bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Burden of Stroke
Authors: Katan Mira , Luft Andreas 
Published: May 2018

AbstractStroke is the second leading cause of death and a major cause of disability worldwide. Its incidence is increasing because the population ages. In addition, more young people are affected by stroke in low- and middle-income countries. Ischemic stroke is more frequent but hemorrhagic stroke is responsible for more deaths and disability-adjusted life-years lost. Incidence and mortality of stroke differ between countries, geographical regions, and ethnic groups. In high-income countries mainly, improvements in prevention, acute treatment, and neurorehabilitation have led to a substantial decrease in the burden of stroke over the past 30 years. This article reviews the epidemiological and clinical data concerning stroke incidence and burden around the globe.
The Pediatric Emergency Care Applied Research Network Registry: A Multicenter Electronic Health Record Registry of Pediatric Emergency Care
Authors: Deakyne Davies Sara , Grundmeier Robert , Campos Diego , Hayes Katie , Bell Jamie , Alessandrini Evaline , Bajaj Lalit , Chamberlain James , Gorelick Marc , Enriquez Rene , Casper T. , Scheid Beth , Kittick Marlena , Dean J. , Alpern Elizabeth ,   the Pediatric Emergency Care Applied Research Network
Published: May 2018

Background Electronic health record (EHR)-based registries allow for robust data to be derived directly from the patient clinical record and can provide important information about processes of care delivery and patient health outcomes.
Methods A data dictionary, and subsequent data model, were developed describing EHR data sources to include all processes of care within the emergency department (ED). ED visit data were deidentified and XML files were created and submitted to a central data coordinating center for inclusion in the registry. Automated data quality control occurred prior to submission through an application created for this project. Data quality reports were created for manual data quality review.
Results The Pediatric Emergency Care Applied Research Network (PECARN) Registry, representing four hospital systems and seven EDs, demonstrates that ED data from disparate health systems and EHR vendors can be harmonized for use in a single registry with a common data model. The current PECARN Registry represents data from 2,019,461 pediatric ED visits, 894,503 distinct patients, more than 12.5 million narrative reports, and 12,469,754 laboratory tests and continues to accrue data monthly.
Conclusion The Registry is a robust harmonized clinical registry that includes data from diverse patients, sites, and EHR vendors derived via data extraction, deidentification, and secure submission to a central data coordinating center. The data provided may be used for benchmarking, clinical quality improvement, and comparative effectiveness research.
Meniscus Repair in Children and Adolescents: A Systematic Review of Treatment Approaches, Meniscal Healing, and Outcomes
Authors: Ferrari Márcio Balbinotti , Murphy Colin P. , Gomes João Luiz Ellera 
Published: May 2018

AbstractAlthough the consequences of traumatic meniscus tears and the importance of meniscal repair are well-established in adults, the same cannot be said for the young population. Better evidence regarding the outcomes following traumatic meniscal tears in children would improve our understanding of this increasing pathology and help define important factors in deciding the best treatment option. A systematic review was performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines using the Cochrane Database of Systematic Review, Cochrane Central Register of Controlled Trials, MEDLINE Ovid, and MEDLINE PubMed databases. Inclusion criteria were as follows: studies reporting the outcomes of meniscal repair in patients 18 years old or younger, with a minimum mean follow-up of 12 months, Portuguese, Spanish, or English languages, and human studies including 10 or more patients. Our search identified 2,534 individual titles. After application of the inclusion and exclusion criteria, 8 studies were included, evaluating 287 patients with repaired meniscal tears. All eight studies were classified as level of evidence IV. The mean methodological index for nonrandomized studies score was 8.6 ± 1.4. Meniscal repair included all meniscal zones and tear patterns. Anterior cruciate ligament tear was the most common associated injury. The all-inside and inside-out techniques were predominantly reported. The majority of the patients reported good to excellent outcomes and had clinical signals of meniscal healing; meniscectomies following meniscal repair were performed in just 44 cases. In conclusion, meniscal tears in pediatrics are not uncommon. Repairs of this injury were associated with good to excellent outcomes in most patients, regardless of the injury pattern, zone, or technique. Reported complications were minimal; however, higher quality studies are needed to confirm the findings of this systematic review. This is a systematic review study with Level IV.
Return to Sport after ACL Surgery: A Comparison between Two Different Reconstructive Techniques
Authors: Baldassarri Matteo , Perazzo Luca , Ghinelli Diego , Ricciarelli Marco , Pilla Federico , Buda Roberto 
Published: May 2018

AbstractThe anterior cruciate ligament reconstruction (ACLR) has become a very common surgical procedure. One of the main success indicators of the surgical procedure is the return to preinjury sporting level. In recent years, reconstructive techniques have been geared toward less morbidity and optimized ligaments process to speed up the recovery of sports activity. This study compares clinical and imaging data, to evaluate the timing of return to sport, of two populations undergoing ACLR using two different techniques: ACLR with hamstring maintaining tibial insertion (MHG) and an all-inside technique with complete hamstring detachment (DHG). Patients were clinically evaluated with Marx rating scale, International Knee Documentation Committee (IKDC) score, and Tegner activity scale at a minimum follow-up (FU) of 4 years. The two groups have homogeneous characteristics: age, sex, type, and level of sports activity. Since November 2012, 59 patients with unilateral ACL insufficiency underwent ACLR: 31 patients using the MHG technique and 28 patients using the DHG technique. In both groups, a significant improvement in the clinical scores of the administered tests was observed. The MHG group reported a higher percentage of normal knees (83.8%) compared with the DHG group (78.6%). IKDC subjective score improved at each FU. Comparing the two techniques, at 12 months' FU the MHG group achieved better IKDC results (89.6) compared with the DHG technique (84.2). Marx and Tegner score values improved over time reaching comparable results at final FU. At final FU, 98% of patients returned to the same preinjury professional sporting level. Both techniques have been able to provide good clinical results. The MHG group, however, had a resumption of sports activity of the same level and intensity slightly longer (6.3 months) than that in the DHG group (5.9 months). Furthermore, the resumption of training and athletic gestures for the type of sport practiced was earlier than the DHG group. However, in the long run the level of sporting activity leveled in both groups, demonstrating the effectiveness of both techniques.
Dyspnea in the Supine Position after Anterior Cervical Discectomy and Fusion
Authors: Zhang Hua 
Published: May 2018

AbstractPosterior occipitocervicothoracic fusion in a flexed position may cause dyspnea, and the onset of obstructive sleep apnea after anterior upper cervical fusion. However, there are no reports of dyspnea occurring after anterior lower cervical fusion. Here, we present an unusual case of dyspnea in the supine position after a C5-C6 anterior cervical discectomy and fusion.
Radiographic Diagnosis of Scapholunate Diastasis in Distal Radius Fractures: Implications for Surgical Practice
Authors: Özkan Sezai , Korteweg Julian , Bloemers Frank , DiGiovanni Nicholas , Mudgal Chaitanya 
Published: May 2018

Background Radiographic diagnosis of scapholunate ligament injury (SLI) in the setting of distal radius fractures (DRFs) is challenging. It remains unclear to what extent radiographic diagnosis of SLI by a radiologist influences surgical decision-making regarding treatment of SLI.
Purpose We aimed to (1) identify the number of times that concerns for the possibility of concurrent SLI in the setting of a DRF had been raised by the radiologists, (2) identify how often the radiologist's diagnosis was confirmed by the treating surgeon, and (3) how many of the patients with a radiographic concern for SLI by the radiologist received operative treatment for the SLI.
Patients and Methods Based on Current Procedural Terminology codes, we identified 2,923 patients that were operatively treated for their DRF in 1 of 3 participating institutions in an urban city in the United States. We reviewed the medical charts of 654 patients who had a mention of scapholunate ligament (SL) distance in their radiography, surgery, or clinical notes. We then measured the SL distance and recorded patient, diagnosis, and treatment characteristics of all these patients.
Results A total of 200 out of 2,923 patients (6.8%) received a radiological diagnosis of SLI. In seven of these patients (3.5%), the surgeon confirmed the diagnosis of the radiologist. Four patients (2%) had operative repair of their SLI.
Conclusion Radiologists demonstrate a low threshold to identify SLI in the setting of DRFs, while the number of SLIs identified by the treating surgeon is a remarkably smaller number.
Level of Evidence Level II, prognostic study.
Skin Punctures in Preterm Infants in the First 2 Weeks of Life
Authors: Butler Daryl , Sheehan Orla , Livingstone Vicki , Dempsey Eugene , Finn Daragh 
Published: May 2018

Objective The objective of this study was to investigate frequency and trends of skin punctures in preterm infants.
Study Design A prospective audit of preterm infants less than 35 weeks admitted over a 6-month period to a tertiary neonatal intensive care unit. Each skin puncture performed in the first 2 weeks of life was documented in a specifically designed audit sheet.
Results Ninety-nine preterm infants were enrolled. Infants born at < 32 weeks' gestation had significantly more skin punctures than infants > 32 weeks (median skin punctures 26.5 vs. 17, p-value < 0.05). The highest frequency of skin punctures occurred during the first week of life for infants > 28 weeks' gestation (medians 17.5 in 28–31 + 6 weeks' gestation, and 15 in > 32 weeks), and during the second week of life for those born at < 28 weeks (median 17.5). Infants with sepsis had more skin punctures (p-value < 0.001), but this was not significant on multivariate analysis. Median skin punctures in the second week of life were statistically higher in the sepsis group on multivariate analysis (odds ratio: 1.07, 95% confidence interval: 1.00–1.14, p = 0.041).
Conclusion Frequency of skin punctures is influenced by gestational age and postnatal age. Skin punctures were not an independent risk factor for sepsis.
The Impact of Frailty on Postoperative Cardiopulmonary Complications in the Emergency General Surgery Population
Authors: Akyar Serra , Armenia Sarah , Ratnani Parita , Merchant Aziz 
Published: May 2018

Background The burden of frail patients undergoing emergency general surgery (EGS) is increasing rapidly and this population is particularly susceptible to postoperative cardiopulmonary complications and mortality. We aimed to determine the association between frailty, as defined by the previously described modified frailty index (mFI), and postoperative respiratory complications (unplanned reintubation, pneumonia, and prolonged ventilation), cardiac complications (myocardial infarction and cardiac arrest), and mortality. We also sought to identify the most significant determinants of frailty in the highest risk patients based on the specific variables comprising the mFI.
Methods We performed a retrospective observational analysis of the prospectively collected American College of Surgeons National Surgical Quality Improvement Program database. Files from 2005 to 2015 identified 132,765 inpatients who underwent EGS. mFI scores were calculated for each patient. The effect of increasing frailty on unplanned reintubation, pneumonia, prolonged ventilation, myocardial infarction, cardiac arrest, and mortality was evaluated using bivariate analysis. Multivariable logistic regression was used to compare mFI with additional predictor variables including race, gender, physical status as defined by the American Society of Anesthesiologists, disseminated cancer, renal failure, smoking status, sepsis, wound presence/classification, dyspnea, and previous ventilator dependence.
Results Unplanned reintubation, pneumonia, prolonged ventilation, myocardial infarction, cardiac arrest, and mortality were significantly associated with frailty, and the odds of each postoperative complication increased with increasing mFI score. Of the frailest patients (mFI ≥3) that experienced cardiopulmonary complications or mortality, the variables of the mFI that contributed most to frailty were hypertension requiring medication and functional status before surgery.
Conclusions A higher mFI score is associated with increased odds of postoperative cardiopulmonary complications and mortality in the EGS population. Specific variables of the mFI can also provide valuable information for assessing odds in the frailest patients undergoing EGS.
Using Bayesian Kriging for Spatial Smoothing in Crop Insurance Rating
Authors: Park Eunchun , Brorsen B. Wade , Harri Ardian 
Published: May 2018

AbstractRating insurance policies depends on the probability of events in the tail of a distribution. A method to measure such tail‐related risk based on Extreme Value Theory could potentially improve insurance rating. It is also widely agreed that there is a spatial structure to crop yield distributions. Considering the spatial structure may provide more precisely rated policies. In this context, this research provides two contributions in rating area yield crop insurance. One is to provide a method that fits the tail of crop yield distributions using the Generalized Pareto Distribution (GPD), a member of the family of extreme value distributions that models only the tail of the distribution. The second is to estimate parameters of the distribution using a Bayesian Kriging approach that provides spatial smoothing of GPD parameters. The proposed model provides estimates of the spatial structure across regions such as the maximum distance of the spatial effect. Based on an out‐of‐sample performance game between a private insurance company and the federal agency the proposed model provides considerable improvement, particularly when rating deeper tail probability.
Association Between Change in Central Nocturnal Blood Pressure and Urine Albumin–Creatinine Ratio by a Valsartan/Amlodipine Combination: A CPET Study
Authors: Fujiwara Takeshi , Yano Yuichiro , Hoshide Satoshi , Kanegae Hiroshi , Hashimoto Junichiro , Kario Kazuomi 
Published: May 2018

Abstract

BACKGROUND
We aimed to assess the association of changes in brachial or central nocturnal systolic blood pressure (SBP) with change in urine albumin–creatinine ratio (UACR) by a valsartan/amlodipine combination (80/5 mg) therapy in hypertensive patients.

METHODS
Twenty-three patients (age range, 47–78 years; mean, 68.0 years; 35% men, 65% with chronic kidney disease) with clinic brachial BP ≥140/90 mm Hg were treated with valsartan/amlodipine combination therapy for 16 weeks. At baseline and 16 weeks later, we measured brachial and central nocturnal SBP using an oscillometric Mobil-O-Graph device and UACR by spot urine in 23 patients.

RESULTS
The changes in brachial nocturnal SBP (r = 0.445, P = 0.033) and those in central nocturnal SBP (r = 0.616, P = 0.002) were significantly associated with change in UACR by intervention. In multivariable-adjusted multiple regression analyses including changes in both brachial and central nocturnal SBP jointly, only central nocturnal SBP change retained a statistically significant association with change in UACR (β = 0.919, P = 0.020).

CONCLUSIONS
Lowering central nocturnal SBP by a valsartan/amlodipine combination therapy was associated with reduction of UACR, independently of brachial nocturnal SBP reduction. Central nocturnal SBP may be a therapeutic target to protect the kidney. A larger scale interventional study will be needed to confirm the kidney protection conferred by lowering central nocturnal SBP.

CLINICAL TRIALS REGISTRATION
Trial Number UMIN000013519.
RIFRAF: a frame-resolving consensus algorithm
Authors: Eren Kemal , Murrell Ben 
Published: May 2018

Abstract

Motivation
Protein coding genes can be studied using long-read next generation sequencing. However, high rates of indel sequencing errors are problematic, corrupting the reading frame. Even the consensus of multiple independent sequence reads retains indel errors. To solve this problem, we introduce Reference-Informed Frame-Resolving multiple-Alignment Free template inference algorithm (RIFRAF), a sequence consensus algorithm that takes a set of error-prone reads and a reference sequence and infers an accurate in-frame consensus. RIFRAF uses a novel structure, analogous to a two-layer hidden Markov model: the consensus is optimized to maximize alignment scores with both the set of noisy reads and with a reference. The template-to-reads component of the model encodes the preponderance of indels, and is sensitive to the per-base quality scores, giving greater weight to more accurate bases. The reference-to-template component of the model penalizes frame-destroying indels. A local search algorithm proceeds in stages to find the best consensus sequence for both objectives.

Results
Using Pacific Biosciences SMRT sequences from an HIV-1 env clone, NL4-3, we compare our approach to other consensus and frame correction methods. RIFRAF consistently finds a consensus sequence that is more accurate and in-frame, especially with small numbers of reads. It was able to perfectly reconstruct over 80% of consensus sequences from as few as three reads, whereas the best alternative required twice as many. RIFRAF is able to achieve these results and keep the consensus in-frame even with a distantly related reference sequence. Moreover, unlike other frame correction methods, RIFRAF can detect and keep true indels while removing erroneous ones.

Availability and implementation
RIFRAF is implemented in Julia, and source code is publicly available at https://github.com/MurrellGroup/Rifraf.jl.

Supplementary information
Supplementary data are available at Bioinformatics online.
MODE-TASK: large-scale protein motion tools
Authors: Ross Caroline , Nizami Bilal , Glenister Michael , Sheik Amamuddy Olivier , Atilgan Ali Rana , Atilgan Canan , Tastan Bishop Özlem 
Published: May 2018

Abstract

Summary
MODE-TASK, a novel and versatile software suite, comprises Principal Component Analysis, Multidimensional Scaling, and t-Distributed Stochastic Neighbor Embedding techniques using Molecular Dynamics trajectories. MODE-TASK also includes a Normal Mode Analysis tool based on Anisotropic Network Model so as to provide a variety of ways to analyse and compare large-scale motions of protein complexes for which long MD simulations are prohibitive. Beside the command line function, a GUI has been developed as a PyMOL plugin.

Availability and implementation
MODE-TASK is open source, and available for download from https://github.com/RUBi-ZA/MODE-TASK. It is implemented in Python and C++. It is compatible with Python 2.x and Python 3.x and can be installed by Conda.

Supplementary information
Supplementary data are available at Bioinformatics online.
GateFinder: projection-based gating strategy optimization for flow and mass cytometry
Authors: Aghaeepour Nima , Simonds Erin F , Knapp David J H F , Bruggner Robert V , Sachs Karen , Culos Anthony , Gherardini Pier Federico , Samusik Nikolay , Fragiadakis Gabriela K , Bendall Sean C , Gaudilliere Brice , Angst Martin S , Eaves Connie J , Weiss William A , Fantl Wendy J , Nolan Garry P 
Published: May 2018

Abstract

Motivation
High-parameter single-cell technologies can reveal novel cell populations of interest, but studying or validating these populations using lower-parameter methods remains challenging.

Results
Here, we present GateFinder, an algorithm that enriches high-dimensional cell types with simple, stepwise polygon gates requiring only two markers at a time. A series of case studies of complex cell types illustrates how simplified enrichment strategies can enable more efficient assays, reveal novel biomarkers and clarify underlying biology.

Availability and implementation
The GateFinder algorithm is implemented as a free and open-source package for BioConductor: https://nalab.stanford.edu/gatefinder.

Supplementary information
Supplementary data are available at Bioinformatics online.
Using multivariate mixed-effects selection models for analyzing batch-processed proteomics data with non-ignorable missingness
Authors: Wang Jiebiao , Wang Pei , Hedeker Donald , Chen Lin S 
Published: May 2018

Summary
In quantitative proteomics, mass tag labeling techniques have been widely adopted in mass spectrometry experiments. These techniques allow peptides (short amino acid sequences) and proteins from multiple samples of a batch being detected and quantified in a single experiment, and as such greatly improve the efficiency of protein profiling. However, the batch-processing of samples also results in severe batch effects and non-ignorable missing data occurring at the batch level. Motivated by the breast cancer proteomic data from the Clinical Proteomic Tumor Analysis Consortium, in this work, we developed two tailored multivariate MIxed-effects SElection models (mvMISE) to jointly analyze multiple correlated peptides/proteins in labeled proteomics data, considering the batch effects and the non-ignorable missingness. By taking a multivariate approach, we can borrow information across multiple peptides of the same protein or multiple proteins from the same biological pathway, and thus achieve better statistical efficiency and biological interpretation. These two different models account for different correlation structures among a group of peptides or proteins. Specifically, to model multiple peptides from the same protein, we employed a factor-analytic random effects structure to characterize the high and similar correlations among peptides. To model biological dependence among multiple proteins in a functional pathway, we introduced a graphical lasso penalty on the error precision matrix, and implemented an efficient algorithm based on the alternating direction method of multipliers. Simulations demonstrated the advantages of the proposed models. Applying the proposed methods to the motivating data set, we identified phosphoproteins and biological pathways that showed different activity patterns in triple negative breast tumors versus other breast tumors. The proposed methods can also be applied to other high-dimensional multivariate analyses based on clustered data with or without non-ignorable missingness.
Valuations on Banach Lattices
Authors: Tradacete Pedro , Villanueva Ignacio 
Published: May 2018

Abstract
We provide a general framework for the study of valuations on Banach lattices. This complements and expands several recent works about valuations on function spaces, including $L_p(\mu )$, Orlicz spaces, and spaces $C(K)$ of continuous functions on a compact Hausdorff space. In particular, we study decomposition properties, boundedness, and integral representation of continuous valuations.