bluuebunny/crossref_metadata_2025_split huggingface dataset:
A unified approach for sparse dynamical system inference from temporal measurements
Authors: Pantazis Yannis , Tsamardinos Ioannis 
Published: January 2019

AbstractMotivationTemporal variations in biological systems and more generally in natural sciences are typically modeled as a set of ordinary, partial or stochastic differential or difference equations. Algorithms for learning the structure and the parameters of a dynamical system are distinguished based on whether time is discrete or continuous, observations are time-series or time-course and whether the system is deterministic or stochastic, however, there is no approach able to handle the various types of dynamical systems simultaneously.ResultsIn this paper, we present a unified approach to infer both the structure and the parameters of non-linear dynamical systems of any type under the restriction of being linear with respect to the unknown parameters. Our approach, which is named Unified Sparse Dynamics Learning (USDL), constitutes of two steps. First, an atemporal system of equations is derived through the application of the weak formulation. Then, assuming a sparse representation for the dynamical system, we show that the inference problem can be expressed as a sparse signal recovery problem, allowing the application of an extensive body of algorithms and theoretical results. Results on simulated data demonstrate the efficacy and superiority of the USDL algorithm under multiple interventions and/or stochasticity. Additionally, USDL’s accuracy significantly correlates with theoretical metrics such as the exact recovery coefficient. On real single-cell data, the proposed approach is able to induce high-confidence subgraphs of the signaling pathway.Availability and implementationSource code is available at Bioinformatics online. USDL algorithm has been also integrated in SCENERY (http://scenery.csd.uoc.gr/); an online tool for single-cell mass cytometry analytics.Supplementary informationSupplementary data are available at Bioinformatics online.
Genome-wide identification of circulating-miRNA expression quantitative trait loci reveals the role of several miRNAs in the regulation of cardiometabolic phenotypes
Authors: Nikpay Majid , Beehler Kaitlyn , Valsesia Armand , Hager Jorg , Harper Mary-Ellen , Dent Robert , McPherson Ruth 
Published: January 2019

Abstract

Aims
To identify genetic variants that have a regulatory impact on circulating microRNAs (miRNAs) and to connect genetic risk to blood traits/biomarkers through the circulating miRNAs.

Methods and results
Leveraging miRNA-Seq data and the 1000 Genomes imputed genotypes, we carried out genome-wide association analysis for SNPs that regulate the expression of circulating miRNAs in a sample of 710 unrelated subjects of European ancestry. Wherever possible, we used data from the Framingham and the Geuvadis studies to replicate our findings. We found at least one genome-wide significant (P < 5e−8) miRNA-eQTL (mirQTL) for 143 circulating miRNAs. Overall each mirQTL explained a small portion (<1%) of variation in miRNA levels; however, we identified a few mirQTLs that explained 4% to 20% of variation in miRNA levels in plasma. Unlike trans-mirQTLs (P = 0.7), cis-mirQTLs tend to be also associated with their counterpart mature miRNAs (P < 0.0001), this suggests trans-mirQTLs exert their effect through processes that affect the stability of mature miRNAs; whereas, cis-mirQTLs mainly regulate the expression of primary-miRNAs. Next, we used the identified mirQTLs to investigate the links between circulating miRNAs with blood traits/biomarkers through Mendelian randomization analysis. We found miR-1908-5p plays an important role in regulating low-density lipoprotein (LDL), total cholesterol (TC), fasting glucose, HbA1c, and several lipid-metabolites in blood, whereas, miR-10b-5p mediates the trans-regulatory effect of the ABO locus on several blood proteins, coronary artery disease, and TC. Moreover, we demonstrated that a higher plasma level of miR-199a is causally associated with lower levels of LDL and TC. Finally, we found miR-143-3p and miR-145-5p are functionally related and mediate the effect of ZFPM2 on a number of its protein targets in blood including VEGFA, SERPINE1, and PDGFs.

Conclusions
This study identifies SNPs that have a regulatory impact on circulating miRNAs, and underlines the role of several circulating miRNAs in mediating the effect of a number of GWAS loci on cardiometabolic phenotypes.
Vedolizumab Trough Levels and Histological Healing During Maintenance Therapy in Ulcerative Colitis
Authors: Pouillon Lieven , Rousseau Hélène , Busby-Venner Hélène , De Carvalho Bittencourt Marcelo , Choukour Myriam , Gauchotte Guillaume , Zallot Camille , Danese Silvio , Baumann Cédric , Peyrin-Biroulet Laurent 
Published: January 2019

Abstract

Background and Aims
Histological healing may be the ultimate therapeutic goal in ulcerative colitis [UC]. We investigated, for the first time, the association between vedolizumab trough levels and histological healing in UC.

Methods
This is a single-centre retrospective cohort study including all consecutive UC patients on vedolizumab maintenance therapy who had a histological evaluation blindly to clinical data and underwent therapeutic drug monitoring, between June 2014 and March 2018. Per-event analysis was performed. Histological healing was defined as a Nancy histological index ≤1.

Results
Thirty-five histological samples were analysed. Median [interquartile range] vedolizumab trough levels were higher in the group with histological healing (31.5 [25–49.1] μg/mL) compared with the group without histological healing (15 [9–26.6] μg/mL, p = 0.02). The higher vedolizumab trough level quartiles tended to be associated with greater rates of histological healing [p = 0.10]. A cut-off vedolizumab trough level of 25 μg/mL predicted histological healing with an accuracy of 74% and an area under the receiver operating curve of 0.62 [95% confidence interval 0.58–0.92, p = 0.004]. Bivariate analysis identified a vedolizumab trough level ≥25 µg/mL [p = 0.006], a partial Mayo score ≤1 [p = 0.008], C-reactive protein level <5 mg/L [p = 0.005] and a Mayo endoscopic subscore ≤1 [p = 0.0004] as factors associated with histological healing.

Conclusions
Histological healing was associated with higher vedolizumab trough levels during maintenance therapy in UC. A vedolizumab trough level threshold of 25 μg/mL proved most optimal to predict histological healing according to the Nancy histological index. Confirmation of these data in larger, independent cohorts is needed.
Testing collinearity of vector time series
Authors: McElroy Tucker S , Jach Agnieszka 
Published: January 2019

Summary
We investigate the collinearity of vector time series in the frequency domain, by examining the rank of the spectral density matrix at a given frequency of interest. Rank reduction corresponds to collinearity at the given frequency. When the time series is nonstationary and has been differenced to stationarity, collinearity corresponds to co-integration at a particular frequency. We examine rank through the Schur complements of the spectral density matrix, testing for rank reduction via assessing the positivity of these Schur complements, which are obtained from a nonparametric estimator of the spectral density. New asymptotic results for the test statistics are derived under the fixed bandwidth ratio paradigm; they diverge under the alternative, but under the null hypothesis of collinearity the test statistics converge to a non-standard limiting distribution. Subsampling is used to obtain the limiting null quantiles. A simulation study and an empirical illustration for 6-variate time series data are provided.
Risk stratification by assessment of coronary artery disease using coronary computed tomography angiography in diabetes and non-diabetes patients: a study from the Western Denmark Cardiac Computed Tomography Registry
Authors: Olesen Kevin K W , Riis Anders H , Nielsen Lene H , Steffensen Flemming H , Nørgaard Bjarne L , Jensen Jesper M , Poulsen Per L , Thim Troels , Bøtker Hans Erik , Sørensen Henrik T , Maeng Michael 
Published: January 2019

AbstractAimsWe examined whether severity of coronary artery disease (CAD) measured by coronary computed tomography angiography can be used to predict rates of myocardial infarction (MI) and death in patients with and without diabetes.Methods and resultsA cohort study of consecutive patients (n = 48 731) registered in the Western Denmark Cardiac Computed Tomography Registry from 2008 to 2016. Patients were stratified by diabetes status and CAD severity (no, non-obstructive, or obstructive). Endpoints were MI and death. Event rates per 1000 person-years, unadjusted and adjusted incidence rate ratios were computed. Median follow-up was 3.6 years. Among non-diabetes patients, MI event rates per 1000 person-years were 1.4 for no CAD, 4.1 for non-obstructive CAD, and 9.1 for obstructive CAD. Among diabetes patients, the corresponding rates were 2.1 for no CAD, 4.8 for non-obstructive CAD, and 12.6 for obstructive CAD. Non-diabetes and diabetes patients without CAD had similar low rates of MI [adjusted incidence rate ratio 1.40, 95% confidence interval (CI): 0.71–2.78]. Among diabetes patients, the adjusted risk of MI increased with severity of CAD (no CAD: reference; non-obstructive CAD: adjusted incidence rate ratio 1.71, 95% CI: 0.79–3.68; obstructive CAD: adjusted incidence rate ratio 4.42, 95% CI: 2.14–9.17). Diabetes patients had higher death rates than non-diabetes patients, irrespective of CAD severity.ConclusionIn patients without CAD, diabetes patients have a low risk of MI similar to non-diabetes patients. Further, MI rates increase with CAD severity in both diabetes and non-diabetes patients; with diabetes patients with obstructive CAD having the highest risk of MI.
Differential association between the progression of coronary artery calcium score and coronary plaque volume progression according to statins: the Progression of AtheRosclerotic PlAque DetermIned by Computed TomoGraphic Angiography Imaging (PARADIGM) study
Authors: Lee Sang-Eun , Sung Ji Min , Andreini Daniele , Budoff Matthew J , Cademartiri Filippo , Chinnaiyan Kavitha , Choi Jung Hyun , Chun Eun Ju , Conte Edoardo , Gottlieb Ilan , Hadamitzky Martin , Kim Yong Jin , Kumar Amit , Lee Byoung Kwon , Leipsic Jonathon A , Maffei Erica , Marques Hugo , Pontone Gianluca , Raff Gilbert , Shin Sanghoon , Stone Peter H , Samady Habib , Virmani Renu , Narula Jagat , Berman Daniel S , Shaw Leslee J , Bax Jeroen J , Lin Fay Y , Min James K , Chang Hyuk-Jae 
Published: January 2019

Abstract

Aims
Coronary artery calcium score (CACS) is a strong predictor of major adverse cardiac events (MACE). Conversely, statins, which markedly reduce MACE risk, increase CACS. We explored whether CACS progression represents compositional plaque volume (PV) progression differently according to statin use.

Methods and results
From a prospective multinational registry of consecutive patients (n = 2252) who underwent serial coronary computed tomography angiography (CCTA) at a ≥ 2-year interval, 654 patients (61 ± 10 years, 56% men, inter-scan interval 3.9 ± 1.5 years) with information regarding the use of statins and having a serial CACS were included. Patients were divided into non-statin (n = 246) and statin-taking (n = 408) groups. Coronary PVs (total, calcified, and non-calcified; sum of fibrous, fibro-fatty, and lipid-rich) were quantitatively analysed, and CACS was measured from both CCTAs. Multivariate linear regression models were constructed for both statin-taking and non-statin group to assess the association between compositional PV change and change in CACS. In multivariate linear regression analysis, in the non-statin group, CACS increase was positively associated with both non-calcified (β = 0.369, P = 0.004) and calcified PV increase (β = 1.579, P < 0.001). However, in the statin-taking group, CACS increase was positively associated with calcified PV change (β = 0.756, P < 0.001) but was negatively associated with non-calcified PV change (β = −0.194, P = 0.026).

Conclusion
In the non-statin group, CACS progression indicates the progression of both non-calcified and calcified PV progression. However, under the effect of statins, CACS progression indicates only calcified PV progression, but not non-calcified PV progression. Thus, the result of serial CACS should be differently interpreted according to the use of statins.
Intraoperative flow profiles of arterial and venous bypass grafts to the left coronary territory
Authors: Amin Sanaz , Madsen Per Lav , Werner Raphael S , Krasopoulos George , Taggart David P 
Published: January 2019

Abstract

OBJECTIVES
The different mechanical and vasodilatory properties of arteries and veins may influence their flow profiles when used for coronary artery bypass grafting (CABG). This may be of significance when assessing the cut-off values for adequate flow. However, conduit-related flow differences are less examined.

METHODS
In a study of 268 patients, transit time flowmetry parameters of 336 arterial and 170 venous conduits all grafted to the left coronary territory were compared. With transit time flowmetry, the mean graft flow (MGF), pulsatility index, percentage of diastolic filling and percentage of backwards flow were measured. Conduit-related differences were further compared according to on- or off-pump CABG (ONCABG versus OPCABG) surgery.

RESULTS
Overall MGF and pulsatility index were comparable between arterial and venous grafts, but in arterial grafts, MGF was higher during ONCABG than during OPCABG (49.1 ± 35.3 ml/min vs 38.8 ± 26.6 ml/min; P = 0.003). Percentage of diastolic filling was higher in arterial grafts than in venous grafts (overall 71.0 ± 7.9% vs 63.7 ± 11.1%; ONCABG 69.9 ± 7.1% vs 63.9 ± 10.4%; OPCABG 71.9 ± 8.3% vs 63.4 ± 12.2%; all P < 0.001). Furthermore, percentage of backwards flow was higher in arterial grafts than in venous grafts in the overall (2.3 ± 3.2% vs 1.7 ± 3.2%, P = 0.002) and in the ONCABG (2.3 ± 3.2% vs 1.3 ± 2.5%, P < 0.001) cohorts. In venous grafts, percentage of backwards flow was lower during ONCABG versus OPCABG (1.3 ± 2.5% vs 2.6 ± 3.9%, P = 0.016).

CONCLUSIONS
No statistically significant difference was observed for MGF and pulsatility index between arterial and venous conduits. However, arterial grafts have significantly higher diastolic filling and backwards flow than venous grafts. Furthermore, arterial grafts have a significantly higher MGF in ONCABG versus OPCABG.
Feeling Young and in Control: Daily Control Beliefs Are Associated With Younger Subjective Ages
Authors: Bellingtier Jennifer A , Neupert Shevaun D 
Published: January 2019

Abstract

Objectives
Daily variations in control beliefs are associated with developmental outcomes. We predicted that on days when older adults feel more in control than their personal average, they would also report feeling younger, and explored the relationship in younger adults.

Method
A total of 116 older and 107 younger adults completed a 9-day daily diary study. On Day 1 participants reported on demographic variables. On Days 2–9, participants reported their daily subjective age, daily control beliefs, daily stressors, and daily physical health symptoms. All measures were completed online via Qualtrics. Results were analyzed using multilevel models.

Results
Controlling for age, gender, education, daily stressors, daily physical health, and average control, there was a significant main effect of daily control beliefs on daily subjective age. Older adults felt significantly younger on days with a greater sense of control than usual, but this effect was absent in younger adults. For younger adults, average exposure to daily stressors and daily fluctuations in physical health were better predictors of daily subjective age.

Discussion
These findings suggest that higher daily control is associated with younger subjective ages in older adults, whereas other factors may play a more central role in the daily variations of younger adults’ subjective ages.
Image conditions and addition theorems for prolate and oblate spheroidal-coordinate separation-of-variables acoustic multiple scattering models with perfectly-reflecting flat surfaces
Authors: Shin Ho-Chul 
Published: January 2019

Abstract
Three-dimensional time-harmonic acoustic multiple scattering problems are considered for a finite number of prolate and oblate spheroidal objects adjacent to flat surfaces. Wave propagation by spheroids is modelled by the method of separation of variables equipped with the addition theorems in the spheroidal coordinates. The effect of flat surfaces is accounted for by using the method of images; hence, the flat surfaces are of (semi-)infinite extent and perfectly reflecting: either rigid or pressure release. Wedge-shaped acoustic domains are constructed including half-space and right-angled corners with the wedge angle of $\pi /n$ rad with positive integer $n$. First, Euler angles are implemented to rotate image spheroids to realize the mirror reflection. Then, the ‘image conditions’ are developed to reduce the number of unknowns by expressing the unknown expansion coefficients of image-scattered fields in terms of real counterparts. Use of image conditions to 2D wedges, therefore, leads to the $4n^2$-fold reduction in the size of a matrix for direct solvers and $2n$-times faster computation than the approach without using them; for 3D wedges, the savings are $16n^2$-fold and $4n$-times, respectively. Multiple scattering models (MSMs) are also formulated for fluid, rigid and pressure-release spheroids under either plane- or spherical-wave incidence; novel addition theorems are also derived for spheroidal wavefunctions by using two rotations of spherical wavefunctions and a $z$-axis translation in-between, which is shown numerically more efficient than other addition theorems based on an arbitrary-direction translation and a single rotation. Finally, MSMs using image conditions are numerically validated by the boundary element method for a configuration populated with both prolate and oblate spheroids.
Fundamental Groups of Small Covers Revisited
Authors: Wu Lisu , Yu Li 
Published: January 2019

Abstract
We study the topology of small covers from their fundamental groups. We find a way to obtain explicit presentations of the fundamental group of a small cover. Then we use these presentations to study the relations between the fundamental groups of a small cover and its facial submanifolds. In particular, we can determine when a facial submanifold of a small cover is $\pi _1$-injective in terms of some purely combinatorial data on the underlying simple polytope. In addition, we find that any three-dimensional small cover has an embedded non-simply connected $\pi _1$-injective surface. Using this result and some results of Schoen and Yau [25], we characterize all the three-dimensional small covers that admit Riemannian metrics with nonnegative scalar curvature.
RETRACTED: Comparing Long-Term Outcomes Following Radical and Partial Nephrectomy for cT1 Renal Cell Carcinoma in Young and Healthy Individuals
Authors: Tan Wei Shen , Berg Sebastian , Cole Alexander P , Krimphove Marieke , Marchese Maya , Lipsitz Stuart R , Nabi Junaid , Sammon Jesse D , Choueiri Toni K , Kibel Adam S , Sun Maxine , Chang Steven , Trinh Quoc-Dien 
Published: January 2019

Abstract

Background
Despite randomized data demonstrating better overall survival favoring radical nephrectomy, partial nephrectomy continues to be the treatment of choice for low-stage renal cell carcinoma.

Methods
We utilized the National Cancer Database to identify patients younger than 50 years diagnosed with low-stage renal cell carcinoma (cT1) treated with radical nephrectomy or partial nephrectomy (2004–2007). Inverse probability of treatment weighting adjustment was performed for all preoperative factors to account for confounding factors. Kaplan-Meier curves and Cox proportional hazards regression analyses were used to compare overall survival of patients in the two treatment arms. Sensitivity analysis was performed to explore the interaction of type of surgery and clinical stage on overall survival.

Results
Among the 3009 patients (median age = 44 years [interquartile range (IQR) = 40–47 years]), 2454 patients (81.6%) were treated with radical nephrectomy and 555 patients (18.4%) with partial nephrectomy. The median follow-up was 108.6 months (IQR = 80.2–124.3 months) during which 297 patients (12.1%) in the radical nephrectomy arm and 58 patients (10.5%) in the partial nephrectomy arm died. Following inverse probability of treatment weighting adjustment, there was no difference in overall survival between patients treated with partial nephrectomy and radical nephrectomy (hazard ratio = 0.83, 95% confidence interval = 0.63 to 1.10, P = .196). There were no statistically significant interactions between type of surgery and clinical stage on treatment outcome.

Conclusions
There was no difference in long-term overall survival between radical and partial nephrectomy in young and healthy patients. This patient cohort may have sufficient renal reserve over their lifetime, and preserving nephrons by partial nephrectomy may be unnecessary.
Pediatric Neuroschistosomiasis: A Case Report and Review of the Literature
Authors: Wen Sophie C H , Anderson Rebecca , Ryan Monique M , Kumbla Surekha , Wray Alison , Steer Andrew 
Published: January 2019

Abstract
Neuroschistosomiasis is a rare but severe manifestation of Schistosoma infection. Diagnosis is challenging and surgical biopsy is often required to confirm diagnosis and exclude malignancy. We present a pediatric case of presumed pseudotumoral cerebral schistosomiasis secondary to Schistosoma mansoni with an excellent therapeutic response to empirical praziquantel and corticosteroid treatment.
History of Exercise Testing
Authors: Thomas Gregory S. , Kligfield Paul , Ellestad Myrvin H. 
Published: January 2019

Abstract
The History of Exercise Testing chapter reviews the development of the exercise test from Einthoven to the contributions of Bruce and Ellestad. Feil and Siegel recognized that myocardial ischemia and thus coronary artery disease (CAD) could be diagnosed by ST depression during exercise. Master and Oppenheimer developed the first standardized exercise test, a 1.5-minute step test to evaluate cardiac capacity and cardiovascular disease. Goldhammer and Scherf recommended the use of exercise testing for the diagnosis of chest pain or angina. Wilson’s development of the six chest leads increased the opportunity to detect ischemia with 12 lead electrocardiography. Bruce developed the multi-stage treadmill test now termed the Bruce protocol. An outcome study of Ellestad demonstrated that 1 mm of ST depression predicted cardiac events and death. Following one hundred years of development, the exercise test remains the foundation of stress testing.
When to Use Exercise Testing—Indications, Guidelines and Appropriate Use Criteria
Authors: Thomas Gregory S. , Wann L. Samuel 
Published: January 2019

Abstract
The chapter When to Use Exercise Testing—Indications, Guidelines, and Appropriate Use Criteria (AUC) reviews and interprets the American College of Cardiology and American Heart Association guidelines and AUC. Exercise testing remains the cornerstone of the evaluation of coronary artery disease (CAD) in patients whose electrocardiogram is interpretable for ischemia and who are expected to be able to achieve ≥85% maximum predicted heart rate with exercise. If either is not the case, or if greater test sensitivity is clinically necessary, pharmacologic testing with myocardial perfusion imaging (MPI) or stress echocardiography is indicated. The Duke Activity Status Index (DASI) score can be used as a tool to determine to predict if a patient can perform the recommended ≥5 metabolic equivalents (METs) on an exercise test. The HEART score can be effectively used to determine low risk patients presenting to the emergency room with chest pain can be safely discharged for outpatient evaluation.