bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-dimensional magnetic reconnection in a collapsing coronal loop system
Authors: O’Flannagain Aidan M. , Maloney Shane A. , Gallagher Peter T. , Browning Philippa , Refojo Jose 
Published: June 2018

Context. Magnetic reconnection is believed to be the primary mechanism by which non-potential energy stored in coronal magnetic fields is rapidly released during solar eruptive events. Unfortunately, owing to the small spatial scales on which reconnection is thought to occur, it is not directly observable in the solar corona. However, larger scale processes, such as associated inflow and outflow, and signatures of accelerated particles have been put forward as evidence of reconnection.
Aims. Using a combination of observations we explore the origin of a persistent Type I radio source that accompanies a coronal X-shaped structure during its passage across the disk. Of particular interest is the time range around a partial collapse of the structure that is associated with inflow, outflow, and signatures of particle acceleration.
Methods. Imaging radio observations from the Nançay Radioheliograph were used to localise the radio source. Solar Dynamics Observatory (SDO) AIA extreme ultraviolet (EUV) observations from the same time period were analysed, looking for evidence of inflows and outflows. Further mpole magnetic reconstructions using SDO HMI observations allowed the magnetic connectivity associated with the radio source to be determined.
Results. The Type I radio source was well aligned with a magnetic separator identified in the extrapolations. During the partial collapse, gradual (1 km s−1) and fast (5 km s−1) inflow phases and fast (30 km s−1) and rapid (80–100 km s−1) outflow phases were observed, resulting in an estimated reconnection rate of ∼0.06. The radio source brightening and dimming was found to be co-temporal with increased soft X-ray emission observed in both Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI) and Geostationary Operational Environmental Satellite (GOES).
Conclusions. We interpret the brightening and dimming of the radio emission as evidence for accelerated electrons in the reconnection region responding to a gradual fall and rapid rise in electric drift velocity, in response to the inflowing and outflowing field lines. These results present a comprehensive example of 3D null-point reconnection.
Water and interstellar complex organics associated with the HH 212 protostellar disc
Authors: Codella C. , Bianchi E. , Tabone B. , Lee C.-F. , Cabrit S. , Ceccarelli C. , Podio L. , Bacciotti F. , Bachiller R. , Chapillon E. , Gueth F. , Gusdorf A. , Lefloch B. , Leurini S. , Pineau des Forêts G. , Rygl K. L. J. , Tafalla M. 
Published: June 2018

Context.The unprecedented combination of high-sensitivity and high angular resolution provided by the ALMA interferometer allows us to shed light on the processes leading to the formation of the jet-disc system associated with a Sun-like mass protostar.Aims.We investigate the physical and chemical properties of the gas associated with water and interstellar complex organic molecules around a protostar on solar system scales.Methods.The HH 212 protostellar system, in Orion B, has been mapped, thanks to ALMA-Band 7 Cycle 1 and Cycle 4 observations of dueterated water (HDO) and acetaldehyde (CH3CHO) emission with an angular resolution down to ~0.′′15 (60 au).Results.Many emission lines due to 14 CH3CHO and 1 HDO transitions at high excitation (Eubetween 163 and 335 K) have been imaged in the inner ~70 au region. The local thermal equilibrium analysis of the CH3CHO emission leads to a temperature of 78 ± 14 K and a column density of 7.6 ± 3.2 × 1015cm−2, which, whenNH2of 1024cm−2is assumed, leads to an abundance ofXCH3CHO≃ 8 × 10−9. The large velocity gradient analysis of the HDO emission also places severe constraints on the volume density,nH2≥ 108cm−3. The line profiles are 5–7 km s−1wide, and CH3CHO and HDO both show a ±2 km s−1velocity gradient over a size of ~70 au (blue-shifted emission towards the north-west and red-shifted emission towards the south-east) along the disc equatorial plane, in agreement with what was found so far using other molecular tracers.Conclusions.The kinematics of CH3CHO and HDO are consistent with the occurrence of a centrifugal barrier, that is, the infalling envelope-rotating disc ring, which is chemically enriched through low-velocity accretion shocks. The emission radius is ~60 au, in good agreement with what was found before for another interstellar complex organic molecule such as NH2CHO. We support a vertical structure for the centrifugal barrier, suggesting the occurrence of two outflowing, expanding, and rotating rings above and below (of about 40–45 au) the optically thick equatorial disc plane. It is tempting to speculate that these rings could probe the basis of a wind launched from this region.
Hot prominence detected in the core of a coronal mass ejection
Authors: Susino R. , Bemporad A. , Jejčič S. , Heinzel P. 
Published: June 2018

Context. We study an erupting prominence embedded in the core of a coronal mass ejection that occurred on August 2, 2000, and focus on deriving the plasma filling factor of the prominence.
Aims. We explore two methods for measuring this factor along the line of sight. They are based on a combination of visible-light and ultraviolet spectroscopic observations.
Methods. Theoretical relationships for resonant scattering and collisional excitation were used to evaluate the intensity of the neutral hydrogen Lyman-α and Lyman-β lines in two prominence points where simultaneous and cospatial LASCO-C2 and UVCS data were available. Thermodynamic and geometrical parameters assumed for the calculation (i.e., electron column density, kinetic temperature, flow velocity, chromospheric Lyα and Lyβ intensities and profiles, and thickness of the prominence along the line of sight) are provided by both observations and the results of a detailed 1D non-local thermal equilibrium (non-LTE) radiative-transfer model of the prominence, developed in our previous work. The geometrical filling factor was derived from comparing the calculated and measured intensities of the two lines. The results were then checked against the non-LTE model in order to verify the reliability of the methods.
Results. The resulting filling factors are consistent with the model in both prominence points when the radiative and collisional components of the total intensity of the hydrogen lines are separated using the Lyα and Lyβ line intensities, which is required to estimate the filling factor. The exploration of the parameter space shows that the results are weakly sensitive to the plasma flow velocity, but depend more strongly on the assumed kinetic temperatures.
Conclusions. The combination of visible-light and ultraviolet Lyα and Lyβ data can be used to approximately estimate the line-of-sight geometrical filling factor in erupting prominences, but the proposed technique, which is model dependent, is reliable only for emission that is optically thin in the lines considered, a condition that is not in general representative of prominence plasma.
Patientinnenteilnahme an Tumorkonferenzen: ein wichtiger Faktor für eine gemeinsame Entscheidungsfindung?
Authors: Heuser Christian , Diekmann Annika , Ansmann Lena , Ernstmann Nicole 
Published: June 2018

Zusammenfassung
Hintergrund Ein zentrales Instrument multidisziplinärer Versorgung in der Onkologie sind multidisziplinäre Tumorkonferenzen (MTK). Die meisten MTK finden ohne die Teilnahme von Patienten statt und es ist unklar, welchen Nutzen und welche Risiken die Patientinnenteilnahme an MTK hat.
Fragestellung Das vorliegende Forschungsvorhaben zielt auf die Beantwortung folgender drei Fragestellungen ab: 1) Wie unterscheiden sich MTK mit und ohne Patientinnenteilnahme hinsichtlich Organisation und Interaktion in der Versorgung von Brust- und gynäkologischen Tumoren? 2) Wie erleben die Patientinnen die Teilnahme? 3) Wie bewerten die an der MTK teilnehmenden Berufsgruppen die Machbarkeit der Teilnahme von Patientinnen an der MTK und die Qualität der Entscheidungsfindung?
Methodik Mit einer Triangulation unterschiedlicher qualitativer und quantitativer Methoden werden MTK in sechs nordrhein-westfälischen Brust- und gynäkologischen Zentren mit und ohne Patientinnenteilnahme untersucht. Der Mixed-Methods-Ansatz sieht teilnehmende Beobachtungen der MTK sowie Experteninterviews mit den teilnehmenden Berufsgruppen und schriftliche Befragungen der Patientinnen vor. Die Patientinnen werden vor der MTK, direkt danach und vier Wochen im Anschluss anhand von standardisierten Kurzfragebögen befragt.
Ergebnisse Aus den Ergebnissen können erste Hinweise auf Machbarkeit, Risiken und Nutzen der Patientinnenteilnahme an MTK für die Patientinnen und die teilnehmenden Berufsgruppen abgeleitet sowie Aufschluss über die konkrete Praxis gemeinsamer Entscheidungsfindung in Tumorkonferenzen abgeleitet werden.
Diskussion Die hier beschriebene explorative Studie ist eine notwendige Vorarbeit für die weitere Erforschung der Auswirkungen der Patientinnenteilnahme auf Outcomes in interventionellen Designs.
Hemostasis in Allergy
Authors: Toubi Elias , Vadasz Zahava 
Published: June 2018

AbstractThe involvement of the hemostatic system in immune-mediated inflammation is widely reported. Many coagulation factors play a role in the pathogenesis of autoimmune diseases, such as systemic vasculitis and systemic lupus erythematosus. Hemostatic disorders are also involved in asthma and chronic spontaneous urticaria (CSU). Factor XIIa (FXIIa) was one of the first coagulation factors implicated in inducing both humoral and cellular responses and is therefore considered a prime new therapeutic target in immune-mediated inflammation. The involvement of coagulation factors, such as tissue factor and fibrinogen, in the pathogenesis of asthma has been reported. The finding of platelet activation in asthma also indicates a link between bronchial inflammation and hemostasis. The pathogenesis of mast cell degranulation and CSU was also shown to be associated with the activation of hemostatic factors such as fibrinogen and FXIIa. Increased plasma levels of D-dimer have been widely reported as a biological marker for the duration and severity of CSU. In addition, endothelial-induced cell activation by the kallikrein–high molecular weight complex and the release of heat shock protein 90 was shown to be involved in mast cell degranulation disorders. In this narrative review, the authors aim to summarize the role of hemostasis in inflammation, asthma, and CSU by focusing on the increasing information linking hemostatic factors and immune-mediated disorders.
Negative Pressure Wound Dressing Reduces Surgical Site Infections in Infants after Closed Abdominal Procedures: A Preliminary Report
Authors: Zoeller Christoph , Yoshizawa Emi , Sethi Mohammad V. , Ure Benno M. , Kuebler Joachim F. 
Published: June 2018

Introduction Negative pressure wound therapy (NPWT) is a novel tool to reduce surgical site infections (SSIs). Although SSIs are a common source of morbidity in infants undergoing laparotomy, the cost of the available NPWT devices has restricted its use to adult high-risk patients. We developed a low-cost method of NPWT in infants and analyzed its impact on the incidence of SSIs in infant patients.
Materials and Methods A consecutive series of infants (age ≤ 12 months) who underwent a clean-contaminated, contaminated, or dirty abdominal procedure via laparotomy from 08/2015 to 12/2016 were included. The choice of the applied dressing, either NPWT or standard surgical dressing (SSD), was made at the surgeon's discretion. SSIs were documented prospectively. The Horan definition and the Clavien-Dindo classification were used. The cost of material was calculated for both groups.
Results Ninety-three consecutive patients were included (65 SSD and 28 NPWT). SSI occurred in 10 patients in the SSD group, Grade I in 7 and Grade II in 3 (Clavien-Dindo classification). No SSI occurred in patients with NPWT (p < 0.05). The cost of an SSD was less than 1 €, and the cost of a NPWT was less than 10 €.
Conclusion The routine use of this modified vacuum wound dressing may be an efficient and affordable technique to decrease SSIs in infants who underwent contaminated abdominal operations.
Democratization of ecosystem services—a radical approach for assessing nature’s benefits in the face of urbanization
Authors: McHale Melissa R. , Beck Scott M. , Pickett Steward T. A. , Childers Daniel L. , Cadenasso Mary L. , Rivers Louie , Swemmer Louise , Ebersohn Liesel , Twine Wayne , Bunn David N 
Published: June 2018

ABSTRACT

Objectives:
(1) To evaluate how ecosystem services may be utilized to either reinforce or fracture the planning and development practices that emerged from segregation and economic exclusion; (2) To survey the current state of ecosystem service assessments and synthesize a growing number of recommendations from the literature for renovating ecosystem service analyses.

Methods:
Utilizing current maps of ecosystem service distribution in Bushbuckridge Local Municipality, South Africa, we considered how a democratized process of assessing ecosystem services will produce a more nuanced representation of diverse values in society and capture heterogeneity in ecosystem structure and function.

Results:
We propose interventions for assessing ecosystem services that are inclusive of a broad range of stakeholders’ values and result in actual quantification of social and ecological processes. We demonstrate how to operationalize a pluralistic framework for ecosystem service assessments.

Conclusion:
A democratized approach to ecosystem service assessments is a reimagined path to rescuing a poorly implemented concept and designing and managing future social-ecological systems that benefit people and support ecosystem integrity. It is the responsibility of scientists who do ecosystem services research to embrace more complex, pluralistic frameworks so that sound and inclusive scientific information is utilized in decision-making.
snpAD: an ancient DNA genotype caller
Authors: Prüfer Kay 
Published: June 2018

Abstract

Motivation
The study of ancient genomes can elucidate the evolutionary past. However, analyses are complicated by base-modifications in ancient DNA molecules that result in errors in DNA sequences. These errors are particularly common near the ends of sequences and pose a challenge for genotype calling.

Results
I describe an iterative method that estimates genotype frequencies and errors along sequences to allow for accurate genotype calling from ancient sequences. The implementation of this method, called snpAD, performs well on high-coverage ancient data, as shown by simulations and by subsampling the data of a high-coverage Neandertal genome. Although estimates for low-coverage genomes are less accurate, I am able to derive approximate estimates of heterozygosity from several low-coverage Neandertals. These estimates show that low heterozygosity, compared to modern humans, was common among Neandertals.

Availability and implementation
The C++ code of snpAD is freely available at http://bioinf.eva.mpg.de/snpAD/.

Supplementary information
Supplementary data are available at Bioinformatics online.
iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC
Authors: Su Zhen-Dong , Huang Yan , Zhang Zhao-Yue , Zhao Ya-Wei , Wang Dong , Chen Wei , Chou Kuo-Chen , Lin Hao 
Published: June 2018

AbstractMotivationLong non-coding RNAs (lncRNAs) are a class of RNA molecules with more than 200 nucleotides. They have important functions in cell development and metabolism, such as genetic markers, genome rearrangements, chromatin modifications, cell cycle regulation, transcription and translation. Their functions are generally closely related to their localization in the cell. Therefore, knowledge about their subcellular locations can provide very useful clues or preliminary insight into their biological functions. Although biochemical experiments could determine the localization of lncRNAs in a cell, they are both time-consuming and expensive. Therefore, it is highly desirable to develop bioinformatics tools for fast and effective identification of their subcellular locations.ResultsWe developed a sequence-based bioinformatics tool called ‘iLoc-lncRNA’ to predict the subcellular locations of LncRNAs by incorporating the 8-tuple nucleotide features into the general PseKNC (Pseudo K-tuple Nucleotide Composition) via the binomial distribution approach. Rigorous jackknife tests have shown that the overall accuracy achieved by the new predictor on a stringent benchmark dataset is 86.72%, which is over 20% higher than that by the existing state-of-the-art predictor evaluated on the same tests.Availability and implementationA user-friendly webserver has been established at http://lin-group.cn/server/iLoc-LncRNA, by which users can easily obtain their desired results.Supplementary informationSupplementary data are available at Bioinformatics online.
Vascular endothelial growth factor regulation of endothelial nitric oxide synthase phosphorylation is involved in isoflurane cardiac preconditioning
Authors: Liu Yanan , Paterson Mark , Baumgardt Shelley L , Irwin Michael G , Xia Zhengyuan , Bosnjak Zeljko J , Ge Zhi-Dong 
Published: June 2018

Abstract

Aims
Previous studies indicate that nitric oxide derived from endothelial nitric oxide synthase (eNOS) serves as both trigger and mediator in anaesthetic cardiac preconditioning. The mechanisms underlying regulation of eNOS by volatile anaesthetics have not been fully understood. Therefore, this study examined the role of vascular endothelial growth factor (VEGF) in isoflurane cardiac preconditioning.

Methods and results
Wistar rats underwent 30 min of coronary artery occlusion followed by 2 h of reperfusion. Isoflurane given prior to ischaemia/reperfusion significantly decreased myocardial infarct size from 60 ± 1% in control to 40 ± 3% (n = 8 rats/group, P < 0.05). The beneficial effects of isoflurane were blocked by neutralizing antibody against VEGF (nVEGF). Coronary arterial endothelial cells (ECs) alone or together with cardiomyocytes (CMs) were subjected to hypoxia/reoxygenation injury. The expression of VEGF and eNOS was analysed by western blot, and nitric oxide was measured by ozone-based chemiluminescence. In co-cultured CMs and ECs, isoflurane administered before hypoxia/reoxygenation attenuated lactate dehydrogenase activity and increased the ratio of phosphorylated eNOS/eNOS and nitric oxide production. The protective effect of isoflurane on CMs was compromised by nVEGF and after VEGF in ECs was inhibited with hypoxia inducible factor-1α short hairpin RNA (shRNA). The negative effect of hypoxia inducible factor-1α shRNA was restored by recombinant VEGF.

Conclusion
Isoflurane cardiac preconditioning is associated with VEGF regulation of phosphorylation of eNOS and nitric oxide production.
A new method to estimate habitat potential for Atlantic salmon (Salmo salar): predicting the influence of dam removal on the Sélune River (France) as a case study
Authors: Forget Guillaume , Baglinière Jean-Luc , Marchand Frédéric , Richard Arnaud , Nevoux Marie 
Published: June 2018

Abstract
Maintaining connectivity in aquatic ecosystems is important to ensure adequate ecological functioning. A large dam removal project in the Sélune River (Normandy, France) would reconnect 827 km2 of catchment area to the sea. Only the downstream section of the Selune is currently available to diadromous fish, which migrate between freshwater and the marine environment. In particular, managers focus on the future potential abundance of Atlantic salmon, Salmo salar, for conservation and fishery purposes. As in stream channel habitat drives carrying capacity of juvenile salmon, salmon abundance is usually inferred from intensive and linear habitat surveys. However, this approach is neither cost-effective for large-scale surveys nor feasible for riverbed sections with low accessibility for measurement with traditional methods, e.g. dam lakes. We used well-defined relationships between gradient, hydrology and channel habitat structure to construct a simple model to estimate potential suitable habitat for juvenile salmon. Using fine-scale habitat data from nearby rivers, we parameterized a linear mixed model to estimate the area of suitable habitat based on simple physical descriptors of river characteristics. We compared our predictions to fine-scale habitat surveys on the upper Sélune. Using only slope and width, our model was able to explain 80% of the variance in suitable habitat. Estimates indicated that dam removal on the Sélune River would generate a threefold increase in suitable habitat for juveniles. This could increase the mean number of adult salmon returning to the river by 1420.9 (s.e. = 1015.5). More generally, this model provides an alternative and cost-effective tool to help better manage salmon populations in rivers impacted by dams.
Spherical Hall Algebras of Weighted Projective Curves
Authors: Lin Jyun-Ao 
Published: June 2018

AbstractIn this article, we deal with the structure of the spherical Hall algebra $\mathbf{U}$ of coherent sheaves with parabolic structures on a smooth projective curve $X$ of arbitrary genus $g$. We provide a shuffle-like presentation of the bundle part $\mathbf{U}^&gt;$ and show the existence of generic spherical Hall algebra of genus $g$. We also prove that the algebra $\mathbf{U}$ contains the characteristic functions on all the Harder–Narasimhan strata. These results together imply Schiffmann’s theorem on the existence of Kac polynomials for parabolic vector bundles of fixed rank and multi-degree over $X$. On the other hand, the shuffle structure we obtain is new and we make links to the representations of quantum affine algebras of type $A$.
Cosmopolitanism beyond the Monolingual Vision
Authors: Bielsa Esperança 
Published: June 2018

AbstractThis article examines how debates on language and democracy have been differently framed within multiculturalist and cosmopolitan frameworks, questioning some of their underlying assumptions and demonstrating a basic continuity with reference to what is approached as the monolingual vision. It then goes on to propose an alternative conception of the language of democracy based on plurilingualism, linguistic hospitality, and translation. Such a conception is not ignorant of the social role of language in the constitution of individual selves and of collective identities, nor does it avoid confronting the politics of language in a highly unequal global space. It recognizes that the grounds of a cosmopolitan democracy can only be built through generalized plurilingual exchanges and sees in the difficulties of understanding and the productive confrontation with the opacity of others and of ourselves the very substance of democracy amongst diversity. This approach also points in the direction of a cosmopolitan sociology that bridges political cosmopolitanism with forms of literary and artistic cosmopolitanism that have remained rather marginal in cosmopolitan thought.