 0.04) and intraneural injection of 2.5 ml (P = 0.045), and highly significant after injection of 5 ml (P = 0.006) when compared to controls. Sustained nerve swelling was observed after intraneural injection, but not after needle trauma and perineural injection.

Conclusions

Isolated mechanical trauma caused by forced needle advancement alone or in combination with intraneural injection of saline was followed by a significant decline in CMAP amplitudes indicating conduction block due to disruption of myelin or axon loss (pseudo‐conduction block).
Differential Effects of Alcohol on Excitatory and Inhibitory Puberty‐Related Peptides in the Basal Hypothalamus of the Female Rat
Authors: Srivastava Vinod K. , Hiney Jill K. , Stevener Kristyn , Dees William L.
Published: November 2015

Background

An increase in development of excitatory inputs along with a decline in inhibitory inputs ultimately govern the timely increased secretion of hypothalamic luteinizing hormone‐releasing hormone (LHRH) at the time of puberty. As chronic alcohol (ALC) exposure acts at the hypothalamic level to suppress LHRH secretion and delay puberty, we assessed its ability to differentially affect the expression of key puberty‐related proteins.

Methods

ALC was administered to female rats from days 27 to 33, at which time animals were killed and tissues collected for protein expression. In the medial basal hypothalamus (MBH), we assessed kisspeptin (Kp) 10, an excitatory peptide critical for prepubertal LHRH secretion, and Lin28b, a peptide with an inhibitory influence on puberty. As a direct mechanism of action of Lin28b was not known, we determined whether its central administration could induce dynorphin (DYN), a peptide that is inhibitory on LHRH secretion. Also, ALC's effect on DYN protein expression was assessed, as well as its effect on DYN release in vitro.

Results

ALC markedly suppressed (p < 0.01) the expression of the excitatory Kp protein, while at the same time increased (p < 0.001) the expression of inhibitory Lin28b protein. Subsequently, we showed for the first time that the central administration of Lin28b stimulated (p < 0.01) the synthesis of DYN. Finally, ALC also induced (p < 0.01) the protein expression and stimulated (p < 0.01) the in vitro release of DYN from the MBH.

Conclusions

These results indicate that ALC can simultaneously and differentially alter both excitatory and inhibitory influences governing pubertal development, show for the first time a mechanism of action by which Lin28b exerts its prepubertal inhibitory tone, and further demonstrate the negative influences of ALC on the pubertal process.
Molecular epidemiological characteristics of Salmonella enterica serovars Enteritidis, Typhimurium and Livingstone strains isolated in a Tunisian university hospital
Authors: Ktari Sonia , Ksibi Boutheina , Gharsallah Houda , Mnif Basma , Maalej Sonda , Rhimi Fouzia , Hammami Adnene
Published: November 2015

Enteritidis, Typhimurium and Livingstone are the main Salmonella enterica serovars recovered in Tunisia. Here, we aimed to assess the genetic diversity of fifty‐seven Salmonella enterica strains from different sampling periods, origins and settings using pulsed‐field gel electrophoresis (PFGE), multi‐locus sequence typing (MLST) and multi‐locus variable‐number tandem repeat analysis (MLVA). Salmonella Enteritidis, isolated from human and food sources from two regions in Sfax in 2007, were grouped into one cluster using PFGE. However, using MLVA these strains were divided into two clusters. Salmonella Typhimurium strains, recovered in 2012 and represent sporadic cases of human clinical isolates, were included in one PFGE cluster. Nevertheless, the MLVA technique, divided Salmonella Typhimurium isolates into six clusters with diversity index reaching (DI = 0.757). For Salmonella Livingstone which was responsible of two nosocomial outbreaks during 2000–2003, the PFGE and MLVA methods showed that these strains were genetically closely related. Salmonella Enteritidis and Salmonella Livingstone populations showed a single ST lineage ST11 and ST543 respectively. For Salmonella Typhimurium, two MLST sequence types ST19 and ST328 were defined. Salmonella Enteritidis and Salmonella Typhimurium strains were clearly differentiated by MLVA which was not the case using PFGE.