bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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.
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
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’.
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

AbstractNetpredictor 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

Abstract
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

Abstract
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

Abstract
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.