bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistent magnetic vortex flow at a supergranular vertex
Authors: Requerey Iker S. , Cobo Basilio Ruiz , Gošić Milan , Bellot Rubio Luis R. 
Published: December 2017

Context. Photospheric vortex flows are thought to play a key role in the evolution of magnetic fields. Recent studies show that these swirling motions are ubiquitous in the solar surface convection and occur in a wide range of temporal and spatial scales. Their interplay with magnetic fields is poorly characterized, however.
Aims. We study the relation between a persistent photospheric vortex flow and the evolution of a network magnetic element at a supergranular vertex.
Methods. We used long-duration sequences of continuum intensity images acquired with Hinode and the local correlation-tracking method to derive the horizontal photospheric flows. Supergranular cells are detected as large-scale divergence structures in the flow maps. At their vertices, and cospatial with network magnetic elements, the velocity flows converge on a central point.
Results. One of these converging flows is observed as a vortex during the whole 24 h time series. It consists of three consecutive vortices that appear nearly at the same location. At their core, a network magnetic element is also detected. Its evolution is strongly correlated to that of the vortices. The magnetic feature is concentrated and evacuated when it is caught by the vortices and is weakened and fragmented after the whirls disappear.
Conclusions. This evolutionary behavior supports the picture presented previously, where a small flux tube becomes stable when it is surrounded by a vortex flow.
Acute Stroke Multimodal Imaging: Present and Potential Applications toward Advancing Care
Authors: Matos Diaz I. , Liang J. , Ostojic L. , Tansy Aaron 
Published: December 2017

AbstractIn the past few decades, the field of acute ischemic stroke (AIS) has experienced significant advances in clinical practice. A core driver of this success has been the utilization of acute stroke imaging with an increasing focus on advanced methods including multimodal imaging. Such imaging techniques not only provide a richer understanding of AIS in vivo, but also, in doing so, provide better informed clinical assessments in management and treatment toward achieving best outcomes. As a result, advanced stroke imaging methods are now a mainstay of routine AIS practice that reflect best practice delivery of care. Furthermore, these imaging methods hold great potential to continue to advance the understanding of AIS and its care in the future.
TSPO-PET Imaging to Assess Cerebral Microglial Activation in Multiple Sclerosis
Authors: Weiner Howard , Bakshi Rohit , Singhal Tarun 
Published: December 2017

AbstractThe adaptive immune system, particularly T cells and more recently B cells, is considered to play a major role in the pathogenesis of multiple sclerosis (MS). In addition to adaptive immune mechanisms, innate central nervous system (CNS) immunity, particularly mediated by microglia, may play a key role in MS pathogenesis. Microglial activation has been demonstrated throughout the MS disease course and at various locations in the CNS, including white and gray matter lesions as well as normal appearing white and gray matter. Activated microglia overexpress an 18 kilodalton mitochondrial translocator protein (TSPO), which is otherwise expressed at low levels during the resting state. Several positron emission tomography (PET) ligands targeting TSPO have been developed to enable the assessment of microglial activation. In this article, we review the biological basis, methodological aspects, and current status of TSPO-PET imaging in MS and discuss future research directions.
Magnetic Resonance Spectroscopy as a Biomarker for Chronic Traumatic Encephalopathy
Authors: Alosco Michael , Jarnagin Johnny , Rowland Benjamin , Liao Huijun , Stern Robert , Lin Alexander 
Published: December 2017

AbstractChronic traumatic encephalopathy (CTE) is a neurodegenerative disease associated with exposure to repetitive head impacts (RHI). Currently, CTE can only be diagnosed after death by postmortem, as validated in vivo biomarkers of CTE do not yet exist. Proton magnetic resonance spectroscopy (MRS) measures brain tissue metabolism in vivo and could facilitate a “probable CTE” diagnosis during life. Here, we propose MRS as one potential biomarker for CTE through a review of CTE neuropathology, and the extant literature that has examined the acute and long-term effects of RHI exposure on brain chemistry. There is preliminary empirical support for MRS in the detection of later-life neurological impairment associated with RHI exposure, but further ante- and postmortem research is needed before MRS can be considered a diagnostic biomarker for CTE.
Role of Endovascular Aortic Repair in the Treatment of Infected Aortic Aneurysms Complicated by Aortoenteric or Aortobronchial Fistulae
Authors: Lee Hsin-Ling , Yang Yu-Jen , Kan Chung-Dann 
Published: December 2017

Background The aim of this study was to compare outcomes and identify factors related to increased mortality of open surgical and endovascular aortic repair (EVAR) of primary mycotic aortic aneurysms complicated by aortoenteric fistula (AEF) or aortobronchial fistula (ABF).
Methods Patients with primary mycotic aortic aneurysms complicated by an AEF or ABF treated by open surgery or endovascular repair between January 1993 and January 2014 were retrospectively reviewed. Outcomes were compared between the open surgery and endovascular groups, and a Cox's proportional hazard model was used to determine factors associated with mortality.
Results A total of 29 patients included 14 received open surgery and 15 received endovascular repair. Positive initial bacterial blood culture results included Salmonella spp., oxacillin-resistant Staphylococcus aureus, and Klebsiella pneumoniae. Mortality within 1 month of surgery was higher in the open surgery than in the endovascular group (43 vs. 7%, respectively, p = 0.035). Shock, additional surgery to repair gastrointestinal (GI) or airway pathology, and aneurysm rupture were associated with a higher risk of death. Compared with patients without resection surgery, the adjusted hazard ratio of death within 4 years in patients with resection for GI/bronchial disease was 0.25. Survival within 6 months was better in the endovascular group (p = 0.016).
Conclusion The results of this study showed that EVAR/thoracic EVAR (TEVAR) is feasible for the management of infected aortic aneurysms complicated by an AEF or ABF, and results in good short-term outcomes. However, EVAR/TEVAR did not benefit long-term survival compared with open surgery.
Cognitive Development in Pediatric Epilepsy Surgery
Authors: Reuner Gitta , Ramantani Georgia 
Published: December 2017

AbstractEpilepsy surgery is a very effective treatment option for children and adolescents with drug-resistant structural epilepsy, resulting in seizure freedom in the majority of cases. Beyond seizure freedom, the postsurgical stabilization or even improvement of cognitive development constitutes a fundamental objective. This study aims to address key features of cognitive development in the context of pediatric epilepsy surgery. Many surgical candidates present with severe developmental delay and cognitive deficits prior to surgery. Recent studies support that global cognitive development remains stable after surgery. Individual developmental trajectories are determined by the degree of presurgical developmental impairment, age at surgery, seizure freedom, antiepileptic drug tapering, and other case-specific factors. Compared with adults, children may better compensate for temporary postsurgical deficits in circumscribed cognitive functions such as memory. Particularly for left-sided temporal resections, children present a clear advantage in terms of postsurgical recovery with regard to verbal learning compared with adults. In the case of severe presurgical developmental impairment, minimal postsurgical improvements are often not measurable, although they are evident to patients' families and have a large impact on their quality of life. Multicenter studies with a standardized assessment protocol and longer follow-up intervals are urgently called for to provide deeper insights into the cognitive development after epilepsy surgery, to analyze the interaction between different predictors, and to facilitate the selection of appropriate candidates as well as the counseling of families.
Management des Delirs auf der Intensivstation
Authors: Braune Stephan , Gurlit Simone 
Published: December 2017

Was ist neu?Ende 2015 wurde die aktualisierte S3-Leitlinie „Analgesie, Sedierung und Delirmanagement in der Intensivmedizin“ publiziert 1.
Erkennung des Delirs Das mehrfach tägliche Delir-Screening mittels validierter Delir-Scores ist die Voraussetzung für ein effektives Delir-Management auf der Intensivstation und ein Qualitätsindikator in der Intensivmedizin.
Management des Delirs Grundlage der Prävention und Therapie des Delirs sind nicht-pharmakologische Basismaßnahmen. Diese werden flankiert von einer effektiven Analgesie, einer zurückhaltenden, ziel- und symptomorientierten Sedierung mit gut steuerbaren, möglichst wenig delirogenen Substanzen sowie bedarfsweise und symptomorientiert einer antipsychotischen Therapie.
Phäochromozytom richtig erkennen, behandeln und nachsorgen
Authors: Megerle Felix , Fassnacht Martin 
Published: December 2017

Was ist neu?
Laborchemische Diagnostik Die Bestimmung der Metanephrine (Überbegriff für Normetanephrin und Metanephrin) im Plasma oder der fraktionierten Metanephrine im 24h-Sammelurin sind Diagnostik der ersten Wahl und haben die Bestimmung von Adrenalin und Noradrenalin bzw. Vanillinmandelsäure endgültig abgelöst. Werte > 3fach der oberen Norm werden als diagnostisch angesehen. Bei leicht bis moderat erhöhten Befunden empfiehlt sich weitere Bestätigungsdiagnostik.
Bildgebende Diagnostik Computertomografie (CT) und Magnetresonanztherapie (MRT) sind ebenbürtige Optionen. Eine funktionelle Bildgebung ist nach den neuen Leitlinien nur bei Malignitätsverdacht bzw. metastasierten Phäochromozytomen oder zur Detektion von Paragangliomen zwingend.
Genetische Diagnostik Bei mind. 30 % der Patienten mit Phäochromozytom lässt sich eine genetische Disposition feststellen. Inzwischen wurden 14 „Phäochromozytom-Paragangliom-Gene“ identifiziert. Daher wird grundsätzlich jedem Patienten eine genetische Aufklärung und Diagnostik angeboten.
Therapie Hier geht die Empfehlung zur minimalinvasiven Resektion, sofern dies technisch möglich ist und kein Malignitätsverdacht besteht. Alle Patienten mit hormonell aktivem Phäochromozytom sollten eine präoperative α-Blockade für 7 – 14 Tage erhalten.
Nachsorge Alle Patienten bedürfen einer regelmäßigen jährlichen Nachsorge für mindestens 10 Jahre. Bei nachgewiesener Mutation, großem Tumor oder jungem Patientenalter wird lebenslängliche Nachsorge empfohlen.
Google and advertising: digital capitalism in the context of Post-Fordism, the reification of language, and the rise of fake news
Authors: Graham Rosie 
Published: December 2017

AbstractGoogle’s dominance over the web allows it to dictate various norms and practices that regulate the state of contemporary capitalism online. The way in which Google operates as a company and generates revenue is often sidelined in academic discussions regarding the cultural implications of how its search engine functions. Almost 90% of Google’s revenue is derived from advertising, despite Larry Page and Sergey Brin’s original academic paper regarding Google in which they argue that advertising produces mixed motives that make it an unfeasible way to fund search engines. This article outlines how Google’s model of advertising reflects and encourages wider changes in capitalism as it shifts from its twentieth-century Fordist incarnation to contemporary Post-Fordist arrangements of labour. In doing so, this article analyses Google’s two main advertising systems, AdWords and AdSense, and proposes that these financial models have significant effects upon online discourse. In discussing AdWords, this article details some of the tensions between the local and the global that develop when tracing flows of information and capital, specifically highlighting Google’s impact on the decline of online language diversity. In outlining AdSense, this article demonstrates how Google’s hegemonic control prescribes which parts of the web can be monetised and which remain unprofitable. In particular, in drawing from existing studies, evidence is provided that Google’s AdSense programme, along with Google’s relationship with Facebook, incentivised the rise of fake news in the 2016 US presidential election. This work builds on existing scholarship to demonstrate that Google’s economic influence has varied and far-reaching effects in a number of contexts and is relevant to scholars in a range of disciplines. As such, this article is intended as a discursive introduction to the topic and does not require specific disciplinary background knowledge. In doing so, this article does not attempt to provide the final word on Google’s relationship to digital capitalism, but rather, demonstrate the profitability of a Post-Fordist perspective, in order to enable a wider engagement with the issues identified.
Direct measurements of meltwater runoff on the Greenland ice sheet surface
Authors: Smith Laurence C. , Yang Kang , Pitcher Lincoln H , Overstreet Brandon T. , Chu Vena W. , Rennermalm Åsa K. , Ryan Jonathan C. , Cooper Matthew G. , Gleason Colin J. , Tedesco Marco , Jeyaratnam Jeyavinoth , van As Dirk , van den Broeke Michiel R. , van de Berg Willem Jan , Noël Brice , Langen Peter L. , Cullather Richard I. , Zhao Bin , Willis Michael J. , Hubbard Alun , Box Jason E. , Jenner Brittany A. , Behar Alberto E. 
Published: December 2017

Significance
Meltwater runoff is an important hydrological process operating on the Greenland ice sheet surface that is rarely studied directly. By combining satellite and drone remote sensing with continuous field measurements of discharge in a large supraglacial river, we obtained 72 h of runoff observations suitable for comparison with climate model predictions. The field observations quantify how a large, fluvial supraglacial catchment attenuates the magnitude and timing of runoff delivered to its terminal moulin and hence the bed. The data are used to calibrate classical fluvial hydrology equations to improve meltwater runoff models and to demonstrate that broad-scale surface water drainage patterns that form on the ice surface powerfully alter the timing, magnitude, and locations of meltwater penetrating into the ice sheet.
Conserved salt-bridge competition triggered by phosphorylation regulates the protein interactome
Authors: Skinner John J. , Wang Sheng , Lee Jiyoung , Ong Colin , Sommese Ruth , Sivaramakrishnan Sivaraj , Koelmel Wolfgang , Hirschbeck Maria , Schindelin Hermann , Kisker Caroline , Lorenz Kristina , Sosnick Tobin R. , Rosner Marsha Rich 
Published: December 2017

Significance
Phosphorylation is a ubiquitous modification that has been implicated in signaling and other functions, but the atomic-level mechanisms are not completely understood. We identify a salt-bridge competition or “theft” mechanism wherein a phosphoserine, but not a phosphomimetic, breaks a pre-existing salt bridge, initiating a partial unfolding event and promoting new protein interactions. Structural elements underlying the theft occurred early in evolution and are found in 10% of homo-oligomers and 30% of hetero-oligomers. These findings identify a facile and evolutionarily accessible mechanism for reorganizing salt bridges and other electrostatic networks with only a single mutation to trigger a functional switch.
What Chern–Simons theory assigns to a point
Authors: Henriques André G. 
Published: December 2017

SignificanceThere are two main classes of 3D topological field theories: Turaev–Viro theories, associated to fusion categories, and Reshetikhin–Turaev theories, associated to modular tensor categories. Since the groundbreaking work by Lurie on the cobordism hypothesis, it has been a major open question to know which topological field theories (TFTs) extend down to points. Turaev–Viro theories can be extended down to points. But for most Reshetikhin–Turaev theories, including Chern–Simons theories, this was believed to be impossible (unless one puts them on the boundary of a 4D TFT). The present paper achieves two things: It shows that Reshetikhin–Turaev theories extend down to points, and it puts Turaev–Viro theories and Reshetikhin–Turaev theories on an equal footing by providing a unified language, bicommutant categories, that applies to both.
Recurring infection with ecologically distinct HPV types can explain high prevalence and diversity
Authors: Ranjeva Sylvia L. , Baskerville Edward B. , Dukic Vanja , Villa Luisa L. , Lazcano-Ponce Eduardo , Giuliano Anna R. , Dwyer Greg , Cobey Sarah 
Published: December 2017

Significance
Human papillomavirus (HPV) is the most common sexually transmitted infection. Understanding the factors underlying the prevalence and diversity of over 200 HPV types is necessary to predict the effects of multivalent vaccines. We investigate HPV transmission dynamics by fitting mechanistic models to data from unvaccinated men. We find that infection risk in a susceptible population is, on average, low and concentrated in high-risk individuals and that, rather than inducing protective immunity, HPV infection strongly increases the risk of future infection by the same type. Thus, high HPV prevalence results from frequent reinfection or persistent infections within individuals. Vaccinating boys before their first HPV exposure may be especially effective in reducing prevalence, and vaccinating previously infected men may also be effective.
Aminoglycoside interactions and impacts on the eukaryotic ribosome
Authors: Prokhorova Irina , Altman Roger B. , Djumagulov Muminjon , Shrestha Jaya P. , Urzhumtsev Alexandre , Ferguson Angelica , Chang Cheng-Wei Tom , Yusupov Marat , Blanchard Scott C. , Yusupova Gulnara 
Published: December 2017

Significance
Aminoglycosides are well known as antibiotics that target the bacterial ribosome. However, they also impact the eukaryotic translation mechanism to promote read-through of premature termination codons (PTCs) in mRNA. Aminoglycosides are therefore considered as potential therapies for PTC-associated human diseases. Here, we performed a comprehensive study of the mechanism of action of aminoglycosides in eukaryotes by applying a combination of structural and functional approaches. Our findings reveal complex interactions of aminoglycosides with eukaryotic 80S ribosome caused by their multiple binding sites, which lead to inhibition of intersubunit movement within the human ribosome that impact nearly every aspect of protein synthesis.
Ant colony optimization and event-based dynamic task scheduling and staffing for software projects
Authors: Ellappan Vijayan , Ashwini J 
Published: December 2017

Abstract
In programming change organizations from medium to inconceivable scale broadens, the issue of wander orchestrating is amazingly unusual and testing undertaking despite considering it a manual system. Programming wander-organizing requirements to deal with the issue of undertaking arranging and in addition the issue of human resource portion (also called staffing) in light of the way that most of the advantages in programming ventures are individuals. We propose a machine learning approach with finds respond in due order regarding booking by taking in the present arranging courses of action and an event based scheduler revives the endeavour arranging system moulded by the learning computation in perspective of the conformity in event like the begin with the Ander, the instant at what time possessions be free starting to ended errands, and the time when delegates stick together otherwise depart the wander inside the item change plan. The route toward invigorating the timetable structure by the even based scheduler makes the arranging method dynamic. It uses structure components to exhibit the interrelated surges of endeavours, slip-ups and singular all through different progression organizes and is adjusted to mechanical data. It increases past programming wander movement ask about by taking a gander at a survey based process with a one of a kind model, organizing it with the data based system for peril assessment and cost estimation, and using a choice showing stage.
FROGS: Find, Rapidly, OTUs with Galaxy Solution
Authors: Escudié Frédéric , Auer Lucas , Bernard Maria , Mariadassou Mahendra , Cauquil Laurent , Vidal Katia , Maman Sarah , Hernandez-Raquet Guillermina , Combes Sylvie , Pascal Géraldine 
Published: December 2017

Abstract

Motivation
Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own.

Results
This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME.

Availability and implementation
Source code and instructions for installation: https://github.com/geraldinepascal/FROGS.git. A companion website: http://frogs.toulouse.inra.fr.

Supplementary information
Supplementary data are available at Bioinformatics online.
SPRING: a kinetic interface for visualizing high dimensional single-cell expression data
Authors: Weinreb Caleb , Wolock Samuel , Klein Allon M 
Published: December 2017

Abstract

Motivation
Single-cell gene expression profiling technologies can map the cell states in a tissue or organism. As these technologies become more common, there is a need for computational tools to explore the data they produce. In particular, visualizing continuous gene expression topologies can be improved, since current tools tend to fragment gene expression continua or capture only limited features of complex population topologies.

Results
Force-directed layouts of k-nearest-neighbor graphs can visualize continuous gene expression topologies in a manner that preserves high-dimensional relationships and captures complex population topologies. We describe SPRING, a pipeline for data filtering, normalization and visualization using force-directed layouts and show that it reveals more detailed biological relationships than existing approaches when applied to branching gene expression trajectories from hematopoietic progenitor cells and cells of the upper airway epithelium. Visualizations from SPRING are also more reproducible than those of stochastic visualization methods such as tSNE, a state-of-the-art tool. We provide SPRING as an interactive web-tool with an easy to use GUI.

Availability and implementation
https://kleintools.hms.harvard.edu/tools/spring.html, https://github.com/AllonKleinLab/SPRING/.

Supplementary information
Supplementary data are available at Bioinformatics online.