bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is surveillance imaging in pediatric patients treated for localized rhabdomyosarcoma useful? The European experience
Authors: Vaarwerk Bas , Mallebranche Coralie , Affinita Maria C. , van der Lee Johanna H. , Ferrari Andrea , Chisholm Julia C. , Defachelles Anne‐Sophie , De Salvo Gian Luca , Corradini Nadège , Minard‐Colin Veronique , Morosi Carlo , Brisse Hervé J. , McHugh Kieran , Bisogno Gianni , van Rijn Rick R. , Orbach Daniel , Merks Johannes H. M. 
Published: November 2019

BackgroundAfter the completion of therapy, patients with localized rhabdomyosarcoma (RMS) are subjected to intensive radiological tumor surveillance. However, the clinical benefit of this surveillance is unclear. This study retrospectively analyzed the value of off‐therapy surveillance by comparing the survival of patients in whom relapse was detected by routine imaging (the imaging group) and patients in whom relapse was first suspected by symptoms (the symptom group).MethodsThis study included patients with relapsed RMS after the completion of therapy for localized RMS who were treated in large pediatric oncology hospitals in France, the United Kingdom, Italy, and the Netherlands and who were enrolled in the International Society of Paediatric Oncology Malignant Mesenchymal Tumor 95 (1995‐2004) study, the Italian Paediatric Soft Tissue Sarcoma Committee Rhabdomyosarcoma 96 (1996‐2004) study, or the European Paediatric Soft Tissue Sarcoma Study Group Rhabdomyosarcoma 2005 (2005‐2013) study. The survival times after relapse were compared with a log‐rank test between patients in the imaging group and patients in the symptom group.ResultsIn total, 199 patients with relapsed RMS were included: 78 patients (39.2%) in the imaging group and 121 patients (60.8%) in the symptom group. The median follow‐up time after relapse was 7.4 years (interquartile range, 3.9‐11.5 years) for survivors (n = 86); the 3‐year postrelapse survival rate was 50% (95% confidence interval [CI], 38%‐61%) for the imaging group and 46% (95% CI, 37%‐55%) for the symptom group (P = .7).ConclusionsAlthough systematic routine imaging is the standard of care after RMS therapy, the majority of relapses were detected as a result of clinical symptoms. This study found no survival advantage for patients whose relapse was detected before the emergence of clinical symptoms. These results show that the value of off‐therapy surveillance is controversial, particularly because repeated imaging may also entail potential harm.
Targeted deep sequencing of cell‐free DNA in serous body cavity fluids with malignant, suspicious, and benign cytology
Authors: Yang Soo‐Ryum , Mooney Kelly L. , Libiran Paolo , Jones Carol D. , Joshi Rohan , Lau Hubert D. , Stehr Henning , Berry Gerald J. , Zehnder James L. , Long Steven R. , Kong Christina S. , Kunder Christian A. 
Published: November 2019

BackgroundLiquid biopsy using cell‐free DNA (cfDNA) presents new opportunities for solid tumor genotyping. While studies have demonstrated the utility of cfDNA from plasma, cfDNA from other body fluids remains underexplored.MethodsWe evaluated the molecular features and clinicopathologic correlates of cfDNA from serous body cavity fluids by performing hybrid capture‐based next‐generation sequencing (NGS) on cfDNA isolated from residual effusion supernatants. Twenty‐one serous effusions from pleural (n = 15), peritoneal (n = 5), and pericardial (n = 1) cavity were analyzed.ResultsThe supernatants provided a median cfDNA concentration of 10.3 ng/µL. Notably, all effusions were sequenced successfully to a median depth >1000×, revealing a broad range of genetic alterations including single nucleotide variants, small insertions and deletions, amplifications, and fusions. Specifically, pathogenic alterations were identified in all malignant fluids (13/13), all fluids suspicious for malignancy (2/2), and 1 benign fluid (1/6) from a patient with metastatic cancer. To validate our findings, we examined matching results from 11 patients who underwent additional testing using formalin‐fixed, paraffin‐embedded (FFPE) specimens. In 8 patients, the paired results between FFPE and supernatant testing were concordant, whereas in the remaining 3 patients, supernatant analysis identified additional variants likely associated with resistance to targeted therapies. Additional comparison between FFPE and supernatant testing showed no difference in DNA concentration (P = .5), depth of coverage (P = .6), or allele frequency of pathogenic mutations (P = .7).ConclusioncfDNA isolated from serous body cavity fluids represents a promising source of genomic input for targeted NGS.
Atlas of the neuromuscular system in the Trachymedusa Aglantha digitale: Insights from the advanced hydrozoan
Authors: Norekian Tigran P. , Moroz Leonid L. 
Published: November 2019

AbstractCnidaria is the sister taxon to bilaterian animals, and therefore, represents a key reference lineage to understand early origins and evolution of the neural systems. The hydromedusa Aglantha digitale is arguably the best electrophysiologically studied jellyfish because of its system of giant axons and unique fast swimming/escape behaviors. Here, using a combination of scanning electron microscopy and immunohistochemistry together with phalloidin labeling, we systematically characterize both neural and muscular systems in Aglantha, summarizing and expanding further the previous knowledge on the microscopic neuroanatomy of this crucial reference species. We found that the majority, if not all (~2,500) neurons, that are labeled by FMRFamide antibody are different from those revealed by anti‐α‐tubulin immunostaining, making these two neuronal markers complementary to each other and, therefore, expanding the diversity of neural elements in Aglantha with two distinct neural subsystems. Our data uncovered the complex organization of neural networks forming a functional “annulus‐type” central nervous system with three subsets of giant axons, dozen subtypes of neurons, muscles, and a variety of receptors fully integrated with epithelial conductive pathways supporting swimming, escape and feeding behaviors. The observed unique adaptations within the Aglantha lineage (including giant axons innervating striated muscles) strongly support an extensive and wide‐spread parallel evolution of integrative and effector systems across Metazoa.
The ENCODE Portal as an Epigenomics Resource
Authors: Jou Jennifer , Gabdank Idan , Luo Yunhai , Lin Khine , Sud Paul , Myers Zachary , Hilton Jason A. , Kagda Meenakshi S. , Lam Bonita , O'Neill Emma , Adenekan Philip , Graham Keenan , Baymuradov Ulugbek K. , R. Miyasato Stuart , Strattan J. Seth , Jolanki Otto , Lee Jin‐Wook , Litton Casey , Y. Tanaka Forrest , Hitz Benjamin C. , Cherry J. Michael 
Published: November 2019

AbstractThe Encyclopedia of DNA Elements (ENCODE) web portal hosts genomic data generated by the ENCODE Consortium, Genomics of Gene Regulation, The NIH Roadmap Epigenomics Consortium, and the modENCODE and modERN projects. The goal of the ENCODE project is to build a comprehensive map of the functional elements of the human and mouse genomes. Currently, the portal database stores over 500 TB of raw and processed data from over 15,000 experiments spanning assays that measure gene expression, DNA accessibility, DNA and RNA binding, DNA methylation, and 3D chromatin structure across numerous cell lines, tissue types, and differentiation states with selected genetic and molecular perturbations. The ENCODE portal provides unrestricted access to the aforementioned data and relevant metadata as a service to the scientific community. The metadata model captures the details of the experiments, raw and processed data files, and processing pipelines in human and machine‐readable form and enables the user to search for specific data either using a web browser or programmatically via REST API. Furthermore, ENCODE data can be freely visualized or downloaded for additional analyses. © 2019 The Authors.Basic Protocol: Query the portalSupport Protocol 1: Batch downloadingSupport Protocol 2: Using the cart to download filesSupport Protocol 3: Visualize dataAlternate Protocol: Query building and programmatic access
A scalable and adaptable allocation framework for heterogeneous resources in a large cluster environment
Authors: Filelis‐Papadopoulos Christos , Xiong Huanhuan , Morrison John 
Published: November 2019

SummaryFinding an appropriate resource to host the next application to be deployed in a Cloud environment can be a nontrivial task. To deliver the appropriate level of service, the functional requirements of the application must be met. Ideally, this process involves filtering the best resource from a number of possible candidates while simultaneously satisfying multiple objectives. If timely responses to resource requests are to be maintained, the sophistication of the filtering mechanism and size of the search space have to be carefully balanced. The quality of the solution will thus not readily scale with growth in cloud resources and filtering complexity. This limitation is becoming more evident with the emergence of hyperscale clouds and the increased complexity needed to accommodate the growing heterogeneity in resources. Moreover, meeting nonfunctional requirements, reflecting the Cloud Service Provider's business objects, is also becoming increasingly critical as service utilization and energy efficiency in a typical cloud deployment are extremely low. This paper proposes a re‐examination of the resource allocation problem by proposing a framework to support distributed resource allocation decisions and that can be dynamically populated with strategies to reflect the ever‐growing number of diverse objectives as they become evident in the evolving cloud infrastructure.
Using time series data to assess recent population dynamics of Bald Eagles in the northeast United States
Authors: Hanley Brenda J. , Dhondt André A. , Dennis Brian , Schuler Krysten L. 
Published: November 2019

AbstractWe explored the use of time series data to study the recent demographics of Bald Eagles in the northeast United States. We merged a stage‐structured population matrix model (PMM) into a combinatorial optimization algorithm (COA) to estimate stage‐wise abundances, survival rates, and other dynamics of the eagle population from 1990 to 2018. The PMM includes biannual periods (breeding and non‐breeding), density dependence, and stage‐wise migration and dispersal. We demonstrated theoretically that the information contained in 17 yr of time series data of the reproductive stage would have contained all the information for the entire population. We then tested the performance of the COA in estimating transient and asymptotic population dynamics using simulated data. Finally, we assessed the COA under differing modeling conditions (without stage‐wise dispersal and in the absence of biological assumptions). We found that time series data of the reproductive class, the skeleton of the PMM, and COA are sole ingredients to reliably estimate stage‐wise abundances and survival, but additional biological assumptions are helpful in honing precision of the estimates. The algorithm is a tool to assess population dynamics when demographic data are limited to counts of reproductive adults.
Comparing the Acute Toxicity of Imidacloprid with Alternative Systemic Insecticides in the Aquatic Insect Chironomus dilutus
Authors: Maloney Erin M. , Sykes Hunter , Morrissey Christy , Peru Kerry M. , Headley John V. , Liber Karsten 
Published: November 2019

Abstract
Acute (96-h) toxicities of 5 systemic insecticides (chlorantraniliprole, cyantraniliprole, flupyradifurone, flubendiamide, and sulfoxaflor) were tested on larval Chironomus dilutus and compared with the neonicotinoid imidacloprid. Three insecticides were less acutely toxic than imidacloprid (2.5–25 times lower). However, chlorantraniliprole and cyantraniliprole were 1.5 to 1.8 times more toxic to C. dilutus. Thus, these ryanodine receptor agonists could pose a higher risk to aquatic insects than their neonicotinoid predecessors, warranting further studies. Environ Toxicol Chem 2020;39:587–594. © 2019 SETAC
Dietary Uptake and Depuration Kinetics of Perfluorooctane Sulfonate, Perfluorooctanoic Acid, and Hexafluoropropylene Oxide Dimer Acid (GenX) in a Benthic Fish
Authors: Hassell Kathryn L. , Coggan Timothy L. , Cresswell Tom , Kolobaric Adam , Berry Kathryn , Crosbie Nicholas D. , Blackbeard Judy , Pettigrove Vincent J. , Clarke Bradley O. 
Published: November 2019

Abstract
Per- and poly-fluoroalkyl substances (PFAS) are ubiquitously distributed throughout aquatic environments and can bioaccumulate in organisms. We examined dietary uptake and depuration of a mixture of 3 PFAS: perfluorooctanoic acid (PFOA; C8HF15O2), perfluorooctane sulfonate (PFOS; C8HF17SO3), and hexafluoropropylene oxide dimer acid (HPFO-DA; C6HF11O3; trade name GenX). Benthic fish (blue spot gobies, Pseudogobius sp.) were fed contaminated food (nominal dose 500 ng g–1) daily for a 21-d uptake period, followed by a 42-d depuration period. The compounds PFOA, linear-PFOS (linear PFOS), and total PFOS (sum of linear and branched PFOS) were detected in freeze-dried fish, whereas GenX was not, indicating either a lack of uptake or rapid elimination (&lt;24 h). Depuration rates (d–1) were 0.150 (PFOA), 0.045 (linear-PFOS), and 0.042 (linear+branched-PFOS) with corresponding biological half-lives of 5.9, 15, and 16 d, respectively. The PFOS isomers were eliminated differently, resulting in enrichment of linear-PFOS (70–90%) throughout the depuration period. The present study is the first reported study of GenX dietary bioaccumulation potential in fish, and the first dietary study to investigate uptake and depuration of multiple PFASs simultaneously, allowing us to determine that whereas PFOA and PFOS accumulated as expected, GenX, administered in the same way, did not appear to bioaccumulate. Environ Toxicol Chem 2020;39:595–603. © 2019 SETAC
Abstract
Individually housed fish were exposed to a mixture of per- and poly-fluoroalkyl substances (PFAS) via contaminated food for a 21-d uptake period, followed by a 42-d depuration period. At regular intervals fish were removed, and freeze-dried whole-body tissue was analyzed. PFOA = perfluorooctanoic acid; LC–MS/MS = liquid chromatography–tandem mass spectrometry.
The “Law of Brevity” in animal communication: Sex-specific signaling optimization is determined by call amplitude rather than duration
Authors: Demartsev Vlad , Gordon Naomi , Barocas Adi , Bar-Ziv Einat , Ilany Tchia , Goll Yael , Ilany Amiyaal , Geffen Eli 
Published: November 2019

AbstractThe efficiency of informational transfer is one of the key aspects of any communication system. The informational coding economy of human languages is often demonstrated by their almost universal fit to Zipf's “Law of Brevity,” expressing negative relationship between word length and its usage frequency. Animal vocal systems, however, provided mixed results in their adherence to this relationship, potentially due to conflicting evolutionary pressures related to differences in signaling range and communicational needs. To examine this potential parallel between human and animal vocal communication, and also to explore how divergent, sex-specific, communicational settings affect signaling efficiency within a species, we examined the complete vocal repertoire of rock hyraxes (Procavia capensis). As male and female hyraxes differ in their sociality levels and male hyraxes vocal repertoire is dominated by sexual advertisement songs, we hypothesized that sex-specific vocal repertoires could be subjected to different signaling optimization pressures. Our results show that the sexes differ in repertoire size, call usage, and adherence to coding efficiency principles. Interestingly, the classic call length/call usage relationship is not consistently found in rock hyraxes. Rather, a negative relationship between call amplitude and call usage is found, suggesting that the efficiency of the vocal repertoire is driven by call amplitude rather than duration. We hypothesize that, in contrast to human speech that is mainly intended for short distance, the need for frequent long-range signaling shapes an animal's vocal repertoire efficiency according to the cost of call amplitude rather than call length. However, call duration may be a secondary factor affecting signaling efficiency, in cases where amplitude is under specific selection pressures, such as sexual selection.
Efficient coupling of direct forcing immersed boundary‐lattice Boltzmann method and finite element method to simulate fluid‐structure interactions
Authors: Qin Jianhua , Andreopoulos Yiannis , Jiang Xiaohai , Dong Guodan , Chen Zhihua 
Published: November 2019

SummaryFluid‐structure interactions (FSI) of rigid and flexible bodies are simulated in this article. For the fluid flow, multidirect forcing immersed boundary method (IBM) is adopted to capture the moving boundary, and lattice Boltzmann method (LBM) is used to evolve the flow field. Compared with our previous no‐penetration IBM, less iterations are required in this work. In addition, larger velocity in lattice units can be used and the nonphysical force oscillations are suppressed due to the C3 6‐point kernel. Multi‐relaxation‐time collision operator and local grid refinement are also adopted in LBM to enhance the numerical stability and efficiency. To improve the efficiency of the FSI coupling algorithm, the mesh of the deformable structure can be coarser than the Lagrangian mesh using Newton‐Cotes formulas to integrate the traction on the structure surface. A variety of benchmarks, including flow around a circular cylinder with Reynold number ranging from 20 to 200, forced oscillation of a circular cylinder, vortex‐induced vibration (VIV) of an elastically mounted circular cylinder in two degrees of freedom, and VIV of an elastic cantilever beam attached to a circular cylinder, are carried out to evaluate the accuracy and stability of the present coupling algorithm. For the benchmark FSI problem considered in this article, a reduction of 54% of the calculation time is achieved using coarser structure mesh. As an application of the FSI coupling algorithm, the mechanism of an elastic beam in the wake of a circular cylinder is discussed.
Systemic risk in global volatility spillover networks: Evidence from option‐implied volatility indices
Authors: Yang Zihui , Zhou Yinggang , Cheng Xin 
Published: November 2019

AbstractWith option‐implied volatility indices, we identify networks of global volatility spillovers and examine time‐varying systemic risk across global financial markets. The U.S. stock market is the center of the network and plays a dominant role in the spread of volatility spillover to other markets. The global systemic risks have intensified since the Federal Reserve exited from quantitative easing, hiked interest rate, and shrank its balance sheet. We further show that the U.S. monetary tightening is an important catalyst for the intensifying global systemic risk. Our findings highlight the pernicious effects of monetary tightening after an era of cheap money.
Hemispheric asymmetries in resting‐state EEG and fMRI are related to approach and avoidance behaviour, but not to eating behaviour or BMI
Authors: Morys Filip , Janssen Lieneke K. , Cesnaite Elena , Beyer Frauke , Garcia‐Garcia Isabel , Kube Jana , Kumral Deniz , Liem Franziskus , Mehl Nora , Mahjoory Keyvan , Schrimpf Anne , Gaebler Michael , Margulies Daniel , Villringer Arno , Neumann Jane , Nikulin Vadim V. , Horstmann Annette 
Published: November 2019

AbstractMuch of our behaviour is driven by two motivational dimensions—approach and avoidance. These have been related to frontal hemispheric asymmetries in clinical and resting‐state EEG studies: Approach was linked to higher activity of the left relative to the right hemisphere, while avoidance was related to the opposite pattern. Increased approach behaviour, specifically towards unhealthy foods, is also observed in obesity and has been linked to asymmetry in the framework of the right‐brain hypothesis of obesity. Here, we aimed to replicate previous EEG findings of hemispheric asymmetries for self‐reported approach/avoidance behaviour and to relate them to eating behaviour. Further, we assessed whether resting fMRI hemispheric asymmetries can be detected and whether they are related to approach/avoidance, eating behaviour and BMI. We analysed three samples: Sample 1 (n = 117) containing EEG and fMRI data from lean participants, and Samples 2 (n = 89) and 3 (n = 152) containing fMRI data from lean, overweight and obese participants. In Sample 1, approach behaviour in women was related to EEG, but not to fMRI hemispheric asymmetries. In Sample 2, approach/avoidance behaviours were related to fMRI hemispheric asymmetries. Finally, hemispheric asymmetries were not related to either BMI or eating behaviour in any of the samples. Our study partly replicates previous EEG findings regarding hemispheric asymmetries and indicates that this relationship could also be captured using fMRI. Our findings suggest that eating behaviour and obesity are likely to be mediated by mechanisms not directly relating to frontal asymmetries in neuronal activation quantified with EEG and fMRI.
Spatial and temporal variations in the groundwater contributing areas of inland wetlands
Authors: Park Junehyeong , Wang Dongdong , Kumar Mukesh 
Published: November 2019

AbstractWater quality and groundwater dynamics in wetlands are strongly influenced by the spatiotemporal distribution of contaminant application, and variations and changes in climate, vegetation, and anthropogenic interventions in its neighborhood. For groundwater‐fed wetlands, this relevant neighborhood at least extends to the groundwater contributing area (GCA) boundary. In spite of its importance, understanding of the nature of GCA dynamics vis‐à‐vis meteorological variations remains largely understudied. This work attempts to map GCA of inland forested wetlands. Following that, two specific questions are answered: (a) Is GCA extent and its variation different than that of the topographic contributing area (TCA)? and (b) Is the temporal dynamics of GCA for different wetlands, all of which are experiencing very similar climatological forcing, similar? Our results show that GCAs for wetlands vary temporally, are much different in extent and shape than the TCA, and on an average are larger than the TCA. Although wetlands in the studied watershed experienced similar meteorological forcings, their covariation with forcings varied markedly. Majority of the wetlands registered an increase in GCA during dry period, but for a few the GCA decreased. This highlights the role of additional physical controls, other than meteorological forcings, on temporal dynamics of GCA. Notably, wetlands with larger TCA are found to generally have larger average GCA as well, thus indicating the dominant role of topography in determining the relative size of average GCA over the landscape. Our results provide a refined picture of the spatiotemporal patterns of GCA dynamics and the controls on it. The information will help improve the prediction of wet period dynamics, recharge, and contamination risk of groundwater‐fed wetlands.