bluuebunny/crossref_metadata_2025_split huggingface dataset:
An initial comparative genomic autopsy of wasting disease in sea stars
Authors: Ruiz‐Ramos Dannise V. , Schiebelhut Lauren M. , Hoff Katharina J. , Wares John P. , Dawson Michael N 
Published: February 2020

AbstractBeginning in 2013, sea stars throughout the Eastern North Pacific were decimated by wasting disease, also known as “asteroid idiopathic wasting syndrome” (AIWS) due to its elusive aetiology. The geographic extent and taxonomic scale of AIWS meant events leading up to the outbreak were heterogeneous, multifaceted, and oftentimes unobserved; progression from morbidity to death was rapid, leaving few tell‐tale symptoms. Here, we take a forensic genomic approach to discover candidate genes that may help explain sea star wasting syndrome. We report the first genome and annotation for Pisaster ochraceus, along with differential gene expression (DGE) analyses in four size classes, three tissue types, and in symptomatic and asymptomatic individuals. We integrate nucleotide polymorphisms associated with survivors of the wasting disease outbreak, DGE associated with temperature treatments in P. ochraceus, and DGE associated with wasting in another asteroid Pycnopodia helianthoides. In P. ochraceus, we found DGE across all tissues, among size classes, and between asymptomatic and symptomatic individuals; the strongest wasting‐associated DGE signal was in pyloric caecum. We also found previously identified outlier loci co‐occur with differentially expressed genes. In cross‐species comparisons of symptomatic and asymptomatic individuals, consistent responses distinguish genes associated with invertebrate innate immunity and chemical defence, consistent with context‐dependent stress responses, defensive apoptosis, and tissue degradation. Our analyses thus highlight genomic constituents that may link suspected environmental drivers (elevated temperature) with intrinsic differences among individuals (age/size, alleles associated with susceptibility) that elicit organismal responses (e.g., coelomocyte proliferation) and manifest as sea star wasting mass mortality.
Wavelet‐based approach of time series model for modal identification of a bridge with incomplete input
Authors: Huang C. S. , Le Q. T. , Su W. C. , Chen C. H. 
Published: February 2020

AbstractIdentification of modal parameters of a bridge from its earthquake responses is crucial for performing damage assessment of the structure. However, all the input base excitations of the bridge may not be measured because of economic concerns and sensor malfunctions. Consequently, evaluating the modal parameters of a bridge under the consideration of incomplete input measurements is a challenging and important task. An approach that combines the continuous Cauchy wavelet transform with an autoregressive time‐varying moving average with exogenous input (AR‐TVMA‐X) model is proposed in this study to identify the modal parameters of a multispan bridge under multiple support earthquake excitations with incomplete measurements. The efficiency and efficacy of the proposed approach are first validated using numerically simulated responses of a three‐span continuous beam subjected to multiple support nonstationary excitations. A standard procedure of using the proposed approach to identify the modal parameters is established according to comprehensive studies on the effects of noise in the data, the number of supports whose excitations are used in the AR‐TVMA‐X model, and the orders of the AR‐TVMA‐X model on the accuracy of identifying the modal parameters. This procedure is further applied to process the earthquake responses of a two‐span cable‐stayed 510‐m‐long bridge to demonstrate the engineering applicability of the proposed approach.
De novo genome assembly of Candida glabrata reveals cell wall protein complement and structure of dispersed tandem repeat arrays
Authors: Xu Zhuwei , Green Brian , Benoit Nicole , Schatz Michael , Wheelan Sarah , Cormack Brendan 
Published: February 2020

AbstractCandida glabratais an opportunistic pathogen in humans, responsible for approximately 20% of disseminated candidiasis. Candida glabrata's ability to adhere to host tissue is mediated by GPI‐anchored cell wall proteins (GPI‐CWPs); the corresponding genes contain long tandem repeat regions. These repeat regions resulted in assembly errors in the reference genome. Here, we performed a de novo assembly of the C. glabrata type strain CBS138 using long single‐molecule real‐time reads, with short read sequences (Illumina) for refinement, and constructed telomere‐to‐telomere assemblies of all 13 chromosomes. Our assembly has excellent agreement overall with the current reference genome, but we made substantial corrections within tandem repeat regions. Specifically, we removed 62 genes of which 45 were scrambled due to misassembly in the reference. We annotated 31 novel ORFs of which 24 ORFs are GPI‐CWPs. In addition, we corrected the tandem repeat structure of an additional 21 genes. Our corrections to the genome were substantial, with the length of new genes and tandem repeat corrections amounting to approximately 3.8% of the ORFeome length. As most corrections were within the coding regions of GPI‐CWP genes, our genome assembly establishes a high‐quality reference set of genes and repeat structures for the functional analysis of these cell surface proteins.
Thrombotic microangiopathy following heart transplant in pediatric Danon disease
Authors: Hummel Kevin , Glotzbach Kristi , Menon Shaji , Griffiths Eric , Lal Ashwin K. 
Published: February 2020

AbstractThis case describes an uncommon acute complication of diffuse thrombotic angiopathy and associated aHUS/TTP in an 11‐year‐old girl with Danon disease who underwent orthotopic heart transplant. Shortly after transplant, despite an uncomplicated operative course, the patient developed severe kidney injury and progressive altered mental status, culminating in cerebral edema, brain herniation, and death. She had received a single dose of tacrolimus (FK506) and a single dose of antithymocyte globulin. Sources of progressive somnolence, including oversedation from impaired renal clearance of opiates, and severe myopathy as has been previously described in Danon disease, were ruled out, and the patient continued to decline. Initial brain CT scan early after transplant showed no signs of cerebral edema, but repeat CT indicated severe cerebral edema. Based on autopsy, diffuse thrombotic angiopathy, with signs of hemolytic anemia with schistocytes, was likely responsible for her deterioration in the broader condition of aHUS/TTP.
Comparison of melphalan‐ And busulfan‐based myeloablative conditioning in children undergoing allogeneic transplantation for acute myeloid leukemia or myelodysplasia
Authors: Oshrine Benjamin , Adams Lauren , Nguyen Anh Thy H. , Amankwah Ernest , Shyr David , Hale Gregory , Petrovic Aleksandra 
Published: February 2020

AbstractBackgroundThe optimal conditioning regimen for alloHCT in children with myeloid malignancies remains undefined.ProcedureWe performed a retrospective review of children undergoing alloHCT for AML and MDS over a 10‐year period (2008‐2018) at our institution, comparing the outcomes of recipients of either a myeloablative busulfan‐ or reduced toxicity mel/thio‐based conditioning regimen.ResultsA total of 49 patients underwent alloHCT for AML/MDS (mel/thio, N = 21; busulfan, N = 28). Mel/thio recipients were selected due to pretransplant comorbidities. Recipients of mel/thio were more likely to have t‐AML, and less likely to have MRD <0.1% at the time of alloHCT (57.1% vs 82.1%). Graft failure was more common in busulfan recipients; engraftment kinetics were similar between groups. Sinusoidal obstructive syndrome was diagnosed in 21% of busulfan and no mel/thio recipients (P = .03). One patient in each group died from TRM. Relapse incidence was comparable (mel/thio—29% vs busulfan—32%); however, relapse occurred significantly later in recipients of mel/thio conditioning (median d + 396 vs d + 137; P = .01). As a result, there was a trend toward improved OS at 1 and 3 years in mel/thio recipients (95% vs 74%, P = .06; and 75% vs 50%, P = .11; respectively).ConclusionIn our single institution, when compared to myeloablative busulfan‐based conditioning, use of a mel/thio‐based reduced toxicity regimen resulted in comparable outcomes, despite higher risk patient and disease characteristics. Mel/thio recipients had both more comorbidities and higher risk disease profile, which did not translate into higher rates of either TRM or relapse.
Biodiversity–Ecosystem Functioning (BEF) approach to further understanding aquaculture–environment interactions with application to bivalve culture and benthic ecosystems
Authors: Lacoste Élise , McKindsey Christopher W. , Archambault Philippe 
Published: February 2020

AbstractCoastal benthic ecosystems may be impacted by numerous human activities, including aquaculture, which continues to expand rapidly. Indeed, today aquaculture worldwide provides more biomass for human consumption than do wild fisheries. This rapid development raises questions about the interactions the practice has with the surrounding environment. In order to design strategies of sustainable ecosystem exploitation and marine spatial planning, a better understanding of coastal ecosystem functioning is needed so that tools to quantify impacts of human activities, including aquaculture, may be developed. To achieve this goal, some possible directions proposed are integrated studies leading to new concepts, model development based on these concepts and comparisons of various ecosystems on a global scale. This review draws on existing literature to (i) briefly summarize the major ecological interactions between off‐bottom shellfish aquaculture and the environment, (ii) introduce research on the influence of benthic diversity on ecosystem functioning (BEF relationships) and (iii) propose a holistic approach to conduct aquaculture–environment studies using a BEF approach, highlighting the need for integrated studies that could offer insights and perspectives to guide future research efforts and improve the environmental management of aquaculture.
From the crisis in acute care to postdischarge resilience – The communication experience of Geriatric patients: A qualitative study
Authors: Gabay Gillie 
Published: February 2020

BackgroundHospital readmissions due to illness among geriatric patients result in human suffering and psychological trauma. Resilience in chronic illness protects geriatric patients from outcomes of trauma leads to psychological and physical well‐being and enables bouncing back to life. While communication has been linked to improved health outcomes, little is known about communication pathways in the context of postdischarge resilience.Aim and objectiveTo explore the role of communication pathways that acute‐care clinicians used with geriatric patients in postdischarge resilience.Methodological design and justificationParticipants were ten geriatric patients who were readmitted several times in the past year. Twenty narrative interviews were conducted, one upon discharge and the other a month thereafter. Data for each phase of interviews were analysed using methods of selection mechanisms and Bricolage.Ethical issuesThe ethics committee approved the study. Participants signed an informed‐consent form for participation and publication.FindingsCommunication in acute care that enhanced health literacy, perceived control and reflection, contributed to higher comprehensibility and manageability during the hospitalisation and postdischarge meaningfulness postdischarge, contributing resilience. Participants who experienced other forms of communication demonstrated anxiety and helplessness with lingering psychological trauma postdischarge.ConclusionsAcute care may provide clinicians with opportunities to alleviate the suffering of geriatric patients and contribute to their postdischarge resilience. The suggested T.E.R model delineates communication pathways to fuel the trajectory from psychological trauma to postdischarge resilience in practice.
Non‐Gaussian geostatistical modeling using (skew) t processes
Authors: Bevilacqua Moreno , Caamaño‐Carrillo Christian , Arellano‐Valle Reinaldo B. , Morales‐Oñate Víctor 
Published: February 2020

AbstractWe propose a new model for regression and dependence analysis when addressing spatial data with possibly heavy tails and an asymmetric marginal distribution. We first propose a stationary process with t marginals obtained through scale mixing of a Gaussian process with an inverse square root process with Gamma marginals. We then generalize this construction by considering a skew‐Gaussian process, thus obtaining a process with skew‐t marginal distributions. For the proposed (skew) t process, we study the second‐order and geometrical properties and in the t case, we provide analytic expressions for the bivariate distribution. In an extensive simulation study, we investigate the use of the weighted pairwise likelihood as a method of estimation for the t process. Moreover we compare the performance of the optimal linear predictor of the t process versus the optimal Gaussian predictor. Finally, the effectiveness of our methodology is illustrated by analyzing a georeferenced dataset on maximum temperatures in Australia.
Single subduction zone for the generation of Devonian ophiolites and high‐P metamorphic belts of the Variscan Orogen (NW Iberia)
Authors: Díez Fernández Rubén , Arenas Ricardo , Sánchez Martínez Sonia , Novo‐Fernández Irene , Albert Richard 
Published: February 2020

AbstractWithin the Variscan Orogen, Early Devonian and Late Devonian high‐P belts separated by mid‐Devonian ophiolites can be interpreted as having formed in a single subduction zone. Early Devonian convergence nucleated a Laurussia‐dipping subduction zone from an inherited lithospheric neck (peri‐Gondwanan Cambrian back‐arc). Slab‐retreat induced upper plate extension, mantle incursion and lower plate thermal softening, favouring slab‐detachment within the lower plate and diapiric exhumation of deep‐seated rocks through the overlying mantle up to relaminate the upper plate. Upper plate extension produced mid‐Devonian suprasubduction ocean floor spreading (Devonian ophiolites), while further convergence resulted in plate coupling and intraoceanic ophiolite imbrication. Accretion of the remaining Cambrian ocean heralded Late Devonian subduction of inner sections of Gondwana across the same subduction zone and the underthrusting of mainland Gondwana (culmination of NW Iberian allochthonous pile). Oblique convergence favoured lateral plate sliding, and explained the different lateral positions along Gondwana of terranes separated by Palaeozoic ophiolites.
Improving geospatial query performance of an interoperable geographic situation‐awareness system for disaster response
Authors: Zhang Chuanrong , Zhao Tian , Usery E. Lynn , Varanka Dalia , Li Weidong 
Published: February 2020

AbstractDisaster response operations require fast and coordinated actions based on real‐time disaster situation information. Although crowdsourced geospatial data applications have been demonstrated to be valuable tools for gathering real‐time disaster situation information, they only provide limited utility for disaster response coordination because of the lack of semantic compatibility and interoperability. To help overcome the semantic incompatibility and heterogeneity problems, we use Geospatial Semantic Web (GSW) technologies. We then combine GSW technologies with Web Feature Service requests to access multiple servers. However, a GSW‐based geographic information system often has poor performance due to the complex geometric computations required. The objective of this research is to explore how to use optimization techniques to improve the performance of an interoperable geographic situation‐awareness system (IGSAS) based on GSW technologies for disaster response. We conducted experiments to evaluate various client‐side optimization techniques for improving the performance of an IGSAS prototype for flood disaster response in New Haven, Connecticut. Our experimental results show that the developed prototype can greatly reduce the runtime costs of geospatial semantic queries through on‐the‐fly spatial indexing, tile‐based rendering, efficient algorithms for spatial join, and caching, especially for those spatial‐join geospatial queries that involve a large number of spatial features and heavy geometric computation.
Onset of Cavity Oscillation From Transverse to Longitudinal Mode in a Supersonic Flow
Authors: Pandian S. , Desikan S. L. N. , Niranjan Sahoo 
Published: February 2020

AbstractExperiments are carried out in supersonic flow past cavities (L/D = 1–3) to comprehend cavity oscillation from transverse to longitudinal mode. To characterize this, time-resolved schlieren images and unsteady pressure measurements are carried out. For L/D = 1, the cavity oscillation is in the transverse direction which is characterized by a single vortex along with low frequency oscillations. In the present studies, for the given length and depth, the L/D = 2 cavity shows both transverse and longitudinal mode of oscillations. This dual nature is ascertained through high-speed schlieren images and large rise in the fluctuating pressure. For L/D = 3, the cavity oscillation is in the longitudinal direction accompanied by low values of fluctuating pressure component and number of discrete modes/tones. Hence, it is believed that the transverse to longitudinal mode of cavity oscillation in the present studies occurs between L/D = 2 and 3. These cavities are driven by a thick shear layer where the vortex convection is found to be nonlinear. The comparison of dominant modes/tones with modified Rossiter and Handa relations indicates the necessity to develop a suitable model for transitional cavities. In-depth analyzes in terms of cross-correlation as well as wavelet transform divulge the basis that generates cavity modes/tones and mode switching phenomena, respectively.
Multilayer Analysis of Phan-Thien-Tanner Immiscible Fluids Under Electro-Osmotic and Pressure-Driven Effects in a Slit Microchannel
Authors: Escandón Juan P. , Gómez Juan R. , Hernández Clara G. 
Published: February 2020

Abstract
Because the pumping of samples by viscous drag forces and the use of flow-focusing for several sheath flows are widely used in microfluidic devices applications, the present investigation treats about the transport of multilayer immiscible viscoelastic fluids into a slit microchannel by electro-osmotic and pressure-driven effects. The mathematical formulation for the steady-state analysis of the flow field is based on the Poisson–Boltzmann equation and the Cauchy momentum equation. Each fluid layer has independent physical and electrical properties and is formed by a mixture of an electrolyte with a fluid that provides a viscoelastic behavior that follows the simplified Phan-Thien-Tanner (sPTT) rheological model. In the problem, the fluids are conductive and the walls of the microchannel are dielectrics, yielding electric double layers in the liquid–liquid and solid–liquid interfaces; therefore, the flow field is controlled by interfacial electrostatic conditions. The semi-analytical results are centered in the description of the velocity profiles and in the flowrate as a function of a series of dimensionless parameters arising from the mathematical modeling, where we can observe that the multilayer flow characteristics are related to the type of electrolyte solutions, since when the flow field is formed by two or more, interesting interfacial effects appear that modify the shape of velocity profiles and change the magnitude of flowrate in favor or against, depending of the positions of each fluid layer; in addition, the flow raises or diminishes by applying an external pressure gradient.
Multiobjective Reliability-Based Design of Ship Structures Subjected to Fatigue Damage and Compressive Collapse
Authors: Garbatov Yordan , Huang Ying Cai 
Published: February 2020

AbstractThis work deals with the reliability-based design and optimization of ship structural components subjected to stochastic loads and accounting for the local fatigue damage and buckling and ultimate global strength of the ship hull. The multi-objective structural optimization is performed in minimizing the component net-section area, lateral deflection, and fatigue damage, avoiding local buckling. The probability of compressive collapse and fatigue damage of the ship hull and associated cost is used as a base to define the best design solution. The Pareto frontier solutions, calculated by the non-dominated sorting genetic algorithm (NSGA-II), are employed in defining the feasible solutions of the design variables. The first-order reliability method (FORM) is employed to estimate the Beta reliability index based on the topology of the structural component as a part of the Pareto frontier solutions. Comparing with the original design solution, the optimized section of the identified best design solution area decreased by 9%.
A Critical Examination of the Hysteresis in Wells Turbines Using Computational Fluid Dynamics and Lumped Parameter Models
Authors: Ghisu Tiziano , Cambuli Francesco , Puddu Pierpaolo , Virdis Irene , Carta Mario , Licheri Fabio 
Published: February 2020

Abstract
The hysteretic behavior of oscillating water column (OWC)-installed Wells turbines has been known for decades. The common explanation invokes the presence of unsteady aerodynamics due to the continuously varying incidence of the flow on the turbine blades. This phenomenon is neither new nor unique to Wells turbines, as an aerodynamic hysteresis is present in rapidly oscillating airfoils and wings, as well as in different types of turbomachinery, such as wind turbines and helicopter rotors, which share significant similarities with a Wells turbine. An important difference is the non-dimensional frequency: the hysteresis appears in oscillating airfoils only at frequencies orders of magnitude larger than the ones Wells turbines operate at. This work contains a re-examination of the phenomenon, using both computational fluid dynamics (CFD) and a lumped parameter model, and shows how the aerodynamic hysteresis in Wells turbines is negligible and how the often measured differences in performance between acceleration and deceleration are caused by the capacitive behavior of the OWC system. Results have been verified with respect to both spatial and temporal discretization, for unstalled and stalled operating conditions.
Numerical Fluid–Structure Interaction Analysis of a Wells Turbine With Flexible Blades
Authors: Kincaid Kellis C. , MacPhee David W. 
Published: February 2020

Abstract
Direct energy conversion from ocean waves requires some method of rectifying the oscillatory motion to produce a unidirectional output. The Wells turbine accomplishes this with horizontally mounted symmetric blades, which produce a net torque output when combined with an oscillating water column. Previous studies have been conducted, which investigate the effects of blade profile, turbine solidity, stator tip gap clearance, and a number of guide vane designs intended to improve performance. Both experimental and computational methods have been employed, with computational models typically relying on commercially available computational fluid dynamics (CFD) code and assuming steady-state flow conditions. In this work, the open-source code foam-extend is used to study the transient behavior of a Wells turbine, with both a standard rigid blade and a blade with a flexible trailing edge. A validated model is established, and the effects of various Young’s Moduli are tested and their flow fields analyzed. Significant performance gains are realized, with a nearly 17% increase in output torque in some cases.