bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prescription Opioid Analgesic Use and Mortality in Systemic Lupus Erythematosus
Authors: Cabacungan Romy J. , Qualls Clifford R. , Sibbitt Wilmer L , Hayward William A. , Gibb James I. , Kettwich Selma D. , Fields Roderick A. , Emil N. Suzanne , Fangtham Monthida , Bankhurst Arthur D 
Published: August 2018

AbstractObjectivesThis research investigated the prevalence of opioid analgesic use in patients with systemic lupus erythematosus (SLE).MethodsThis 5-year prospective cohort study of 275 SLE patients focused on prescription opioid use and 5-year outcome. Associations were determined with univariable regression analysis and then multivariable models were created to determine independent effects on dependent variablesResultsPrescription opioid use was common in SLE with 24% using opioid analgesics chronically and 76% not using opioids. Opioid users had a higher rate of tobacco use (p<0.01), cocaine use (p<0.002), mean pain scores (p<0.001), disease activity (SLEDAI-2K) (p<0.001), disease damage (SLICC/ACRDI) (p<0.001), non-adherence to medical therapy (p<0.01), and total deaths at 5 years (opioids: 48.0%, no opioids 19.0%, p<0.001). Logistic regression analysis predicting death revealed opioid use (hazard ratio 2.6, p<0.001) and SLEDAI-2K (1.1, p<0.001) respectively; and opioid use (hazard ratio 2.5, p<0.002), SLEDAI-2K (hazard ratio 1.1, p<0.001), and non-adherence (hazard ratio 1.6, p=0.11), respectively. Multivariable Cox Model analysis estimating probability of death with covariates: opioid use (hazard ratio 2.6, p<0.001) and SLEDAI-2K (hazard ratio 1.1, p<0.001); opioid use (hazard ratios 3.0, p<0.001), and cocaine use (hazard ratio 3.2, p<0.001). The Kaplan-Meir survival analysis revealed a significantly higher probability of death for SLE patients using opioid analgesics.ConclusionsPrescription opioid analgesic use is common in SLE and is associated with markedly increased mortality. Preferably, non-opioid approaches to treat chronic pain should be used in SLE patients.Clinical trial registration numberThis was not a clinical trial.KEY MESSAGES:1. Chronic opioid analgesic use is common in SLE (24%).2. Opioid use is associated with greater disease severity, tobacco use, non-adherence, and increased mortality.3. Opioids should be used cautiously in SLE; alternative non-opioid management of pain is recommended.ACKNOWLEDGMENTS AND FUNDING INFORMATION:This work was supported by US National Institutes of Health research grants to Dr. Sibbitt (R01 NS035708) and to the Clinical and Translational Research Center (UL1TR001449).
Somatically Mutated Genes Under Positive and Negative Selection Found by Transcriptome Sequence Analysis Include Oncogene and Tumor Suppressor Candidates
Authors: Drubin Casey W. , Ramu Avinash , Rockweiler Nicole B. , Conrad Donald F. 
Published: August 2018

AbstractIntroductionOncogenic somatic mutations confer proliferative advantage and undergo positive clonal selection. We developed software and applied new analytical approaches to identify: (1) somatic mutations in diverse tissues, (2) somatically mutated genes under positive and negative selection, (3) post-transcriptional modifications in the mitochondrial transcriptome, and (4) inherited germline alleles predisposing people to higher somatic mutation burden or higher levels of post-transcriptional modification.MethodsTranscriptome sequence data (Genotype Tissue Expression project) for 7051 tissue samples from 549 postmortem donors and representing 44 tissue types were used. Germline mutations were inferred from whole-exome DNA sequencing and SNP arrays. DNA somatic mutations were inferred from variant allele frequencies (VAF) in RNA-seq data. Post-transcriptional modifications were inferred from Polymorphism Information Content (PIC) at the p9 sites of mitochondrial tRNA sequences. Positive and negative clonal selection was evaluated using a nonsynonomous/synonomous mutation rate (dN/dS) model. Genome-wide association studies (GWAS) were assessed with mitochondrial PIC for post-transcriptional modification level, or using the total number of somatic mutations observed per donor for somatic mutation burden.ResultsOur dN/dS model identified 78 genes under negative selection for somatic mutations (dN/dS < 1, padj< 0.05) and 14 under positive selection (dN/dS > 1, padj<0.05). Our GWAS identified 2 sites associated with post-transcriptional modification (1 approaching significance with p=5.99×10−8, 1 with p<5×10−8) and ∼20 sites associated with somatic mutation burden (p<5×10−8).ConclusionsTo our knowledge these are the first genome-wide association studies on normal somatic mutation burden. These studies were an attempt to increase understanding of the somatic mutation process. Our work identified somatic mutations at the global organismal level that may promote cell proliferation in a tissue-specific manner. By identifying tissue-specific mutations in actively expressed genes that appear before cancer phenotype is detected, this work also identifies gene candidates that might initiate tumorigenesis.
tmap: topological analysis of population-scale microbiome data
Authors: Liao Tianhua , Wei Yuchen , Luo Mingjing , Zhao Guoping , Zhou Haokui 
Published: August 2018

AbstractPopulation-scale microbiome study poses specific challenges in data analysis, from enterotype analysis, identification of driver species, to microbiome-wide association of host covariates. Application of advanced data mining techniques to high-dimensional complex dataset is expected to meet the rapid advancement in large scale and integrative microbiome research. Here, we present tmap, a topological data analysis framework for population-scale microbiome study. This framework can capture complex shape of large scale microbiome data into a compressive network representation. We also develop network-based statistical analysis for driver species identification and microbiome-wide association analysis. tmap can be used for exploring variations in a population-scale microbiome landscape to study host-microbiome association.Availability and implementationtmap is available at GitHub (https://github.com/GPZ-Bioinfo/tmap), accompanied with online documentation and tutorial (http://tmap.readthedocs.io).Contacthttp://hk.zhou@siat.ac.cn
CryoEM structures of open dimers of Gyrase A in complex with DNA illuminate mechanism of strand passage
Authors: Soczek Katarzyna M. , Grant Tim , Rosenthal Peter B. , Mondragon Alfonso 
Published: August 2018

AbstractGyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of conformational changes that consist of concerted gate openings, DNA cleavage, and DNA strand passage events. Structures where the transported DNA molecule (T-segment) is trapped by the A subunit have not been observed. Here we present the cryoEM structures of two oligomeric complexes of open gyrase A dimers and DNA. The protein subunits in these complexes were solved to 4 Å and 5.16 Å resolution. One of the complexes traps a linear DNA molecule, a putative T-segment, which interacts with the open gyrase A dimers in two states, representing steps either prior to or after passage through the DNA-gate. The structures locate the T-segment in important intermediate conformations of the catalytic cycle and provide insights into gyrase-DNA interactions and mechanism.
Mutual synchronization pattern as a complementary indicator of the short-term blood pressure – heart rate feedback regulation activity
Authors: Pyko Nikita S , Pyko Svetlana A , Markelov Oleg A , Mamontov Oleg V , Bogachev Mikhail I 
Published: August 2018

AbstractWe suggest a complementary indicator of the blood pressure – heart rate feedback regulation based on their synchronization pattern assessed by Hilbert transform. We determine the synchronization coefficient Sync as the fraction of time fragments where the standard deviation of the differences between instantaneous phases of blood pressure and pulse intervals are below a certain threshold. While BRS characterizes the intensity of the pulse intervals response to the blood pressure changes during observed feedback responses, the Sync likely indicates how often such responses are activated in the first place. Data from 95 tilt test records indicate that in both healthy subjects and patients with moderate autonomic dysfunction BRS and Sync are typically reciprocal suggesting that low intensity of the feedback responses characterized by low BRS is rather compensated by their more frequent activation indicated by higher Sync. In contrast, in diabetes patients with autonomic neuropathy BRS and Sync are positively correlated likely indicating the breakdown of this compensation in some of the diabetic patients. Therefore we suggest that Sync could be used as an additional indicator of the blood pressure – heart rate feedback regulation activity that is complementary to the widely used baroreflex sensitivity (BRS).
Regional low-frequency oscillations in human rapid-eye movement sleep
Authors: Bernardi Giulio , Betta Monica , Ricciardi Emiliano , Pietrini Pietro , Tononi Giulio , Siclari Francesca 
Published: August 2018

AbstractAlthough the EEG slow wave of sleep is typically considered to be a hallmark of Non Rapid Eye Movement (NREM) sleep, recent work in mice has shown that slow waves can also occur in REM sleep. Here we investigated the presence and cortical distribution of low-frequency (1-4 Hz) oscillations in human REM sleep by analyzing high-density EEG sleep recordings obtained in 28 healthy subjects. We identified two clusters of low-frequency oscillations with distinctive properties: 1) a fronto-central cluster characterized by ∼2.5-3.0 Hz, relatively large, notched delta waves (so-called ‘sawtooth waves’) that tended to occur in bursts, were associated with increased gamma activity and rapid eye movements, and upon source modeling, displayed an occipito-temporal and a fronto-central component; and 2) a medial occipital cluster characterized by more isolated, slower (<2 Hz) and smaller waves that were not associated with rapid eye movements, displayed a negative correlation with gamma activity and were also found in NREM sleep. Thus, low-frequency oscillations are an integral part of REM sleep in humans, and the two identified subtypes (sawtooth and medial-occipital slow waves) may reflect distinct generation mechanisms and functional roles. Sawtooth waves, which are exclusive to REM sleep, share many characteristics with ponto-geniculo-occipital (PGO) waves described in animals and may represent the human equivalent or a closely related event while medio-occipital slow waves appear similar to NREM sleep slow waves.
Research of leakage magnetic field in deenergized transformer
Authors: Horiszny Jacek 
Published: August 2018

Purpose
The paper presents the analysis of magnetic field that surrounds the power transformer after it has been switched off. The purpose of this paper is to determine the possibility of defining the residual fluxes in the legs of the transformer based on the measurement of this field. It was also intended to determine the type and the location of magnetic sensors.

Design/methodology/approach
Numerical analysis of the magnetic field was performed. A three-dimensional model of the transformer’s magnetic core was created in the Flux 3D simulation program. The analysis was concerned with an oil-filled transformer and a dry transformer. The magnetic field of Earth was taken into account.

Findings
The research has shown that magnetic induction of the leakage field produced by residual magnetization of the core is comparable to the magnetic induction of the Earth’s field. It was also found that the measurement of the magnetic induction should be performed as close as possible to the core. The interior of the tank turned out to be a convenient space for the placement of the sensors.

Research limitations/implications
The influence of external ferromagnetic objects, and devices generating magnetic field, on the measurement was not considered. It should be taken into account in the future work.

Originality/value
On the basis of the analysis, it was proposed to measure the magnetic induction vector of the leakage field at three points. The sensors should be placed in front of the columns at a position that is half of their height. The measurement can be performed with satisfactory accuracy by sensors located on the surface of the windings.
A passive SPICE model for rectennas
Authors: Pereira Polyanna Mara , Campelo Felipe , Mori Takuya , Igarashi Hajime , Adriano Ricardo 
Published: August 2018

Purpose
This paper aims to present a SPICE model to represent antennas in receiving mode. The model can be used to evaluate the performance of the antenna when it is coupled to several different nonlinear electric circuits. The proposed methodology is particularly suitable for rectenna applications, as it allows the analysis of different configurations for a rectenna more efficiently than using full-wave analysis simulators coupled directly to each rectifier circuit.

Design/methodology/approach
The model presented uses reciprocity theory to calculate the ideal voltage source of the Thevenin-equivalent circuit for an antenna. Vector fitting is then used to approximate the model to rational functions that can be converted to Resistor, Inductor and Capacitor circuits. Additional components are added to the circuit to prevent numerical instability.

Findings
Two rectennas are used to illustrate the performance of the proposed model, one based on a 2.45-GHz rectangular patch antenna and another based on a planar spiral antenna. The second antenna has impedance with positive and negative real parts along the frequency range, which could lead to numerical instabilities. The proposed method is shown to be stable while working with these negative resistance values, which may appear during circuit parameterization.

Research limitations/implications
The equivalent SPICE circuit model for the antenna makes it easy to simulate nonlinear circuits connected to the antenna and perform transient analyses. The computational cost of antenna analysis is reduced, being more computationally efficient than methods that involve full-wave simulation. This characteristic makes it an interesting approach for working with rectennas, or any application where the time constant of the circuit is much longer than the period of the incident wave.

Originality/value
For most antenna applications, the numerical stability of the circuit can be achieved using passive enforcement. However, depending on the phase response of the antenna, the impedance that represents its far-field characteristic may present a negative real part, in which case, passive enforcement will fail. In this paper, the problem of numerical instability is solved by introducing an offset resistance and a current-controlled voltage source to the model.
Risk reliability-based underwater inspection method for jacket platforms in Indonesia
Authors: Tawekal Jessica Rikanti , Tawekal Ricky Lukman 
Published: August 2018

Purpose
The purpose of this paper is to carry out the application of risk reliability-based underwater inspection (RReBUI).

Design/methodology/approach
The consequence of failure factor is calculated qualitatively in accordance with the risk-based underwater inspection (RBUI) method but the criteria are modified as an adjustment to the addition and combination of production and reliability information of the analyzed platforms. The probability of failure (PoF) is determined quantitatively by calculating the structure reliability index based on collapse failure mechanism in which the uncertainty of wave load is considered. The PoF criteria from the RBUI are re-modified to adjust the criterion with the highest and lowest reliability indexes obtained in RReBUI study. Selection of exposure category of the platform is still the same as the RBUI method.

Findings
The models of three offshore jacket platforms located in each of Java Sea and Natuna Sea were used for the RReBUI application. These six models were previously used in the traditional RBUI application. The results of RReBUI analysis indicated that including the environmental characteristics in the risk assessment resulted in more reliable inspection interval plans.

Originality/value
The drawback of RBUI is that it cannot be used for platforms spread over a distance or different areas, as the failure parameters of these platforms cannot be compared. Furthermore, the RBUI method does not consider the environmental characteristics in its risk assessment. Unlike RBUI, the purpose of RReBUI method is to assess the reliability of a platform based on both structural and environment characteristics. Therefore, the RReBUI method determines the risk of every platform quantitatively without having to compare the failure parameters based on expert justification. The application of RReBUI for jacket platforms has never been developed in Indonesia.
Method for computing the shear capacity of prestressed reinforced concrete beams based on truss-arch model
Authors: Wang Jiawei , Liu Jinliang , Zhang Guanhua , Jia Yanmin 
Published: August 2018

Purpose
The calculation of the shear capacity of inclined section for prestressed reinforced concrete beams is an important topic in the design of concrete members. The purpose of this paper, based on the truss-arch model, is to analyze the shear mechanism in prestressed reinforced concrete beams and establish the calculation formula for shear capacity.

Design/methodology/approach
Considering the effect of the prestressed reinforcement axial force on the angle of the diagonal struts and regression coefficient of softening cocalculation of shear capacity is established. According to the shape of the cracks of prestressed reinforced concrete beams under shear compression failure, the tie-arch model for the calculation of shear capacity is established. Shear-failure-test beam results are collected to verify the established formula for shear bearing capacity.

Findings
Through theoretical analysis and experimental beam verification, it is confirmed in this study that the truss-arch model can be used to analyze the shear mechanism of prestressed reinforced concrete members accurately. The calculation formula for the angle of the diagonal struts chosen by considering the effect of prestress is accurate. The relationship between the softening coefficient of concrete and strength of concrete that is established is correct. Considering the effect of the destruction of beam shear plasticity of the concrete on the surface crack shape, the tie-arch model, which is established where the arch axis is parabolic, is applicable.

Originality/value
The formula for shear capacity of prestressed reinforced concrete beams based on this theoretical model can guarantee the effectiveness of the calculation results when the structural properties vary significantly. Engineers can calculate the parameters of prestressed reinforced concrete beams by using the shear capacity calculation formula proposed in this paper.
Study on behaviour of geometrically scaled glass reinforced epoxy tubes subjected to non-coincident quasi static-indentation
Authors: Almaskari Fahad , Hafeez Farrukh 
Published: August 2018

Purpose
The purpose of this paper is to study the behaviour of glass reinforced epoxy tubes subjected to repeated indentation loads at two non-coincident indentations 180° apart.

Design/methodology/approach
Four geometrically scaled specimens ranging from 100 to 400 mm diameter were used in repeated indentation tests. Force, displacement and damage growth were recorded for loading and unloading until the indenter returned to its original starting point.

Findings
Similar scaled trends were observed between the non-coincidental loadings. Unlike reported response form coincidental loadings, the responses from non-coincidental loadings yield lower values for bending stiffness and peak load.

Research limitations/implications
The differences in behaviour of the specimen between non-coincident loadings were attributed to reductions in fracture toughness and circumferential modulus.

Practical implications
Distant non-interacting damage and delamination around the circumference does reduce the structural performance.

Originality/value
Behaviour of composite tubes under different loading conditions, for example low speed impact or quasi static indentation, is widely studied, however little attention has been given to the repeated loading incidents.
Non-linear delamination in two-dimensional functionally graded multilayered beam
Authors: Rizov Victor 
Published: August 2018

Purpose
A delamination fracture analysis of two-dimensional functionally graded multilayered end-loaded split beam configuration with non-linear mechanical behaviour of material is conducted. The beam is made of an arbitrary number of longitudinal layers. Perfect adhesion between layers is assumed. The material is two-dimensional functionally graded in the cross-section of each layer. Also, each layer has individual thickness and material properties. A delamination crack is located arbitrary along the beam height. The paper aims to discuss these issues.

Design/methodology/approach
The delamination fracture behaviour is investigated analytically in terms of the strain energy release rate by analysing the balance of the energy. An additional analysis of the delamination fracture is performed by applying the J-integral approach for verification.

Findings
The solutions derived are used to evaluate the effects of crack location, material gradients and material non-linearity on the delamination fracture behaviour of end-loaded split beam. The effect of material gradient on the distribution of the J-integral value along the crack front is elucidated too.

Originality/value
Delamination in the multilayered functionally graded end-loaded split beam exhibiting non-linear mechanical behaviour of the material is analysed assuming that the material property is distributed non-linearly in both thickness and width directions in each layer.
The narrative rhythm of terror: a study of the Stockholm terrorist attack and the “Last Night in Sweden” event
Authors: Cassinger Cecilia , Eksell Jorgen , Mansson Maria , Thufvesson Ola 
Published: August 2018

PurposeThe purpose of this paper is to examine how the mediatisation of terror attacks affects the brand image of tourism cities.Design/methodology/approachInformed by theories of mediatisation and space, the study analyses two different types of terror attacks in Sweden during 2017 as media events. The focus of analysis is on identifying spatial and temporal patterns that underpin the narrative rhythm of the discussions of the events on Twitter and online news platforms.FindingsThe findings demonstrate that the unfolding of the events can be divided into three phases of varying intensity in rhythm and implications for city brand image. The manifestation of an imaginary terror attack in a digital environment had a greater impact on the narratives of the city than an actual one.Research limitations/implicationsRythmanalysis is introduced as a useful device to examine how urban space is mediatised through social media and online news flows.Originality/valueThe study contributes with novel knowledge on the mediatisation of city space on digital media platforms in a post-truth world. It shows that city administrations need to deal with both real and imaginary terror attacks, especially when there is an already established negative image of the city.