bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of an External Radiation Dose Estimation Model for Children Returning to Their Homes in Areas Affected by the Fukushima Nuclear Accident
Authors: Mori Airi , Takahara Shogo , Yoshida Hiroko , Sanada Yukihisa , Munakata Masahiro 
Published: June 2019

Abstract
On 1 April 2017, around 6 y after the Fukushima Daiichi nuclear power station accident, evacuation orders for large affected areas were lifted, and areas to which people could return were expanded. In the current study, a dose estimation model based on a probabilistic approach has been developed to estimate the external radiation doses children would receive after returning to these areas. The target groups are children from infants to high school students, and the target areas are nine municipalities including evacuation areas as of 5 September 2015. The estimation period is for 4 y starting 1 April 2017. Validation of the model in an area for which individual personal dosimetry measurements were available showed that it is valid for infants, kindergarteners, 3rd and 4th grade elementary school students, 5th and 6th grade elementary school students, and junior high school students. Considering the statement of the International Commission on Radiological Protection, the estimated radiation doses for these five age groups were taken to be the 95th percentiles of the predicted distributions as an index of conservative judgement. As a result of our estimations, the 95th percentile doses to all age groups were less than 20 mSv y−1 in all periods and in all areas. The 95th percentile doses in some areas were less than 1 mSv y−1, which is the long-term dosimetric target set by the Japanese government. It should be noted that our results are preliminary, being based on several assumptions and limitations regarding environmental contamination conditions and the behavioral patterns of children. To estimate the children’s doses precisely, further considerations for these assumptions and limitations will be needed.
Acoustic radiation forced impulse-based splenic prediction model using data mining for the noninvasive prediction of esophageal varices in hepatitis C virus advanced fibrosis
Authors: Darweesh Samar K. , Yosry Ayman , Salah Mohammed , Zayed Naglaa , Khairy Ahmad , Awad Abubakr , Mabrouk Mahasen , Albuhairi Ahmed 
Published: June 2019

Background
Esophageal varices (EV) are serious complications of hepatitis C virus (HCV) cirrhosis. Endoscopic screening is expensive, invasive, and uncomfortable. Accordingly, noninvasive methods are mandatory to avoid unnecessary endoscopy. Acoustic radiation forced impulse (ARFI) imaging using point shear wave elastography as demonstrated with virtual touch quantification is a possible noninvasive EV predictor. We aimed to validate the reliability of liver stiffness (LS) and spleen stiffness (SS) by an ARFI-based study together with other noninvasive parameters for EV prediction in HCV patients. Also, we aimed to evaluate the diagnostic performance of a new simple prediction model (incorporating SS) using data mining analysis.

Patients and methods
This cross-sectional study included 200 HCV patients with advanced fibrosis. Labs, endoscopic, ultrasonographic, LS, and SS data were collected. Their accuracy in diagnosing EV was assessed and a data mining analysis was carried out.

Results
Ninety patients (22/46% of F3/F4 patients) had EV (39/30/18/3 patients had grade I/II/III/IV, respectively). LS and SS by ARFI showed high significance in differentiating not only patients with/without EV (P = 0.000 for both) but also correlated with the grading of varices (R = 0.31 and 0.45, respectively; P = 0.000 for both). Spleen longitudinal diameter (SD), splenic vein diameter (SVD), platelets to spleen diameter ratio, LOK index, and FIB-4 score were the best ultrasonographic and biochemical predictors for the prediction of EV [area under receiver operating characteristic (AUROC) 0.79, 0.76, 0.76, 0.74, and 0.71, respectively]. SS (using ARFI) had better diagnostic performance than LS for the prediction of EV (AUROC = 0.76 and 0.70, respectively). The diagnostic performance increased using data mining to construct a simple prediction model: high probability for EV if [(SD cm) × 0.17 + (SVD mm) × 0.06 + (SS) × 0.97] more than 6.35 with AUROC 0.85.

Conclusion
SS by ARFI represents a reliable noninvasive tool for the prediction of EV in HCV patients, especially when incorporated into a new data mining-based prediction model.
Training and Interpreting Machine Learning Algorithms to Evaluate Fall Risk After Emergency Department Visits
Authors: Patterson Brian W. , Engstrom Collin J. , Sah Varun , Smith Maureen A. , Mendonça Eneida A. , Pulia Michael S. , Repplinger Michael D. , Hamedani Azita G. , Page David , Shah Manish N. 
Published: June 2019

Background:Machine learning is increasingly used for risk stratification in health care. Achieving accurate predictive models do not improve outcomes if they cannot be translated into efficacious intervention. Here we examine the potential utility of automated risk stratification and referral intervention to screen older adults for fall risk after emergency department (ED) visits.Objective:This study evaluated several machine learning methodologies for the creation of a risk stratification algorithm using electronic health record data and estimated the effects of a resultant intervention based on algorithm performance in test data.Methods:Data available at the time of ED discharge were retrospectively collected and separated into training and test datasets. Algorithms were developed to predict the outcome of a return visit for fall within 6 months of an ED index visit. Models included random forests, AdaBoost, and regression-based methods. We evaluated models both by the area under the receiver operating characteristic (ROC) curve, also referred to as area under the curve (AUC), and by projected clinical impact, estimating number needed to treat (NNT) and referrals per week for a fall risk intervention.Results:The random forest model achieved an AUC of 0.78, with slightly lower performance in regression-based models. Algorithms with similar performance, when evaluated by AUC, differed when placed into a clinical context with the defined task of estimated NNT in a real-world scenario.Conclusion:The ability to translate the results of our analysis to the potential tradeoff between referral numbers and NNT offers decisionmakers the ability to envision the effects of a proposed intervention before implementation.
“There Is No Before Cancer… There Is Only Cancer.” Perceived Late Effects of Pediatric Cancer on Survivors
Authors: Molinaro Monica L. , Fletcher Paula C. 
Published: June 2019

Background
Although “late effects” connotes experiencing effects later in life, they can emerge immediately after active treatment. The effects that survivors experience have been reported but rarely from the point of view of the survivors regarding their life after treatment.

Objective
To examine the perceived late effects of pediatric cancer on survivors and their self-identified primary support persons in order to understand the multifaceted nature of living after a pediatric cancer diagnosis.

Methods
Using a pragmatic interpretive phenomenology approach, 10 survivors of pediatric cancer (aged 21–28 years) and 9 of their support persons (aged 23–73 years) participated, completing background questionnaires and semistructured, one-on-one interviews. Interview transcripts were analyzed thematically.

Results
Both survivors and support persons acknowledged that survivors experienced negative physical and cognitive health outcomes that require follow-up care. Survivors acknowledged that their cancer experience and residual effects have changed the trajectory of their lives.

Conclusions
Research on young adult survivors of pediatric cancer and the residual/late effects and emotional outcomes they experience is warranted. Longitudinal research can aid in understanding how effects develop or worsen over time.

Implications for Practice
The findings of this study support The Children’s Oncology Group Long-term Follow-up Guidelines for practitioners. As the frontline caring for these individuals and families, nurses’ involvement in transitional care out of treatment is necessary. Continued involvement and understanding of long-term pediatric cancer survivorship for nurses are also imperative for continuity for survivors and families.
Clinical Nurse Specialist–Facilitated Collaborative Skin Assessments for Respiratory Care Devices
Authors: Mahramus Hunt Tara L. , Penoyer Daleen A. 
Published: June 2019

Purpose/Aim:
To evaluate a collaborative skin assessment intervention between respiratory therapists and registered nurses.

Design:
A quality improvement design was used to determine feasibility of a collaborative skin assessment.

Methods:
The collaborative skin assessment intervention included skin assessments, documentation of findings, and use of a treatment guideline for patients using a respiratory care device. Perceptions of the collaborative intervention and pressure injury numbers were measured after a 2-month intervention period.

Results:
Respiratory therapists and registered nurses reported satisfaction with the collaborative intervention; stating it was best practice and could prevent respiratory care device–related pressure injuries. However, timing the skin assessment together was difficult. One device-related pressure injury occurred during the intervention period.

Conclusions:
Respiratory therapists and nurses should partner to perform skin assessments under respiratory devices each shift and develop a plan of care to prevent skin injury. Protocol orders to prevent and treat skin alterations found under respiratory care devices and a dedicated area in the medical record to document skin assessments may be helpful to support efforts to prevent injuries. Additionally, as a result of these efforts, pressure injuries specific to endotracheal tubes declined greater than 50% in 2 critical care units in the year following this quality improvement project.
Understanding Emerging Environmental Health Concerns and Environmental Public Health–Tracking Priorities Among State and Local Professionals in Colorado
Authors: Murphy Jacquelyn A. , Peel Jennifer L. , Butts Tom , McKenzie Lisa M. , Litt Jill S. 
Published: June 2019

Context:
Colorado is experiencing dramatic changes related to population growth, climate change, and expanded industrial activity. Local and state public health professionals are trying to address a growing array of unique public health issues with stagnant or limited resources.

Objectives:
To understand, through perspectives from local and state public health professionals, the alignment of contemporary environmental and community health issues with state and local capacity and state environmental public health–tracking priorities.

Design:
During 2014-2015, we conducted semistructured interviews which informed the development of a statewide survey of Colorado's professionals from public health, emergency management, forestry, and transportation.

Setting:
This work took place in Colorado.

Participants:
Fifteen professionals from public (n = 9), academic (n = 4), and private (n = 2) sectors were interviewed. Forty-seven professionals, representing 34 counties and 40 public agencies, completed the 25-minute online survey.

Main Outcome Measures:
Environmental and community health concerns; contributing factors to environmental concerns; strengths and limitations of capacity to respond to issues; and frequency of community engagement activities.

Results:
Top environmental health concerns were indoor air pollution (eg, radon), outdoor air pollution, and waste management. Transportation, extreme weather (eg, wildfires), and oil and gas development were most frequently reported as major contributing factors to concerns. Obesity, physical inactivity, and mental illness were the top community health concerns. To remain prepared for emerging challenges, professionals cited a need for more spatiotemporal-refined data related to their top concerns in the environmental public health–tracking database, and support from local, state, and federal agencies, in addition to personnel and funding. To address concerns, participants reported frequently working with government officials, advisory committees, and media outlets.

Conclusions:
This project illuminates opportunities to strengthen connections between the state's environmental public health–tracking priorities and local-level capacity related to professionals' top concerns. It also suggests reinforcing and broadening partnerships to improve data infrastructure and inform environmental public health priorities.
Mitigating Ethical Risks in Public-Private Partnerships in Public Health
Authors: Yassanye Diana M. , Anason Andrea P. , Barrett Drue H. 
Published: June 2019

Context:
Partnerships between the public and private sectors are necessary in public health and health care. Each partner provides skills, resources, and capabilities. When the public sector, including government, enters into a partnership with a nongovernmental or corporate entity, it is important to determine in advance whether there are real or perceived ethical, financial, or programmatic risks to the organization that might need mitigation.

Program:
This article describes how the Centers for Disease Control and Prevention has approached assessing ethical considerations of public-private partnerships, especially those involving monetary or in-kind gifts.

Implementation:
There are practices that can be applied no matter the size or structure of the organization that can lead to transparency and accountability for a potential partnership.

Discussion:
Examples in this article include a list of practical considerations to review before entering into a new partnership, as well as illustrative anecdotes.
The influence of thermal extremes on coral reef fish behaviour in the Persian Gulf
Authors: D’Agostino Daniele , Burt John A. , Tom Reader , Vaughan Grace O. , Chapman Ben B. , Veronica Santinelli , Cavalcante Geórgenes H. , Feary David A. 
Published: June 2019

AbstractDespite increasing environmental variability within marine ecosystems, little is known about how coral reef fish species will cope with future climate scenarios. The Arabian/Persian Gulf is an extreme environment, providing an opportunity to study fish behaviour on reefs with seasonal temperature ranges which include both values above the mortality threshold of Indo-Pacific reef fish, and values below the optimum temperature for growth. Summer temperatures in the Gulf are comparable to those predicted for the tropical ocean by 2090-2099. Using field observations in winter, spring and summer, and laboratory experiments, we examined the foraging activity, distance from refugia and resting time ofPomacentrus trichrourus(pale-tail damselfish). Observations of fish behaviour in natural conditions showed that individuals substantially reduced distance from refugia and feeding rate and increased resting time at sub-optimal environmental temperatures in winter (average SST = 21°C) and summer (average SST = 34°C), while showing high movement and feeding activity in spring (average SST= 27°C). Diet was dominated by plankton in winter and spring, while fish used both plankton and benthic trophic resources in summer. These findings were corroborated under laboratory conditions: in a replicated aquarium experiment, time away from refugia and activity were significantly higher at 28°C (i.e., spring temperature conditions) compared to 21 °C (i.e., winter temperature conditions). Our findings suggest thatP. trichrourusmay have adapted to the Arabian/Persian Gulf environment by downregulating costly activity during winter and summer and upregulating activity and increasing energy stores in spring. Such adaptive behavioural plasticity may be an important factor in the persistence of populations within increasing environmentally variable coral reef ecosystems.
Properties of the full random effect modelling approach with missing covariates
Authors: Nyberg Joakim , Jonsson E. Niclas , Karlsson Mats O. , Häggström Jonas ,   members of the HBGDki Community
Published: June 2019

SummaryTwo full model approaches was compared with respect to their ability to handle missing covariate information. The reference data analysis approach was the full model method in which the covariate effects are estimated conventionally using fixed effects, and missing covariate data is imputed with the median of the non-missing covariate information. This approach was compared to a novel full model method which treats the covariate data as observed data and estimates the covariates as random effects. A consequence of this way of handling the covariates is that no covariate imputation is required and that any missingness in the covariates is handled implicitly. The comparison between the two analysis methods was based on simulated data from a model of height for age z-scores as a function of age. Data was simulated with increasing degrees of randomly missing covariate information (0-90%) and analyzed using each of the two analysis approaches. Not surprisingly, the precision in the parameter estimates from both methods decreased with increasing degrees of missing covariate information. However, while the bias in the parameter estimates increased in a similar fashion for the reference method, the full random effects approach provided unbiased estimates for all degrees of covariate missingness.
hypeR: An R Package for Geneset Enrichment Workflows
Authors: Federico Anthony , Monti Stefano 
Published: June 2019

ABSTRACTSummaryGeneset enrichment is a popular method for annotating high-throughput sequencing data. Existing tools fall short in providing the flexibility to tackle the varied challenges researchers face in such analyses, particularly when analyzing many signatures across multiple experiments. We present a comprehensive R package for geneset enrichment workflows that offers multiple enrichment, visualization, and sharing methods in addition to novel features such as hierarchical geneset analysis and built-in markdown reporting. hypeR is a one-stop solution to performing geneset enrichment for a wide audience and range of use cases.Availability and implementationThe most recent version of the package is available at https://github.com/montilab/hypeR.Supplementary informationComprehensive documentation and tutorials, are available at https://montilab.github.io/hypeR-docs.
Resistance to change? The impact of group medication on AMR gene dynamics during commercial pig production
Authors: Pollock Jolinda , Muwonge Adrian , Hutchings Michael R. , Mainda Geoffrey , Bronsvoort Barend M. , Duggan Laura C. , Gally David L. , Corbishley Alexander 
Published: June 2019

AbstractThe anthropogenic selection of antimicrobial resistance (AMR) genes is under intense scrutiny, particularly in livestock production, where group antimicrobial administration is used to control disease. Whilst large epidemiological studies provide important data on the diversity and distribution of AMR genes, we have little insight into how group antimicrobial administration impacts AMR gene abundance and diversity within a system. Here, faecal microbiome and AMR gene dynamics were tracked for six months through a standard production cycle on a commercial pig unit. Our results demonstrate that specific AMR genes have reached an equilibrium across this farming system to the extent that the levels measured were maintained from suckling through to slaughter, despite increases in microbiome diversity in early development. These levels were not influenced by antibiotic use, either during the production cycle or following whole herd medication. Some AMR genes were found at levels higher than that of the bacterial 16S rRNA gene, indicating widespread distribution across the most common bacterial genera. The targeted AMR genes were also detected in nearby soil samples, several with decreasing abundance with increasing distance from the unit, demonstrating that the farm acts as a point source of AMR gene ‘pollution’. Metagenomic sequencing of a subset of samples identified 144 AMR genes, with higher gene diversity in the piglet samples compared to the sow samples. Critically, despite overwhelming and stable levels of resistance alleles against the main antimicrobials used on this farm, these compounds continue to control the bacterial pathogens responsible for production losses and compromised welfare.ImportanceGroup antibiotic treatment has been used for decades to control bacterial diseases that reduce the productivity and compromise the welfare of livestock. Recent increases in antibiotic resistant infections in humans has resulted in concerns that antibiotic use in livestock may contribute to the development of untreatable bacterial infections in humans. There is however little understanding as to how the genes that bacteria require to become resistant to antibiotics respond during and after group antibiotic treatment of livestock, particularly in systems where high levels of antibiotics have been used for a prolonged period of time. We show that in such a system, levels of specific antibiotic resistance genes are high irrespective of group antibiotic treatments, whilst dramatic reductions in antibiotic use also fail to reduce the levels of these genes. These findings have important implications for public policy relating to the use of antibiotic in livestock farming.
Large-scalein-vitroproduction of red blood cells from human peripheral blood mononuclear cells
Authors: Heshusius Steven , Heideveld Esther , Burger Patrick , Thiel-Valkhof Marijke , Sellink Erica , Varga Eszter , Ovchynnikova Elina , Visser Anna , Martens Joost H.A. , von Lindern Marieke , van den Akker Emile 
Published: June 2019

AbstractTransfusion of donor-derived red blood cells is the most common form of cellular therapy. Donor availability and the potential risk of alloimmunization and other transfusion-related complications may, however, limit the availability of transfusion units especially for chronically transfused patients.In-vitrocultured, customizable red blood cells would negate these concerns and introduce precision medicine. Large-scale, cost effective production depends on optimization of culture conditions. We developed a defined medium and adapted our protocols to GMP culture requirements, which reproducibly provided pure erythroid cultures from peripheral blood mononuclear cells without prior CD34+isolation, and a 3×107-fold increase in erythroblasts in 25 days. Expanded erythroblast cultures could be differentiated to CD71dimCD235a+CD44+CD117−DRAQ5−red blood cells in 12 days. More than 90% of the cells enucleated and expressed adult hemoglobin as well as the correct blood group antigens. Deformability and oxygen binding capacity of cultured red blood cells was comparable toin-vivoreticulocytes. Daily RNA sampling during differentiation followed by RNA-seq provided a high-resolution map/resource of changes occurring during terminal erythropoiesis. The culture process was compatible with upscaling using a G-Rex bioreactor with a capacity of 1L per reactor, allowing transition towards clinical studies and small-scale applications.