bluuebunny/crossref_metadata_2025 huggingface dataset:
simPATHy: a new method for simulating data from perturbed biological PATHways
Authors: Salviato Elisa , Djordjilović Vera , Chiogna Monica , Romualdi Chiara
Published: October 2016

In the omic era, one of the main aims is to discover groups of functionally related genes that drive the difference between different conditions. To this end, a plethora of potentially useful multivariate statistical approaches has been proposed, but their evaluation is hindered by the absence of a gold standard. Here, we propose a method for simulating biological data – gene expression, RPKM/FPKM or protein abundances – from two conditions, namely, a reference condition and a perturbation of it. Our approach is built upon probabilistic graphical models and is thus especially suited for testing topological approaches.

Availability and Implementation

The simPATHy is an R package, it is open source and freely available on CRAN.

Supplementary information

Supplementary data are available at Bioinformatics online.
Improving cross-study prediction through addon batch effect adjustment or addon normalization
Authors: Hornung Roman , Causeur David , Bernau Christoph , Boulesteix Anne-Laure
Published: October 2016

Motivation

To date most medical tests derived by applying classification methods to high-dimensional molecular data are hardly used in clinical practice. This is partly because the prediction error resulting when applying them to external data is usually much higher than internal error as evaluated through within-study validation procedures. We suggest the use of addon normalization and addon batch effect removal techniques in this context to reduce systematic differences between external data and the original dataset with the aim to improve prediction performance.

Results

We evaluate the impact of addon normalization and seven batch effect removal methods on cross-study prediction performance for several common classifiers using a large collection of microarray gene expression datasets, showing that some of these techniques reduce prediction error.

Availability and Implementation

All investigated addon methods are implemented in our R package bapred.

Supplementary information

Supplementary data are available at Bioinformatics online.
CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data
Authors: Shah Ankeeta , Qian Yingzhi , Weyn-Vanhentenryck Sebastien M , Zhang Chaolin
Published: October 2016

UV cross-linking and immunoprecipitation (CLIP), followed by high-throughput sequencing, is a powerful biochemical assay that maps in vivo protein-RNA interactions on a genome-wide scale. The CLIP Tool Kit (CTK) aims at providing a set of tools for flexible, streamlined and comprehensive CLIP data analysis. This software package extends the scope of our original CIMS package.

Availability and Implementation

The software is implemented in Perl. The source code and detailed documentation are available at http://zhanglab.c2b2.columbia.edu/index.php/CTK.
Electrical remodelling in patients with iatrogenic left bundle branch block
Authors: Engels Elien B. , Poels Thomas T. , Houthuizen Patrick , de Jaegere Peter P.T. , Maessen Jos G. , Vernooy Kevin , Prinzen Frits W.
Published: October 2016

Aims

Left bundle branch block (LBBB) is induced in approximately one-third of all transcatheter aortic valve implantation (TAVI) procedures. We investigated electrophysiological remodelling in patients with TAVI-induced LBBB.

Methods and results

This retrospective study comprises 107 patients with initially narrow QRS complex of whom 40 did not and 67 did develop persistent LBBB after TAVI. 12-lead electrocardiograms (ECGs) taken before TAVI, within 24 hours (‘acute’), and 1–12 months after TAVI (‘chronic’) were used to reconstruct vectorcardiograms. From these vectorcardiograms, QRS and T-wave area were calculated as comprehensive indices of depolarization and repolarization abnormalities, respectively. TAVI-induced LBBB resulted in significant acute depolarization and repolarization changes while further repolarization changes were observed with longer lasting LBBB. The amount of long-term repolarization changes (remodelling) was highly variable between patients. The change in T-wave area between acute and chronic LBBB ranged from +57% to − 77%. After dividing the LBBB cohort into tertiles based on the change in T-wave area, only baseline QRS area was larger in the tertile with no significant change in T-wave area. During longer lasting LBBB, the spatial vector gradient (SVG) changed orientation towards the direction of the QRS-vector, indicating that later-activated regions developed shorter action potential duration.

Conclusion

This study in patients with TAVI-induced LBBB shows that repolarization changes develop within months after onset of LBBB, and that these changes are highly variable between individual patients.
Postcolonial Genetic Criticism: The (un)making of Ahmadou Kourouma’s
Les Soleils des Indépendances
Authors: Corcoran Patrick
Published: October 2016

This article explores the interface between two fields of enquiry that have developed with rather differing sets of priorities: textual genetics and postcolonial studies. Textual genetics has placed the emphasis on writing as a process, deeply influenced by a whole range of factors both literary and non-literary. Its attendant desacralization of the notion of the ‘definitive’ text as the prime object of study, or as a privileged site for the understanding of a writing project, further problematizes the nature of textuality. Postcolonial approaches to literary study, on the other hand, have frequently foregrounded the importance of the social, political, and cultural contexts from which texts emerge and to which they respond, thereby often deflecting attention from strictly literary concerns. The detailed consideration of the genesis of Ahmadou Kourouma’s first novel,
Les Soleils des indépendances
, presented here, involves a process of ‘un-making’ that sees the original manuscript of the novel relegated to the status of an
avant-texte
of the shorter version, published by Seuil in 1970. The study of this particular
dossier de genèse
suggests that where textual genetics would appear to correspond most closely to the preoccupations of postcolonial studies is at a macro-structural level.
Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses
Authors: Rahaman Jordon , Siltberg-Liberles Jessica
Published: October 2016

Within the last 15 years, two related coronaviruses (Severe Acute Respiratory Syndrome [SARS]-CoV and Middle East Respiratory Syndrome [MERS]-CoV) expanded their host range to include humans, with increased virulence in their new host. Coronaviruses were recently found to have little intrinsic disorder compared with many other virus families. Because intrinsically disordered regions have been proposed to be important for rewiring interactions between virus and host, we investigated the conservation of intrinsic disorder and secondary structure in coronaviruses in an evolutionary context. We found that regions of intrinsic disorder are rarely conserved among different coronavirus protein families, with the primary exception of the nucleocapsid. Also, secondary structure predictions are only conserved across 50–80% of sites for most protein families, with the implication that 20–50% of sites do not have conserved secondary structure prediction. Furthermore, nonconserved structure sites are significantly less constrained in sequence divergence than either sites conserved in the secondary structure or sites conserved in loop. Avoiding regions symptomatic of conformational flexibility such as disordered sites and sites with nonconserved secondary structure to identify potential broad-specificity antiviral targets, only one sequence motif (five residues or longer) remains from the >10,000 starting sites across all coronaviruses in this study. The identified sequence motif is found within the nonstructural protein (NSP) 12 and constitutes an antiviral target potentially effective against the present day and future coronaviruses. On shorter evolutionary timescales, the SARS and MERS clades have more sequence motifs fulfilling the criteria applied. Interestingly, many motifs map to NSP12 making this a prime target for coronavirus antivirals.
De-identification of patient notes with recurrent neural networks
Authors: Dernoncourt Franck , Lee Ji Young , Uzuner Ozlem , Szolovits Peter
Published: October 2016

Objective: Patient notes in electronic health records (EHRs) may contain critical information for medical investigations. However, the vast majority of medical investigators can only access de-identified notes, in order to protect the confidentiality of patients. In the United States, the Health Insurance Portability and Accountability Act (HIPAA) defines 18 types of protected health information that needs to be removed to de-identify patient notes. Manual de-identification is impractical given the size of electronic health record databases, the limited number of researchers with access to non-de-identified notes, and the frequent mistakes of human annotators. A reliable automated de-identification system would consequently be of high value.

Materials and Methods: We introduce the first de-identification system based on artificial neural networks (ANNs), which requires no handcrafted features or rules, unlike existing systems. We compare the performance of the system with state-of-the-art systems on two datasets: the i2b2 2014 de-identification challenge dataset, which is the largest publicly available de-identification dataset, and the MIMIC de-identification dataset, which we assembled and is twice as large as the i2b2 2014 dataset.

Results: Our ANN model outperforms the state-of-the-art systems. It yields an F1-score of 97.85 on the i2b2 2014 dataset, with a recall of 97.38 and a precision of 98.32, and an F1-score of 99.23 on the MIMIC de-identification dataset, with a recall of 99.25 and a precision of 99.21.

Conclusion: Our findings support the use of ANNs for de-identification of patient notes, as they show better performance than previously published systems while requiring no manual feature engineering.
Multicentre dose audit for clinical trials of radiation therapy in Asia
Authors: Mizuno Hideyuki , Fukuda Shigekazu , Fukumura Akifumi , Nakamura Yuzuru-Kutsutani , Jianping Cao , Cho Chul-Koo , Supriana Nana , Dung To Anh , Calaguas Miriam Joy , Devi C.R. Beena , Chansilpa Yaowalak , Banu Parvin Akhter , Riaz Masooma , Esentayeva Surya , Kato Shingo , Karasawa Kumiko , Tsujii Hirohiko
Published: October 2016

A dose audit of 16 facilities in 11 countries has been performed within the framework of the Forum for Nuclear Cooperation in Asia (FNCA) quality assurance program. The quality of radiation dosimetry varies because of the large variation in radiation therapy among the participating countries. One of the most important aspects of international multicentre clinical trials is uniformity of absolute dose between centres. The National Institute of Radiological Sciences (NIRS) in Japan has conducted a dose audit of participating countries since 2006 by using radiophotoluminescent glass dosimeters (RGDs). RGDs have been successfully applied to a domestic postal dose audit in Japan. The authors used the same audit system to perform a dose audit of the FNCA countries. The average and standard deviation of the relative deviation between the measured and intended dose among 46 beams was 0.4% and 1.5% (k = 1), respectively. This is an excellent level of uniformity for the multicountry data. However, of the 46 beams measured, a single beam exceeded the permitted tolerance level of ±5%. We investigated the cause for this and solved the problem. This event highlights the importance of external audits in radiation therapy.
Testing Models of Quasar Hosts With Strong Gravitational Lensing by Quasar Hosts
Authors: Cen Renyue , Safarzadeh Mohammadtaher
Published: October 2016

We perform a statistical analysis of strong gravitational lensing by quasar hosts of background galaxies, in the two competing models of dark matter halos of quasars, HOD and CS models. Utilizing the BolshoiP Simulation we demonstrate that strong gravitational lensing provides a potentially very powerful test of models of quasar hosting halos. For quasars at z = 0.5, the lensing probability by quasars of background galaxies in the HOD model is higher than that of the CS model by two orders of magnitude or more for lensing image separations in the range of θ ∼ 1.2 − 12 arcsec. To observationally test this, we show that, as an example, at the depth of the CANDELS wide field survey and with a quasar sample of 1000 at z = 0.5, the two models can be differentiated at 3 − 4σ confidence level. This observational capability is within the reach of HSC and WFIRST Survey.
Engineering of temperature- and light-switchable Cas9 variants
Authors: Richter Florian , Fonfara Ines , Bouazza Boris , Schumacher Charlotte Helene , Bratovič Majda , Charpentier Emmanuelle , Möglich Andreas
Published: October 2016

Sensory photoreceptors have enabled non-invasive and spatiotemporal control of numerous biological processes. Photoreceptor engineering has expanded the repertoire beyond natural receptors, but to date no generally applicable strategy exists towards constructing light-regulated protein actuators of arbitrary function. We hence explored whether the homodimeric Rhodobacter sphaeroides light-oxygen-voltage (LOV) domain (RsLOV) that dissociates upon blue-light exposure can confer light sensitivity onto effector proteins, via a mechanism of light-induced functional site release. We chose the RNA-guided programmable DNA endonuclease Cas9 as proof-of-principle effector, and constructed a comprehensive library of RsLOV inserted throughout the Cas9 protein. Screening with a high-throughput assay based on transcriptional repression in Escherichia coli yielded paRC9, a moderately light-activatable variant. As domain insertion can lead to protein destabilization, we also screened the library for temperature-sensitive variants and isolated tsRC9, a variant with robust activity at 29°C but negligible activity at 37°C. Biochemical assays confirmed temperature-dependent DNA cleavage and binding for tsRC9, but indicated that the light sensitivity of paRC9 is specific to the cellular setting. Using tsRC9, the first temperature-sensitive Cas9 variant, we demonstrate temperature-dependent transcriptional control over ectopic and endogenous genetic loci. Taken together, RsLOV can confer light sensitivity onto an unrelated effector; unexpectedly, the same LOV domain can also impart strong temperature sensitivity.
Effect of Processing on Antinutrient Compounds in Pulses
Authors: Patterson Carol Ann , Curran Julianne , Der Tanya
Published: October 2016

Processing of pulses (peas, beans, lentils, chickpeas, and faba beans) is necessary to reduce or eliminate the antinutrient compounds. Conventional processing including soaking, dehulling, boiling, and pressure cooking as well as germination and fermentation reduce the levels of phytate, protease inhibitors, phenolics, condensed tannins, lectins, and saponins. Recent research has investigated how innovative processes such as extrusion, microwave heating, micronization, and irradiation affect the antinutrient content. Germination tends to be most effective at reducing phytate levels, regardless of pulse type. Mixed results on the effectiveness of extrusion, microwave heating, and micronization have been reported. More work is needed to understand how processing of consumer‐ready foods containing pulse ingredients affects levels of antinutrient compounds.
Comprehensive Sclerotinia Stem Rot Screening of Soybean Germplasm Requires Multiple Isolates of Sclerotinia sclerotiorum
Authors: Willbur J. F. , Ding S. , Marks M. E. , Lucas H. , Grau C. R. , Groves C. L. , Kabbage M. , Smith D. L.
Published: October 2016

Sclerotinia sclerotiorum population variability directly affects Sclerotinia stem rot (SSR) resistance breeding programs. In the north-central United States, however, soybean germplasm selection has often involved only a single isolate. Forty-four S. sclerotiorum isolates from Illinois, Michigan, Minnesota, Nebraska, Wisconsin, Poland, and across 11 different host species were evaluated for variation in isolate in vitro growth, in vitro oxalate production, and in planta aggressiveness on the susceptible soybean ‘Williams 82’. Significant differences (P < 0.0001) were detected in isolate in planta aggressiveness, in vitro growth, and in vitro oxalate production. Furthermore, diverse isolate characteristics were observed within all hosts and locations of collection. Aggressiveness was not correlated to colony growth and was only weakly correlated (r = 0.26, P < 0.0001) to isolate oxalate production. In addition, the host or location of collection did not explain isolate aggressiveness. Isolate oxalic acid production, however, may be partially explained by the host (P < 0.05) and location (P < 0.01) of collection. Using a representative subset of nine S. sclerotiorum isolates and soybean genotypes exhibiting susceptible or resistant responses (determined using a single isolate), a significant interaction (P = 0.04) was detected between isolates and genotypes when SSR severity was evaluated. Our findings suggest that screening of S. sclerotiorum-resistant soybean germplasm should be performed with multiple isolates to account for the overall diversity of S. sclerotiorum isolates found throughout the soybean-growing regions of the United States.
Talking with your post-op patients about sex
Authors: Espinosa Julie
Published: October 2016

Pick up the must-have information to discuss sexual function with your postoperative patients.
A center of excellence model for LGBT patient care
Authors: Lockhart Lisa , Davis Charlotte
Published: October 2016

Together we can be a positive link to change perceptions about healthcare delivery for our lesbian, gay, bisexual, and transgender patients and families.
The Pressure Is On!
Authors: Ottinger Daniele , Hicks Jamie , Wilson Sarah , Sperber Kim , Power Keely
Published: October 2016

Background:

Premature infants have an increased risk for developing skin breakdown. Perceivably noninvasive interventions may have detrimental effects on the infant's skin.

Purpose:

This case presentation describes an extreme case of nasal breakdown associated with nasal continuous positive airway pressure (nCPAP).

Methods:

Highlighted is the vital importance of proper placement, along with appropriate apparatus size, in the efforts to prevent skin breakdown. Ensuring that pressure points are avoided is imperative to prevent nCPAP-related injuries, along with treating the area in the event of skin denudation. A literature search was conducted to determine best practice options to prevent these injuries.

Findings:

There is little information in the literature to guide treatment and prevention of this type of breakdown.

Implications for Practice:

Avoidance of pressure in a localized area is the most commonly found recommendation.

Implications for Research:

There are extensive opportunities for adding to our current knowledge in terms of prevention and treatment of skin breakdown associated with device utilization in the neonatal intensive care unit, especially with the increasing use of nCPAP.
When Less Is More
Authors: Zuckerman Scott L. , Laufer Ilya , Sahgal Arjun , Yamada Yoshiya J. , Schmidt Meic H. , Chou Dean , Shin John H. , Kumar Naresh , Sciubba Daniel M.
Published: October 2016

Study Design.

Systematic review.

Objective.

The aim of this study was to review the techniques, indications, and outcomes of minimally invasive surgery (MIS) and separation surgery with subsequent radiosurgery in the treatment of patients with metastatic spine disease.

Summary of Background Data.

The utilization of MIS techniques in patients with spine metastases is a growing area within spinal oncology. Separation surgery represents a novel paradigm where radiosurgery provides long-term control after tumor is surgically separated from the neural elements.

Methods.

PubMed, Embase, and CINAHL databases were systematically queried for literature reporting MIS techniques or separation surgery in patients with metastatic spine disease. PRISMA guidelines were followed.

Results.

Of the initial 983 articles found, 29 met inclusion criteria. Twenty-five articles discussed MIS techniques and were grouped according to the primary objective: percutaneous stabilization (8), tubular retractors (4), mini-open approach (8), and thoracoscopy/endoscopy (5). The remaining 4 studies reported separation surgery. Indications were similar across all studies and included patients with instability, refractory pain, or neurologic compromise. Intraoperative variables, outcomes, and complications were similar in MIS studies compared to traditional approaches, and some MIS studies showed a statistically significant improvement in outcomes. Studies of mini-open techniques had the strongest evidence for superiority.

Conclusions.

Low-quality evidence currently exists for MIS techniques and separation surgery in the treatment of metastatic spine disease. Given the early promising results, the next iteration of research should include higher-quality studies with sufficient power, and will be able to provide higher-level evidence on the outcomes of MIS approaches and separation surgery.

Level of Evidence:N/A
Expression Patterns of Biomarkers in Primary Tumors and Corresponding Metastases in Breast Cancer
Authors: Kümler Iben , Balslev Eva , Knop Ann S. , Brünner Nils , Klausen Tobias W. , Jespersen Sofie S. , Nielsen Signe L. , Nielsen Dorte L.
Published: October 2016

Tumor heterogeneity has been shown for several cancers including breast cancer (BC). Despite the fact that expression of tumor markers may change throughout the metastatic process, rebiopsies at the time of recurrence are still not performed routinely at all institutions. The aims of the study were to evaluate changes in biomarker profiles during the metastatic process and to investigate whether previous anthracycline or endocrine therapy given in the adjuvant setting could affect the biomarker profile in metastatic lesions. We investigated the expression pattern of ER, HER2, TOP2a, TOP1, p53, Bcl-2, and Ki-67 in 110 paired samples of primary BC and corresponding asynchronous metastases. We found discordant expressions in primary tumor and metastasis for all biomarkers, although only significant for Ki-67. Changes in the expression profile of the metastatic lesions would have altered treatment decisions in 14% of patients. We found no effect of previous anthracycline or endocrine therapy on the expression profiles. Our data confirm that discordant expressions of biomarkers are common in BC and often carry therapeutic consequences. This emphasizes the need for biopsies from metastatic lesions, even in cases where the localization of the metastatic process is not easily accessible.
Pulmonary Adenocarcinoma With Enteric Differentiation: Immunohistochemistry and Molecular Morphology
Authors: Nottegar Alessia , Tabbò Fabrizio , Luchini Claudio , Brunelli Matteo , Bria Emilio , Veronese Nicola , Santo Antonio , Cingarlini Sara , Gilioli Eliana , Ogliosi Chiara , Eccher Albino , Montagna Licia , Pedron Serena , Doglioni Claudio , Cangi Maria G. , Inghirami Giorgio , Chilosi Marco
Published: October 2016

Pulmonary adenocarcinoma with enteric differentiation (PAED) is a rare subtype of lung adenocarcinoma recently recognized in the WHO classification. It is defined as an adenocarcinoma in which the enteric component exceeds 50% and have to show the expression of at least 1 immunohistochemical marker of enteric differentiation. Although the definition of this tumor type is very important, above all in the differential diagnosis between a primary lung tumor and a metastasis of colorectal adenocarcinoma, this cancer still lacks a distinctive immunohistochemical and molecular signature. We recruited the largest series in the literature of PAEDs according to the morphology and the positivity for intestinal markers. Then, we evaluated the immunohistochemical and molecular profile of these adenocarcinomas. In our series, CDX-2 and CK7 were the immunohistochemical markers mostly expressed by PAEDs. There was an inverse relationship between the expression of pnuemocytes markers, such as TTF-1, and intestinal markers. Molecular analysis revealed KRAS as the most frequently mutated gene (>60% of cases), with very few cases harboring abnormalities affecting EGFR, BRAF, and ALK genes. PAEDs are morphologically very heterogenous. The immunohistochemical profile based on CDX-2 and CK7 positivity of PAEDs appears very robust to support this diagnosis, and it is applicable also on small biopsies. KRAS appears as the most important mutated gene in such tumors.
Primary Carcinoid Tumor of the Renal Pelvis Arising From Intestinal Metaplasia: An Unusual Histogenetic Pathway?
Authors: Kuba Maria G. , Wasserman Allison , Vnencak-Jones Cindy L. , Bridge Julia A. , Gellert Lan , Hameed Omar , Giannico Giovanna A.
Published: October 2016

Objectives:

Primary carcinoid tumor of the renal pelvis is a rare neoplasm with few cases reported in the literature. Here we present the clinical and histopathologic findings of a primary carcinoid tumor arising in the left renal pelvis of a horseshoe kidney in a 61-year-old female patient.

Materials and Methods:

Pathologic features were evaluated with standard hematoxylin and eosin sections and immunohistochemical studies. A literature review was performed to place our case in context to previous reports.

Results:

The tumor was associated with intestinal metaplasia with high-grade dysplasia and neuroendocrine hyperplasia. Molecular testing for microsatellite instability and loss of heterozygosity were negative.

Conclusions:

This report portrays a unique presentation of carcinoid tumor arising from intestinal metaplasia of the pelvic urothelium, and supports its histogenesis from urothelial intestinal metaplasia and neuroendocrine hyperplasia.
An International Interprofessional Study of Mental Models and Factors Delaying Neuroimaging of Critically Head-Injured Children Presenting to Emergency Departments
Authors: Auerbach Marc , Cole Joanne , Violano Pina , Roney Linda , Doherty Catherine , Shepherd Michael , MacKinnon Ralph
Published: October 2016

Objectives

Thousands of head-injured children are cared for by interprofessional teams in emergency departments every day. Teams must balance performing time-consuming interventions with safe transport for neuroimaging. This study aims to describe and compare providers' perspectives on the transfer of head-injured children to neuroimaging and factors contributing to delays.

Methods

Participants were interprofessional health care providers involved in the care of head-injured children at sites in the United Kingdom, the United States, and New Zealand. They first viewed a 3-minute video of a child with a severe head injury presenting to their resuscitation bay. Next, they were presented with 5 physiologically different simulated scenarios and asked to report whether interventions were required before transporting each patient to neuroimaging. Then, they reported team and system factors contributing to delays in neuroimaging.

Results

Two hundred forty of 296 providers completed the intervention. The percentage of providers reporting that they would directly transport to neuroimaging without intervention was 89% for “stable,” 49% for “Cushing's triad,” 26% for “hypoxic,” 25% for “tachycardic,” and 5% for “extremis.” There were differences noted in responses by profession for the hypoxia and tachycardia cases. No differences were noted between trainees and attending physicians for any cases. The most frequent factors reported as delaying neuroimaging were team decision making and waiting for equipment, medications, and scanner availability.

Conclusions

There is variability in providers' perspectives on the interventions required before transporting severely head-injured patients for imaging. Diverse team and system factors contribute to delays in imaging.
Home Fire Safety Practices and Smoke Detector Program Awareness in an Urban Pediatric Emergency Department Population
Authors: Wood Rachel Lynn , Teach Stephen J. , Rucker Alexandra , Lall Ambika , Chamberlain James M. , Ryan Leticia Manning
Published: October 2016

Objectives

Risk factors for residential fire death (young age, minority race/ethnicity, and low socioeconomic status) are common among urban pediatric emergency department (ED) patients. Community-based resources are available in our region to provide free smoke detector installation. The objective of our study was to describe awareness of these resources and home fire safety practices in this vulnerable population.

Methods

In this cross-sectional study, a brief survey was administered to a convenience sample of caregivers accompanying patients 19 years of age or younger in an urban pediatric ED in Washington, DC. Survey contents focused on participant knowledge of available community-based resources and risk factors for residential fire injury.

Results

Five hundred eleven eligible caregivers were approached, and 401 (78.5%) agreed to participate. Patients accompanying the caregivers were 48% male, 77% African American, and had a mean (SD) age of 6.5 (5.9) years. Of study participants, 256 (63.8%) lived with children younger than 5 years. When asked about available community-based resources for smoke detectors, 240 (59.9%) were unaware of these programs, 319 (79.6%) were interested in participating, and 221 (55.1%) enrolled. Presence of a home smoke detector was reported by 396 respondents (98.7%); however, 346 (86.3%) reported testing these less often than monthly. Two hundred fifty-six 256 (63.8%) lacked a carbon monoxide detector, and 202 (50.4%) had no fire escape plan. Sixty-five (16%) reported indoor smoking, and 92 (22.9%) reported space heater use.

Conclusions

In this urban pediatric ED population, there is limited awareness of community-based resources but high rates of interest in participating once informed. Whereas the self-reported prevalence of home smoke detectors is high in our study population, other fire safety practices are suboptimal.
Reentry Tachycardia in Children
Authors: Hien Maximilian D. , Benito Castro Fernando , Fournier Philippe , Filleron Anne , Tran Tu-Anh
Published: October 2016

Objectives

We report on a rare but severe complication of adenosine use in a child with reentry tachycardia.

Methods and Results

Treatment with adenosine, which is the standard medical therapy of atrioventricular reentry tachycardia, led to the development of an irregular wide complex tachycardia, caused by rapid ventricular response to atrial fibrillation. The girl was finally stabilized with electrical cardioversion. We analyze the pathomechanism and discuss possible treatment options.

Conclusions

Atrial fibrillation, as well as its conduction to the ventricles, can be caused by adenosine. Rapid ventricular response in children with Wolff-Parkinson-White syndrome is more frequent than previously believed. A patient history of atrial fibrillation is a contraindication for cardioversion with adenosine and needs to be assessed in children with reentry tachycardia. High-risk patients may potentially profit from prophylactic comedication with antiarrhythmic agents, such as flecainide, ibutilide, or vernakalant, before adenosine administration.
Prospective memory mediated by interoceptive accuracy: a psychophysiological approach
Authors: Umeda Satoshi , Tochizawa Saiko , Shibata Midori , Terasawa Yuri
Published: October 2016

Previous studies on prospective memory (PM), defined as memory for future intentions, suggest that psychological stress enhances successful PM retrieval. However, the mechanisms underlying this notion remain poorly understood. We hypothesized that PM retrieval is achieved through interaction with autonomic nervous activity, which is mediated by the individual accuracy of interoceptive awareness, as measured by the heartbeat detection task. In this study, the relationship between cardiac reactivity and retrieval of delayed intentions was evaluated using the event-based PM task. Participants were required to detect PM target letters while engaged in an ongoing 2-back working memory task. The results demonstrated that individuals with higher PM task performance had a greater increase in heart rate on PM target presentation. Also, higher interoceptive perceivers showed better PM task performance. This pattern was not observed for working memory task performance. These findings suggest that cardiac afferent signals enhance PM retrieval, which is mediated by individual levels of interoceptive accuracy.

This article is part of the themed issue ‘Interoception beyond homeostasis: affect, cognition and mental health’.
Respiratory modulation of startle eye blink: a new approach to assess afferent signals from the respiratory system
Authors: Schulz André , Schilling Thomas M. , Vögele Claus , Larra Mauro F. , Schächinger Hartmut
Published: October 2016

Current approaches to assess interoception of respiratory functions cannot differentiate between the physiological basis of interoception, i.e. visceral-afferent signal processing, and the psychological process of attention focusing. Furthermore, they typically involve invasive procedures, e.g. induction of respiratory occlusions or the inhalation of CO
2
-enriched air. The aim of this study was to test the capacity of startle methodology to reflect respiratory-related afferent signal processing, independent of invasive procedures. Forty-two healthy participants were tested in a spontaneous breathing and in a 0.25 Hz paced breathing condition. Acoustic startle noises of 105 dB(A) intensity (50 ms white noise) were presented with identical trial frequency at peak and on-going inspiration and expiration, based on a new pattern detection method, involving the online processing of the respiratory belt signal. The results show the highest startle magnitudes during on-going expiration compared with any other measurement points during the respiratory cycle, independent of whether breathing was spontaneous or paced. Afferent signals from slow adapting phasic pulmonary stretch receptors may be responsible for this effect. This study is the first to demonstrate startle modulation by respiration. These results offer the potential to apply startle methodology in the non-invasive testing of interoception-related aspects in respiratory psychophysiology.

This article is part of the themed issue ‘Interoception beyond homeostasis: affect, cognition and mental health’.
The conserved N-terminus of human rhinovirus capsid protein VP4 contains membrane pore-forming activity and is a target for neutralizing antibodies
Authors: Panjwani Anusha , Asfor Amin S. , Tuthill Tobias J.
Published: October 2016

Human rhinovirus is the causative agent of the common cold and belongs to the non-enveloped picornavirus family. A trigger such as receptor binding or low pH initiates conformational changes in the capsid that allow the virus to attach to membranes and form a pore for the translocation of viral RNA into the cytoplasm. We previously showed that recombinant capsid protein VP4 was able to form membrane pores. In this study, we show the N-terminus but not C-terminus of VP4 formed pores with properties similar to full-length VP4 and consistent with the size required for transfer of RNA. Sera against the N-terminus but not C-terminus of VP4 were shown to neutralize virus infectivity. Together, this suggests that the N-terminus of VP4 is responsible for membrane activity. This study contributes to an improved understanding of the mechanisms for involvement of VP4 in entry and its potential as an antiviral target.
Netpredictor: R and Shiny package to perform Drug-Target Bipartite network analysis and prediction of missing links
Authors: Seal Abhik , Wild David J.
Published: October 2016

Netpredictor is an R package for prediction of missing links in any given bipartite network. The package provides utilities to compute missing links in a bipartite and well as unipartite networks using Random Walk with Restart and Network inference algorithm. The package also allows computation of Bipartite network properties, visualization of communities for two different sets of nodes, and calculation of significant interactions between two sets of nodes using permutation based testing. The R standalone package (including detailed introductory vignettes) and associated R Shiny web application is available under the GPL-2 Open Source license and is freely available to download from github Netpredictor repository and Shiny Netpredictor repository respectively.
Sorption of Aluminum to Plasma Membrane Vesicles Isolated from Roots of Scout 66 and Atlas 66 Cultivars of Wheat
Authors: Yermiyahu U. , Brauer D. K. , Kinraide T. B.
Published: October 2016

To further elucidate the mechanisms of differential genotypic tolerance to Al, plasma membrane (PM) vesicles were isolated from whole roots, root tips, and tipless roots of Al3+-sensitive and Al3+-tolerant cultivars (cv) of wheat (Triticum aestivum L. cv Scout 66 and cv Atlas 66, respectively). Vesicles from cv Scout root tips sorbed more Al than vesicles prepared from any other source. The intrinsic surface-charge density of vesicles isolated from cv Scout was 26% more negative than vesicles from cv Atlas (-37.2 versus -29.5 millicoulombs m-2). Growth experiments indicated that cv Scout is slightly more sensitive to La3+ than is cv Atlas, that the cultivars are equally sensitive to H+, and that cv Atlas is slightly more sensitive to SeO42-. The difference in sensitivity to Al3+ was very large; for a 50% inhibition, a 16-fold greater activity of Al3+ was required for cv Atlas. Using a newly developed Gouy-Chapman-Stern model for ion sorption to the PM together with growth-response curves, we estimate that the difference in surface-charge density can account for the slightly greater sensitivity of cv Scout to cationic toxicants and the slightly greater sensitivity of cv Atlas to anionic toxicants. According to our estimates the differences in PM surface negativity and Al sorptive capacity probably account for some of the difference in sensitivity to Al3+, but the greater part of the difference probably arises from other tolerance mechanisms expressed in cv Atlas root tips that reduce the amount of Al3+ that can reach the PM.
Elevated CO2 Effects during Leaf Ontogeny (A New Perspective on Acclimation)
Authors: Miller A. , Tsai C. H. , Hemphill D. , Endres M. , Rodermel S. , Spalding M.
Published: October 2016

For many plants growth in elevated CO2 leads to reduced rates of photosynthesis. To examine the role that leaf ontogeny plays in the acclimation response, we monitored photosynthesis and some related parameters at short intervals throughout the ontogenetic development of tobacco (Nicotiana tabacum L.) leaves under ambient (350 [mu]L L-1)- and high (950 [mu]L L-1)-CO2 conditions. The pattern of photosynthetic rate over time was similar between the two treatments and consistent with the expected pattern for a typical dicot leaf. However, the photosynthesis pattern in high-CO2-grown tobacco was shifted temporally to an earlier maximum and subsequent senescent decline. Ribulose-1,5-biphosphate carboxylase/oxygenase activity appeared to be the main factor regulating photosynthetic rates in both treatments. Therefore, we propose a new model for interpreting the acclimation response. Lowered photosynthetic rates observed during acclimation appear to be the result of a shift in the timing of the normal photosynthetic stages of leaf ontogeny to an earlier onset of the natural decline in photosynthetic rates associated with senescence.
Increased Salt and Drought Tolerance by D-Ononitol Production in Transgenic Nicotiana tabacum L
Authors: Sheveleva E. , Chmara W. , Bohnert H. J. , Jensen R. G.
Published: October 2016

A cDNA encoding myo-inositol O-methyltransferase (IMT1) has been transferred into Nicotiana tabacum cultivar SR1. During drought and salt stress, transformants (I5A) accumulated the methylated inositol D-ononitol in amounts exceeding 35 [mu]mol g-1 fresh weight In I5A, photosynthetic CO2 fixation was inhibited less during salt stress and drought, and the plants recovered faster than wild type. One day after rewatering drought-stressed plants, I5A photosynthesis had recovered 75% versus 57% recovery with cultivar SR1 plants. After 2.5 weeks of 250 mM NaCl in hydroponic solution, I5A fixed 4.9 [plus or minus] 1.4 [mu]mol CO2 m-2 s-1, whereas SR1 fixed 2.5 [plus or minus] 0.6 [mu]mol CO2 m-2 s-1. myo-Inositol, the substrate for IMT1, increases in tobacco under stress. Preconditioning of I5A plants in 50 mM NaCl increased D-ononitol amounts and resulted in increased protection when the plants were stressed subsequently with 150 mM NaCl. Pro, Suc, Fru, and Glc showed substantial diurnal fluctuations in amounts, but D-ononitol did not. Plant transformation resulting in stress-inducible, stable solute accumulation appears to provide better protection under drought and salt-stress conditions than strategies using osmotic adjustment by metabolites that are constitutively present.
Genetic Transformation of Wheat Mediated by Agrobacterium tumefaciens
Authors: Cheng M. , Fry J. E. , Pang S. , Zhou H. , Hironaka C. M. , Duncan D. R. , Conner T. W. , Wan Y.
Published: October 2016

A rapid Agrobacterium tumefaciens-mediated transformation system for wheat was developed using freshly isolated immature embryos, precultured immature embryos, and embryogenic calli as explants. The explants were inoculated with a disarmed A. tumefaciens strain C58 (ABI) harboring the binary vector pMON18365 containing the β-glucuronidase gene with an intron, and a selectable marker, the neomycin phosphotransferase II gene. Various factors were found to influence the transfer-DNA delivery efficiency, such as explant tissue and surfactants present in the inoculation medium. The inoculated immature embryos or embryogenic calli were selected on G418-containing media. Transgenic plants were regenerated from all three types of explants. The total time required from inoculation to the establishment of plants in soil was 2.5 to 3 months. So far, more than 100 transgenic events have been produced. Almost all transformants were morphologically normal. Stable integration, expression, and inheritance of the transgenes were confirmed by molecular and genetic analysis. One to five copies of the transgene were integrated into the wheat genome without rearrangement. Approximately 35% of the transgenic plants received a single copy of the transgenes based on Southern analysis of 26 events. Transgenes in T1 progeny segregated in a Mendelian fashion in most of the transgenic plants.
Patterns and thresholds of grazing‐induced changes in community structure and ecosystem functioning: species‐level responses and the critical role of species traits
Authors: Li Wenhuai , Xu Fengwei , Zheng Shuxia , Taube Friedhelm , Bai Yongfei
Published: October 2016

Overgrazing has resulted in widespread decline in biodiversity and ecosystem functioning in grasslands world‐wide in recent decades. However, few studies have examined the patterns and thresholds of grazing‐induced changes in community structure and ecosystem functioning along a grazing gradient and based on species‐level responses and plant functional traits.

To identify the thresholds of grazing intensity (GI) at both species and community levels, we conducted a grazing manipulation experiment with seven levels of GI (0–9 sheep ha−1) and two topographies (flat vs. slope) in a typical steppe. Four plant functional traits were measured, including specific leaf area (SLA), plant height, leaf nitrogen content (LNC) and stem: leaf ratio.

The threshold of GI that significantly altered community composition was at 3·75 sheep ha−1 for the flat system and 3·0 sheep ha−1 for the slope system. For both flat and slope systems, the threshold GI for changes in primary productivity was at 3·0 sheep ha−1, beyond which the productivity decreased substantially.

At the species level, the abundances of common species, most of which are perennial grasses, declined at moderate grazing intensities (3·0–4·5 sheep ha−1). The abundances of most rare species, which are perennial forbs, declined at low grazing intensities (1·5–3·0 sheep ha−1). SLA and LNC are good predictors of species‐level responses to grazing. Low SLA and high LNC species are negatively affected by high GI, while high SLA and low LNC species are little affected by grazing. The negative effect of GI on species’ abundance was greater in the slope system than in the flat system.

Synthesis and applications. Our results indicate that the structural and functioning thresholds of grazing intensity depend on plant traits and species composition, which is mediated by topographic location. These findings, integrating plant functional traits and threshold approaches, have important implications for determining sustainable grazing intensity in grassland management and biodiversity conservation in semi‐arid regions.
Participatory Budgeting in Australian Local Government: An Initial Assessment and Critical Issues
Authors: Christensen Helen E. , Grant Bligh
Published: October 2016

Participatory budgeting (PB), a process whereby governments seek direct input from citizens into financial decisions, is gaining a foothold in the community engagement practices of Australian local governments. Following questions of definition, we survey the theoretical terrain, locating PB within several components of local democracy. We then provide details of six PB processes in New South Wales, Victoria, and Western Australia. We identify several questions for the future of PB in Australian local governments, including the role of deliberative practices as part of the broader work of councils, the issue of the adaptability of councils and leaders, the impacts upon state and local governments, and the role of third parties. The article concludes by reflecting on how PB sits with democratic practices at the local level if it continues to be implemented.
“Soldiers of Christ” from the Byzantine Perspective: Monks, Emperors, and Conflict in the Early Byzantine Empire
Authors: Roberts Walter
Published: October 2016

This article is an exploration of concept of monks as “soldiers of Christ” in Byzantine Anatolia during the late sixth and early seventh centuries CE. Through a case study of Theodore of Sykeon, this article will explore monks as agents of continuity in the Byzantine Anatolia of the late sixth and early seventh centuries through Theodore's conflicts with the emperors, imperial authorities, and the regional episcopal hierarchy. The conflicts Theodore had with various authority figures of his time were about helping them see the right path of supporting Catholic orthodoxy as the normative belief system of Byzantine society and integrating his rural community of Sykeon into the wider web of imperial and episcopal urban patronage. Thus, conflict in this context was a catalyst for social order and stability rather than a symptom of social collapse. This article also fits into the historiography of the holy man as local patron in Late Antiquity, suggesting an alternate interpretation of this phenomenon as first put forward in Peter Brown's seminal works on this subject.