bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accounting for tumor purity improves cancer subtype classification from DNA methylation data
Authors: Zhang Weiwei , Feng Hao , Wu Hao , Zheng Xiaoqi 
Published: May 2017

Abstract
Motivation: Tumor sample classification has long been an important task in cancer research. Classifying tumors into different subtypes greatly benefits therapeutic development and facilitates application of precision medicine on patients. In practice, solid tumor tissue samples obtained from clinical settings are always mixtures of cancer and normal cells. Thus, the data obtained from these samples are mixed signals. The ‘tumor purity’, or the percentage of cancer cells in cancer tissue sample, will bias the clustering results if not properly accounted for.
Results: In this article, we developed a model-based clustering method and an R function which uses DNA methylation microarray data to infer tumor subtypes with the consideration of tumor purity. Simulation studies and the analyses of The Cancer Genome Atlas data demonstrate improved results compared with existing methods.
Availability and implementation: InfiniumClust is part of R package InfiniumPurify, which is freely available from CRAN (https://cran.r-project.org/web/packages/InfiniumPurify/index.html).
Contact: hao.wu@emory.edu or xqzheng@shnu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact process with exogenous infection and the scaled SIS process
Authors: Zhang June , Moura José M.F. , Zhang June 
Published: May 2017

Abstract
Propagation of contagion in networks depends on the graph topology. This article is concerned with studying the time-asymptotic behaviour of the extended contact processes on static, undirected, finite-size networks. This is a contact process with nonzero exogenous infection rate (also known as the $\epsilon$-susceptible-infected-susceptible model). The only known analytical characterization of the equilibrium distribution of this process is for complete networks. For large networks with arbitrary topology, it is infeasible to numerically solve for the equilibrium distribution since it requires solving the eigenvalue-eigenvector problem of a matrix that is exponential in $N$, the size of the network. We derive a condition on the infection rates under which, depending on the degree distribution of the network, the equilibrium distribution of extended contact processes on arbitrary, finite-size networks is well approximated by a closed-form formulation. We confirm the goodness of the approximation with small networks answering inference questions like the distribution of the percentage of infected individuals and the most-probable equilibrium configuration. We then use the approximation to analyse the equilibrium distribution of the extended contact process on the 4941-node US Western power grid.
Spatio-temporal models reveal subtle changes to demersal communities following the Exxon Valdez oil spill
Authors: Shelton Andrew O , Hunsicker Mary E , Ward Eric J , Feist Blake E , Blake Rachael , Ward Colette L , Williams Benjamin C , Duffy-Anderson Janet T , Hollowed Anne B , Haynie Alan C 
Published: May 2017

Abstract
Toxic pollutants such as crude oil have direct negative effects for a wide array of marine life. While mortality from acute exposure to oil is obvious, sub-lethal consequences of exposure to petroleum derivatives for growth and reproduction are less evident and sub-lethal effects in fish populations are obscured by natural environmental variation, fishing, and measurement error. We use fisheries independent surveys in the Gulf of Alaska to examine the consequences of the 1989 Exxon Valdez oil spill (EVOS) for demersal fish. We delineate areas across a range of exposure to EVOS and use spatio-temporal models to quantify the abundance of 53 species-groups over 31 years. We compare multiple community metrics for demersal fish in EVOS and Control areas. We find that areas more exposed to EVOS have more negative trends in total groundfish biomass than non-EVOS areas, and that this change is driven primarily by reductions in the abundance of the apex predator guild. We show no signature of increased variability or increased levels of synchrony within EVOS areas. Our analysis supports mild consequences of EVOS for groundfish communities, but suggests that long time-series and assessments of changes at the community level may reveal sub-lethal effects in marine communities.
Deep thinking: a systematic review of mesophotic coral ecosystems
Authors: Turner Joseph A , Babcock Russell C , Hovey Renae , Kendrick Gary A 
Published: May 2017

Abstract
Mesophotic coral ecosystems (MCEs) occur at depths beyond those typically associated with coral reefs. Significant logistical challenges associated with data collection in deep water have resulted in a limited understanding of the ecological relevance of these deeper coral ecosystems. We review the trends in this research, covering the geographic spread of MCE research, the focus of these studies, the methods used, how MCEs differ in terms of species diversity and begin to assess connectivity of coral populations. Clear locational biases were observed, with studies concentrated in a few discrete areas mainly around the Atlantic region. The focus of MCE studies has diversified in recent years and more detailed aspects of MCE ecology are now being investigated in particular areas of research. Advances in technology are also reflected in the current range of research, with a wider variety of methods now employed. However, large information gaps are present in entire regions and particularly in relation to the threats, impacts and subsequent management of MCEs. Analysis of species diversity shows that initial definitions based on depth alone may not be appropriate globally, while further taxonomic resolution may also be required to deduce the full biodiversity of major groups in certain regions. Genetic studies to date show species-specific results, although distinct deeper populations do appear to exist, which raises questions regarding the potential of MCEs to act as refugia.
Validation of deep-sea coral and sponge distribution models in the Aleutian Islands, Alaska
Authors: Rooper Christopher N , Wilborn Rachel , Goddard Pamela , Williams Kresimir , Towler Richard , Hoff Gerald R 
Published: May 2017

Abstract
Spatial management of vulnerable benthic ecosystem components such as deep-sea corals and sponges requires adequate maps of their distribution. These maps are often based on statistical models of survey data. The objective of this project was to validate the predictions of existing presence or absence and abundance models of deep-sea corals and sponges in the Aleutian Islands that were based on bottom trawl survey data. Model validation was conducted by comparing bottom trawl survey model predictions to the observations of an in situ camera survey conducted at randomly selected locations. The measures of goodness of fit (area-under-the-receiver-operator-curve, AUC) for the bottom trawl survey model predictions of camera survey observations ranged from 0.59 to 0.77 (for sponges and coral, respectively) and indicated that the bottom trawl survey models predicted the probability of presence for corals accurately across the Aleutian Islands. The bottom trawl survey models explained as little as 3% of the variability in Stylasteridae density and up to 17% of the variability in coral density. These results indicate that models of deep-sea coral distributions based on presence and absence data from bottom trawl surveys can be accurate and can provide useful information for spatial management of these vulnerable taxa. However, for some other taxa, such as sponges, care should be taken interpreting the results of bottom trawl survey models. An interesting finding of this study was that the residuals from the bottom trawl survey model-camera density relationships were negative in areas that remained open to fishing after 2005, possibly indicating an effect of continued bottom trawling on the abundance of corals in these areas. This study highlights the importance of validating models of species distribution using independent surveys, so that the results can be used with confidence to support decision-making processes.
Silicon-bearing molecules in the shock L1157-B1: first detection of SiS around a Sun-like protostar
Authors: Podio L. , Codella C. , Lefloch B. , Balucani N. , Ceccarelli C. , Bachiller R. , Benedettini M. , Cernicharo J. , Faginas-Lago N. , Fontani F. , Gusdorf A. , Rosi M. 
Published: May 2017

Abstract
The shock L1157-B1 driven by the low-mass protostar L1157-mm is a unique environment to investigate the chemical enrichment due to molecules released from dust grains. IRAM-30m and Plateau de Bure Interferometer observations allow a census of Si-bearing molecules in L1157-B1. We detect SiO and its isotopologues and, for the first time in a shock, SiS. The strong gradient of the [SiO/SiS] abundance ratio across the shock (from ≥180 to ∼25) points to a different chemical origin of the two species. SiO peaks where the jet impacts the cavity walls ([SiO/H2] ∼ 10−6), indicating that SiO is directly released from grains or rapidly formed from released Si in the strong shock occurring at this location. In contrast, SiS is only detected at the head of the cavity opened by previous ejection events ([SiS/H2] ∼ 2 × 10−8). This suggests that SiS is not directly released from the grain cores but instead should be formed through slow gas-phase processes using part of the released silicon. This finding shows that Si-bearing molecules can be useful to distinguish regions where grains or gas-phase chemistry dominates.
Microsurgical Management of Large, Fusiform, Partially Thrombosed Middle Cerebral Artery (M2) Aneurysm with End-to-End M2 Anastomosis: 3-Dimensional Operative Video
Authors: Singh Harminder , da Silva Harley Brito , Straus David C. , Zeinalizadeh Mehdi , Sekhar Laligam N. 
Published: May 2017

Abstract
Technique of Minimally Invasive Cervical Foraminotomy
Authors: Ross Donald A , Bridges Kelly J 
Published: May 2017

Abstract

BACKGROUND
Posterior cervical foraminotomy is a long utilized and commonly performed procedure, but has been supplanted in many cases by anterior procedures. With the advent of minimally invasive techniques, posterior foraminotomy may again deserve a prominent place in the treatment of cervical foraminal stenosis.

OBJECTIVE
To report in detail a successfully utilized minimally invasive technique and the results in a large series of patients, by a single author.

METHODS
The technique is described and illustrated in detail. A retrospective review of the use of this technique in a large series is reported.

RESULTS
Precise details of the technique are described with specific attention to complication avoidance. In over 360 cases, there have been no nerve root injuries other than idiopathic C5 palsies, no wound infections, and a single durotomy that required no specific treatment.

CONCLUSION
Minimally invasive posterior cervical foraminotomy is a well-tolerated and effective procedure which can be performed with minimal complications when attention to detail is maintained.
Refining Operative Strategies for Optic Nerve Decompression: A Morphometric Analysis of Transcranial and Endoscopic Endonasal Techniques Using Clinical Parameters
Authors: Gogela Steven L , Zimmer Lee A , Keller Jeffrey T , Andaluz Norberto 
Published: May 2017

Abstract

BACKGROUND
Various approaches can be considered for decompression of the intracanalicular optic nerve. Although clinical experience has been reported, no quantitative study has yet compared the extent of decompression achieved by an endoscopic endonasal versus transcranial approach.

OBJECTIVE
Toward this aim, our morphometric analysis compared both approaches by quantifying the circumferential degree of optic canal decompression that is possible before any meningeal violation, which would result in cerebrospinal fluid (CSF) leak.

METHODS
From 10 cadaver heads, 20 optic canals were sequentially decompressed using an endoscopic endonasal approach and pterional craniotomy with extradural clinoidectomy. Dissections ended before violation of the sphenoid sinus during the transcranial approach, and before intracranial transgression from the endonasal corridor. Based on our study criteria, decompressions were not maximal for either approach, but were maximal before violating the other compartment. Decompression achieved from each approach was quantified using CT scans for each stage.

RESULTS
Greater circumferential bony optic canal decompression was obtained from transcranial (245.2°) than endonasal (114.8°) routes (P < .001). By endonasal perspective, the anatomical point where the optic nerve traverses intracranially was approximated by the medial border of the anterior ascending cavernous internal carotid artery.

CONCLUSION
Our morphometric analysis comparing optic canal decompression for endonasal and transcranial corridors provides important guidance for this location. Ample visualization and wide exposure can be achieved via a transcranial approach with limited risk of CSF leak. A landmark, where the intracanalicular segment ends and optic nerve traverses intracranially, can mark the extent of decompression safely obtained before risking CSF leak.
An effectiveness hierarchy of preventive interventions: neglected paradigm or self-evident truth?
Authors: Capewell Simon , Capewell Ann 
Published: May 2017

Abstract
Non-communicable disease prevention strategies usually target the four major risk factors of poor diet, tobacco, alcohol and physical inactivity. Yet, the most effective approaches remain disputed. However, increasing evidence supports the concept of an effectiveness hierarchy. Thus, ‘downstream’ preventive activities targeting individuals (such as 1:1 personal advice, health education, ‘nudge’ or primary prevention medications) consistently achieve a smaller population health impact than interventions aimed further ‘upstream’ (for instance, smoke-free legislation, alcohol minimum pricing or regulations eliminating dietary transfats). These comprehensive, policy-based interventions reach all parts of the population and do not depend on a sustained ‘agentic’ individual response. They thus tend to be more effective, more rapid, more equitable and also cost-saving. This effectiveness hierarchy is self-evident to many professionals working in public health. Previously neglected in the wider world, this effectiveness hierarchy now needs to be acknowledged by policy makers.
Reliability of Radiographic Assessments of Adolescent Midshaft Clavicle Fractures by the FACTS Multicenter Study Group
Authors: Li Ying , Donohue Kyna S. , Robbins Christopher B. , Pennock Andrew T. , Ellis Henry B. , Nepple Jeffrey J. , Pandya Nirav , Spence David D. , Willimon Samuel Clifton , Heyworth Benton E. ,   Function After Adolescent Clavicle Trauma and Surgery (FACTS) Multicenter Study Group
Published: May 2017

Objectives:
There is a recent trend toward increased surgical treatment of displaced midshaft clavicle fractures in adolescents. The primary purpose of this study was to evaluate the intrarater and interrater reliability of clavicle fracture classification systems and measurements of displacement, shortening, and angulation in adolescents. The secondary purpose was to compare 2 different measurement methods for fracture shortening.

Methods:
This study was performed by a multicenter study group conducting a prospective, comparative, observational cohort study of adolescent clavicle fractures. Eight raters evaluated 24 deidentified anteroposterior clavicle radiographs selected from patients 10–18 years of age with midshaft clavicle fractures. Two clavicle fracture classification systems were used, and 2 measurements for shortening, 1 measurement for superior–inferior displacement, and 2 measurements for fracture angulation were performed. A minimum of 2 weeks after the first round, the process was repeated. Intraclass correlation coefficients were calculated.

Results:
Good to excellent intrarater and interrater agreement was achieved for the descriptive classification system of fracture displacement, direction of angulation, presence of comminution, and all continuous variables, including both measurements of shortening, superior–inferior displacement, and degrees of angulation. Moderate agreement was achieved for the Arbeitsgemeinschaft für Osteosynthesefragen classification system overall. Mean shortening by 2 different methods were significantly different from each other (P < 0.0001).

Conclusions:
Most radiographic measurements performed by investigators in a multicenter, prospective cohort study of adolescent clavicle fractures demonstrated good-to-excellent intrarater and interrater reliability. Future consensus on the most accurate and clinically appropriate measurement method for fracture shortening is critical.
Effects of Tibial Rotational–guided Growth on the Geometries of Tibial Plateaus and Menisci in Rabbits
Authors: Sevil-Kilimci Figen , Cobanoglu Mutlu , Ocal Mehmet K. , Korkmaz Deniz , Cullu Emre 
Published: May 2017

Background:
There are studies on the use of oblique plate over epiphyses for rotational deformities but the effects of this method on bone are not yet known. The purpose of this study was to determine the effect and rebound effect of rotational-guided growth on the geometries of the tibial plateaus and menisci in a rabbit model of tibial axial rotation.

Methods:
Thirty male rabbits were 6 weeks old when medial and lateral plates were applied to the proximal tibias of the left side. After 4 weeks, 15 rabbits were euthanized (group 1), and the plates from the tibias of the remaining 15 rabbits (group 2) were removed. The rabbits in group 2 were euthanized 4 weeks later.

Results:
In the rabbits of group 1, the most striking differences were a decrease in the lateral tibial slope (from 28.3 to 10.8 degrees) and decrease in the ratio of the lateral plateau covered by the meniscus (from 71.9% to 61.3%). After removing the plates (group 2), the observed values of the rebound effects were 25.9 and 29.8 degrees for the lateral tibial slope, and 76.5% and 77.2% for the ratio of the lateral plateau covered by the meniscus. However, the meniscal geometries continued to change.

Conclusions:
The rotational-guided growth provided by using plates caused a change in the tibial plateau geometry, and the rebound effect, except in the meniscal geometry, was observed after removing the plates in the growing period of the rabbits. Rotational-guided growth for the restoration of tibial axial rotation deformities may be suggested after determining the clinical effects of the increasing meniscal variables.

Level of Evidence:
Clinical relevance: the rotational-guided growth needs close follow-up because of possible changes in anatomy of the bone.
Prospective Evaluation of a Multifaceted Intervention to Improve Outcomes in Intensive Care: The Promoting Respect and Ongoing Safety Through Patient Engagement Communication and Technology Study*
Authors: Dykes Patricia C. , Rozenblum Ronen , Dalal Anuj , Massaro Anthony , Chang Frank , Clements Marsha , Collins Sarah , Donze Jacques , Fagan Maureen , Gazarian Priscilla , Hanna John , Lehmann Lisa , Leone Kathleen , Lipsitz Stuart , McNally Kelly , Morrison Conny , Samal Lipika , Mlaver Eli , Schnock Kumiko , Stade Diana , Williams Deborah , Yoon Catherine , Bates David W. 
Published: May 2017

Objectives:
Studies comprehensively assessing interventions to improve team communication and to engage patients and care partners in ICUs are lacking. This study examines the effectiveness of a patient-centered care and engagement program in the medical ICU.

Design:
Prospective intervention study.

Setting:
Medical ICUs at large tertiary care center.

Patients:
Two thousand one hundred five patient admissions (1,030 before and 1,075 during the intervention) from July 2013 to May 2014 and July 2014 to May 2015.

Interventions:
Structured patient-centered care and engagement training program and web-based technology including ICU safety checklist, tools to develop shared care plan, and messaging platform. Patient and care partner access to online portal to view health information, participate in the care plan, and communicate with providers.

Measurements and Main Results:
Primary outcome was aggregate adverse event rate. Secondary outcomes included patient and care partner satisfaction, care plan concordance, and resource utilization. We included 2,105 patient admissions, (1,030 baseline and 1,075 during intervention periods). The aggregate rate of adverse events fell 29%, from 59.0 per 1,000 patient days (95% CI, 51.8–67.2) to 41.9 per 1,000 patient days (95% CI, 36.3–48.3; p < 0.001), during the intervention period. Satisfaction improved markedly from an overall hospital rating of 71.8 (95% CI, 61.1–82.6) to 93.3 (95% CI, 88.2–98.4; p < 0.001) for patients and from 84.3 (95% CI, 81.3–87.3) to 90.0 (95% CI, 88.1–91.9; p < 0.001) for care partners. No change in care plan concordance or resource utilization.

Conclusions:
Implementation of a structured team communication and patient engagement program in the ICU was associated with a reduction in adverse events and improved patient and care partner satisfaction.
Extracorporeal Membrane Oxygenation for Acute Decompensated Heart Failure
Authors: Dangers Laurence , Bréchot Nicholas , Schmidt Matthieu , Lebreton Guillaume , Hékimian Guillaume , Nieszkowska Ania , Besset Sébastien , Trouillet Jean-Louis , Chastre Jean , Leprince Pascal , Combes Alain , Luyt Charles-Edouard 
Published: May 2017

Objective:
Long-term outcomes of patients treated with venoarterial-extracorporeal membrane oxygenation for acute decompensated heart failure (i.e., cardiogenic shock complicating chronic cardiomyopathy) have not yet been reported. This study was undertaken to describe their outcomes and determine mortality-associated factors.

Design:
Retrospective analysis of data prospectively collected.

Setting:
Twenty-six–bed tertiary hospital ICU.

Patients:
One hundred five patients implanted with venoarterial-extracorporeal membrane oxygenation for acute decompensated heart failure.

Intervention:
None.

Measurements and Main Results:
From March 2007 to January 2015, 105 patients were implanted with venoarterial-extracorporeal membrane oxygenation for acute decompensated heart failure in our ICU (67% of them had an intraaortic balloon pump to unload the left ventricle). Their 1-year survival rate was 42%; most of the survivors were transplanted either directly or after switching to central bilateral centrifugal pump, ventricular-assist device, or total artificial heart. Most deaths occurred early after multiple organ failure. Multivariable analyses retained (odds ratio [95% CI]) pre–extracorporeal membrane oxygenation Sequential Organ Failure Assessment score of more than 11 (3.3 [1.3–8.3]), idiopathic cardiomyopathy (0.4 [0.2–1]), cardiac disease duration greater than 2 years pre–extracorporeal membrane oxygenation (2.8 [1.2–6.9]), and pre–extracorporeal membrane oxygenation blood lactate greater than 4 mmol/L (2.6 [1.03–6.4]) as independent predictors of 1-year mortality. Only 17% of patients with pre–extracorporeal membrane oxygenation Sequential Organ Failure Assessment scores of 14 or more survived, whereas 52% of those with scores less than 7 and 60% of those with scores 7 or more and less than 11 were alive 1 year later.

Conclusions:
Among this selected cohort of 105 patients implanted with venoarterial-extracorporeal membrane oxygenation for acute decompensated heart failure, 1-year survival was 42%, but better for patients with pre–extracorporeal membrane oxygenation Sequential Organ Failure Assessment scores of less than 11. Venoarterial-extracorporeal membrane oxygenation should be considered for patients with acute decompensated heart failure, but timing of implantation is crucial.