bluuebunny/crossref_metadata_2025_split huggingface dataset:
Die Progression der Nierenerkrankung – wie ist sie zu verhindern? - Allgemeine therapeutische Ansätze für jeden CKD-Patienten
Authors: Schneider Markus , Hilgers Karl 
Published: November 2017

ZusammenfassungIst aufgrund eines chronischen Nierenversagens eine Nierenersatztherapie notwendig, ist dies mit einer vergleichsweise schlechten Lebensqualität und einer hohen Mortalitätsrate assoziiert. Daher ist die Verlangsamung der Progression einer chronischen Nierenerkrankung ein wichtiges Ziel. Eine besonders wichtige Intervention ist die Einstellung des Blutdrucks mit einem Zielwert von maximal 140/90 mmHg, bei Patienten mit einer Albuminurie sogar von maximal 130/80 mmHg. Besteht eine Albuminurie, sollten bevorzugt Inhibitoren des Renin-Angiotensin-Systems eingesetzt werden – und zwar abhängig vom Diabetesstatus und von der Schwere der Albuminurie (Patienten Diabetes und Albuminurie ≥ 30 mg/Tag; Patienten ohne Diabetes, aber mit einer Albuminurie > 300 mg/Tag). Mineralocorticoid- und Endothelinrezeptorenblocker scheinen neue antiproteinurische Strategien zu ermöglichen, wenn auch ihre positiven Effekte auf die Nierenfunktion noch zu validieren sind. Ein HbA1c-Zielwert von etwa 7,0 % kann bei Patienten mit einer diabetischen Nierenerkrankung ebenfalls dazu beitragen, die Progression der Niereninsuffizienz zu verlangsamen. Darüber hinaus gilt heute die SGLT-2-Inhibition mit Empagliflozin als kardiovaskulär und renal protektiv. Aktuellen Studiendaten zufolge können auch eine Korrektur der metabolischen Azidose und das Vermeiden eines akuten Nierenversagens die Patienten vor einer Progression des Nierenschadens schützen.
Prenylated Flavonoids and Phenolic Compounds from the Rhizomes of Marine Phanerogam Cymodocea nodosa
Authors: Smadi Abla , Ciavatta Maria , Bitam Fatma , Carbone Marianna , Villani Guido , Gavagnin Margherita 
Published: November 2017

AbstractChemical investigation of the rhizomes of the marine phanerogam Cymodocea nodosa resulted in the isolation of two new prenylated flavon-di-O-glycosides, cymodioside A (1) and B (2), along with known phenolic compounds 3–7, some of which never reported from seagrasses to date. The structures of compounds 1 and 2 were established by extensive nuclear magnetic resonance analysis. In addition, the absolute configuration of 4-(2,5-dihydroxyhexyl) benzene-1,2-diol (7), which was not previously reported in the literature, has been now determined.
Thinking globally, acting locally
Authors: Baider Fabienne H. 
Published: November 2017

AbstractThe aim of this study is to show how trans-national right-wing linguistic strategies and global xenophobic attitudes are reworked at national levels, and how, as a result, specialized country- and culture-specific coercion and legitimization strategies arise. Using a detailed, quantitative-qualitative method of analysis, we look at the Greek Cypriot extreme-right party ELAM to see how the party’s anti-migration rhetoric construes any foreign presence as threat, by proximizing it linguistically as ‘invasion.’ This strategy allows the conflation of the current ‘Other’ (migrants) with archetypical adversaries, such as Turkey. Indeed, anchoring the migration issue in the main national narrative, i.e., the long-standing Cypriot conflict, gives their xenophobic language conceptual coherence and strengthens its textual cohesion. In particular two figures of speech are the basis of this invasion script, the wordmetanasteftiko‘the immigration phenomenon’ conceptualized as thekipriako(the Cyprus problem, i.e., the political division of the island). This parallelism opens the way for a number of inferences, while it also enables a conceptual shift from therealphenomenon known asglobalizationandmulticulturalismto the imagined idea of a (white/Western) genocide. Data include comments responding to ELAM followers’ YouTube videos and mainstream press representations. Methodology includes corpus linguistics and discourse analysis focused on the fundamental metaphors found in the data such asmigration as unbearable weightandmigration as dirt.
“We mustn’t fool ourselves”
Authors: Bolonyai Agnes , Campolong Kelsey 
Published: November 2017

AbstractThe historic wave of refugees reaching Europe in 2015 was met with a volatile mixture of ethno-nationalist, anti-Muslim fearmongering and political infighting within the European Union (EU). Perhaps no one was more influential in promulgating fear and anti-refugee sentiment than Viktor Orbán, the Prime Minister of Hungary, whose inflammatory rhetoric and uncompromising, illiberal political stance helped escalate the refugee-crisis in a discursive battle of political wills, ideologies, and identity politics within the EU. This paper explores how Orbán employs political discourse practices and strategies to enact his right-wing populist (RWP) ideology and anti-immigrant ‘politics of fear’ (Wodak 2015) vis-à-vis EU politicians’ pro-migration discourses. Adopting a broad critical discourse-analytic approach, we demonstrate Orbán’s iterative production of discourses of threat and defense underlying discourses of fear (law and order, cultural/religious difference), and discourses of oppositional political identities and ideologies throughfractal recursion. We argue that recursive performance of RWP stances creates a recognizable political style characteristic of Orbán’s RWP political persona or type.
Donald Trump supporters and the denial of racism
Authors: Subtirelu Nicholas Close 
Published: November 2017

Abstract
Donald Trump’s campaign to become president of the United States was shocking for many people. His negative representations of racialized immigrant groups were one of the most controversial aspects of the campaign, leading to frequent accusations of racism. This study explores how his supporters responded to such accusations. Discussions of racism within a pro-Trump reddit community, called “The_Donald”, were analyzed. The_Donald users adamantly denied that Trump’s statements or proposed policies were racist. Their dismissal of these accusations drew on and extended the logic of color-blind racism. They argued that such accusations were merely cynical political tactics and advocated that Trump supporters respond to them as such. Their favored response strategies superficially resembled genuine debate but were apparently intended to incite emotional responses from accusers and to compel them to disengage from conversations. The article discusses these strategies in light of the ongoing polarization of political debate around immigration.
DDR: efficient computational method to predict drug–target interactions using graph mining and machine learning approaches
Authors: Olayan Rawan S , Ashoor Haitham , Bajic Vladimir B 
Published: November 2017

Abstract

Motivation
Finding computationally drug–target interactions (DTIs) is a convenient strategy to identify new DTIs at low cost with reasonable accuracy. However, the current DTI prediction methods suffer the high false positive prediction rate.

Results
We developed DDR, a novel method that improves the DTI prediction accuracy. DDR is based on the use of a heterogeneous graph that contains known DTIs with multiple similarities between drugs and multiple similarities between target proteins. DDR applies non-linear similarity fusion method to combine different similarities. Before fusion, DDR performs a pre-processing step where a subset of similarities is selected in a heuristic process to obtain an optimized combination of similarities. Then, DDR applies a random forest model using different graph-based features extracted from the DTI heterogeneous graph. Using 5-repeats of 10-fold cross-validation, three testing setups, and the weighted average of area under the precision-recall curve (AUPR) scores, we show that DDR significantly reduces the AUPR score error relative to the next best start-of-the-art method for predicting DTIs by 31% when the drugs are new, by 23% when targets are new and by 34% when the drugs and the targets are known but not all DTIs between them are not known. Using independent sources of evidence, we verify as correct 22 out of the top 25 DDR novel predictions. This suggests that DDR can be used as an efficient method to identify correct DTIs.

Availability and implementation
The data and code are provided at https://bitbucket.org/RSO24/ddr/.

Supplementary information
Supplementary data are available at Bioinformatics online.
bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files
Authors: Lindenbaum Pierre , Redon Richard 
Published: November 2017

Abstract

Motivation
Reformatting and filtering bioinformatics files are common tasks for bioinformaticians. Standard Linux tools and specific programs are usually used to perform such tasks but there is still a gap between using these tools and the programming interface of some existing libraries.

Results
In this study, we developed a set of tools namely bioalcidae, samjs and vcffilterjs that reformat or filter files using a JavaScript engine or a pure java expression and taking advantage of the java API for high-throughput sequencing data (htsjdk).

Availability and implementation
https://github.com/lindenb/jvarkit.
PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
Authors: Castillo-Lara S , Abril J F 
Published: November 2017

AbstractMotivationPlanarians are emerging as a model organism to study regeneration in animals. However, the little available data of protein–protein interactions hinders the advances in understanding the mechanisms underlying its regenerating capabilities.ResultsWe have developed a protocol to predict protein–protein interactions using sequence homology data and a reference Human interactome. This methodology was applied on 11 Schmidtea mediterranea transcriptomic sequence datasets. Then, using Neo4j as our database manager, we developed PlanNET, a web application to explore the multiplicity of networks and the associated sequence annotations. By mapping RNA-seq expression experiments onto the predicted networks, and allowing a transcript-centric exploration of the planarian interactome, we provide researchers with a useful tool to analyse possible pathways and to design new experiments, as well as a reproducible methodology to predict, store, and explore protein interaction networks for non-model organisms.Availability and implementationThe web application PlanNET is available at https://compgen.bio.ub.edu/PlanNET. The source code used is available at https://compgen.bio.ub.edu/PlanNET/downloads.Supplementary informationSupplementary data are available at Bioinformatics online.
SATORI: a system for ontology-guided visual exploration of biomedical data repositories
Authors: Lekschas Fritz , Gehlenborg Nils 
Published: November 2017

Abstract

Motivation
The ever-increasing number of biomedical datasets provides tremendous opportunities for re-use but current data repositories provide limited means of exploration apart from text-based search. Ontological metadata annotations provide context by semantically relating datasets. Visualizing this rich network of relationships can improve the explorability of large data repositories and help researchers find datasets of interest.

Results
We developed SATORI—an integrative search and visual exploration interface for the exploration of biomedical data repositories. The design is informed by a requirements analysis through a series of semi-structured interviews. We evaluated the implementation of SATORI in a field study on a real-world data collection. SATORI enables researchers to seamlessly search, browse and semantically query data repositories via two visualizations that are highly interconnected with a powerful search interface.

Availability and implementation
SATORI is an open-source web application, which is freely available at http://satori.refinery-platform.org and integrated into the Refinery Platform.

Supplementary information
Supplementary data are available at Bioinformatics online.
The OncoPPi Portal: an integrative resource to explore and prioritize protein–protein interactions for cancer target discovery
Authors: Ivanov Andrei A , Revennaugh Brian , Rusnak Lauren , Gonzalez-Pecchi Valentina , Mo Xiulei , Johns Margaret A , Du Yuhong , Cooper Lee A D , Moreno Carlos S , Khuri Fadlo R , Fu Haian 
Published: November 2017

Abstract

Motivation
As cancer genomics initiatives move toward comprehensive identification of genetic alterations in cancer, attention is now turning to understanding how interactions among these genes lead to the acquisition of tumor hallmarks. Emerging pharmacological and clinical data suggest a highly promising role of cancer-specific protein–protein interactions (PPIs) as druggable cancer targets. However, large-scale experimental identification of cancer-related PPIs remains challenging, and currently available resources to explore oncogenic PPI networks are limited.

Results
Recently, we have developed a PPI high-throughput screening platform to detect PPIs between cancer-associated proteins in the context of cancer cells. Here, we present the OncoPPi Portal, an interactive web resource that allows investigators to access, manipulate and interpret a high-quality cancer-focused network of PPIs experimentally detected in cancer cell lines. To facilitate prioritization of PPIs for further biological studies, this resource combines network connectivity analysis, mutual exclusivity analysis of genomic alterations, cellular co-localization of interacting proteins and domain–domain interactions. Estimates of PPI essentiality allow users to evaluate the functional impact of PPI disruption on cancer cell proliferation. Furthermore, connecting the OncoPPi network with the approved drugs and compounds in clinical trials enables discovery of new tumor dependencies to inform strategies to interrogate undruggable targets like tumor suppressors. The OncoPPi Portal serves as a resource for the cancer research community to facilitate discovery of cancer targets and therapeutic development.

Availability and implementation
The OncoPPi Portal is available at http://oncoppi.emory.edu.
Myriads:P-value-based multiple testing correction
Authors: Carvajal-Rodríguez Antonio 
Published: November 2017

AbstractMotivationThere are many multiple testing correction methods. Some of them are robust to various dependencies in the data while others are not. Some of the implementations have problems for managing high dimensional list of P-values as currently demanded by microarray and other omic technologies.ResultsThe program Myriads, formerly SGoF+, provides some of the most important P-value-based correction methods jointly with a test of dependency and a P-value simulator. Myriads easily manage hundreds of thousands of P-values.Availability and implementationhttp://myriads.webs.uvigo.esSupplementary informationSupplementary data are available at Bioinformatics online.
MOCASSIN-prot: a multi-objective clustering approach for protein similarity networks
Authors: Keel Brittney N , Deng Bo , Moriyama Etsuko N 
Published: November 2017

AbstractMotivationProteins often include multiple conserved domains. Various evolutionary events including duplication and loss of domains, domain shuffling, as well as sequence divergence contribute to generating complexities in protein structures, and consequently, in their functions. The evolutionary history of proteins is hence best modeled through networks that incorporate information both from the sequence divergence and the domain content. Here, a game-theoretic approach proposed for protein network construction is adapted into the framework of multi-objective optimization, and extended to incorporate clustering refinement procedure.ResultsThe new method, MOCASSIN-prot, was applied to cluster multi-domain proteins from ten genomes. The performance of MOCASSIN-prot was compared against two protein clustering methods, Markov clustering (TRIBE-MCL) and spectral clustering (SCPS). We showed that compared to these two methods, MOCASSIN-prot, which uses both domain composition and quantitative sequence similarity information, generates fewer false positives. It achieves more functionally coherent protein clusters and better differentiates protein families.Availability and implementationMOCASSIN-prot, implemented in Perl and Matlab, is freely available at http://bioinfolab.unl.edu/emlab/MOCASSINprot.Supplementary informationSupplementary data are available at Bioinformatics online.
Efficiently counting all orbits of graphlets of any order in a graph using autogenerated equations
Authors: Melckenbeeck Ine , Audenaert Pieter , Colle Didier , Pickavet Mario 
Published: November 2017

AbstractMotivationGraphlets are a useful tool to determine a graph’s small-scale structure. Finding them is exponentially hard with respect to the number of nodes in each graphlet. Therefore, equations can be used to reduce the size of graphlets that need to be enumerated to calculate the number of each graphlet touching each node. Hočevar and Demšar first introduced such equations, which were derived manually, and an algorithm that uses them, but only graphlets with four or five nodes can be counted this way.ResultsWe present a new algorithm for orbit counting, which is applicable to graphlets of any order. This algorithm uses a tree structure to simplify finding orbits, and stabilizers and symmetry-breaking constraints to ensure correctness. This method gives a significant speedup compared to a brute force counting method and can count orbits beyond the capacity of other available tools.Availability and implementationAn implementation of the algorithm can be found at https://github.com/biointec/jesse.
shinyCircos: an R/Shiny application for interactive creation of Circos plot
Authors: Yu Yiming , Ouyang Yidan , Yao Wen 
Published: November 2017

Abstract

Summary
Creation of Circos plot is one of the most efficient approaches to visualize genomic data. However, the installation and use of existing tools to make Circos plot are challenging for users lacking of coding experiences. To address this issue, we developed an R/Shiny application shinyCircos, a graphical user interface for interactive creation of Circos plot. shinyCircos can be easily installed either on computers for personal use or on local or public servers to provide online use to the community. Furthermore, various types of Circos plots could be easily generated and decorated with simple mouse-click.

Availability and implementation
shinyCircos and its manual are freely available at https://github.com/venyao/shinyCircos. shinyCircos is deployed at https://yimingyu.shinyapps.io/shinycircos/ and http://shinycircos.ncpgr.cn/ for online use.
Pharmacologic Neuroprotection
Authors: Stocchetti Nino , Carbonara Marco 
Published: November 2017

Abstract
Acute cerebral injury sets into motion a cascade of deleterious biochemical events that cause further neuronal damage and amplify deleterious effects. This cascade develops over time and potentially may be attenuated or limited by pharmacologic manipulation. The neuroprotective properties of several molecules have been clearly demonstrated in experimental models of various pathologies. Based on these findings, many promising compounds have been tested in clinical trials. Large randomized controlled trials, however, have repeatedly failed to provide evidence of clinical efficacy. The authors present an overview of neuroprotective agents studied in traumatic brain injury, subarachnoid hemorrhage, ischemic stroke, and hypoxic-ischemic encephalopathy in adults due to cardiac arrest. They review the molecular mechanisms involved in secondary neuronal injury and how drugs targeting these mechanisms have been evaluated in clinical trials. Finally, the chapter briefly analyzes the possible reasons for repeated failures in translating experimental success into clinical benefit.
Imaging Assessment of Brain Injury
Authors: Warner Matthew A. , de la Plata Carlos Marquez , Liebeskind David S , Diaz-Arrastia Ramon 
Published: November 2017

Abstract
Imaging plays a pivotal role in discerning the extent and nature of brain injuries. Advances in neuroimaging techniques have improved sensitivity for detecting smaller lesions, improved the anatomical specificity of lesions in white matter, and improved the prognostic value of detected lesions. Novel quantitative methods allow measurements of hemorrhage and infarct volume in the acute phase of injury, and regional brain atrophy and functional disconnectedness months after injury. It is likely that the success of future clinical trials of neuroprotective therapies will be dependent on reliable and validated neuroimaging biomarkers of injury and recovery. This chapter describes neuroimaging modalities that are currently being utilized in clinical and experimental settings and their implications for the development and testing of neuroprotection strategies.
Tissue Biomarkers and Neuroprotection
Authors: Petzold Axel 
Published: November 2017

Abstract
This chapter reviews the evidence for using biomarkers to measure damage to the central nervous system (CNS) in neurocritical care and perioperative medicine. A conceptual framework is provided to guide the optimal timing of blood, cerebrospinal fluid, and structural imaging biomarker assessment in relation to the onset of injury. A selection of well-validated, cell type–specific biomarkers of CNS tissue damage are reviewed, including their composition, biokinetics, and specificity for neurons, axons, astrocytes, and microglia. Each of these biomarkers will be reviewed in the pertinent clinical settings of stroke, traumatic brain injury, cardiac arrest, Guillain-Barré syndrome, and neurological complications of critical illness and surgery.
Neurological and Functional Outcomes Assessment
Authors: Uysal Suzan , Mayer Stephan A. 
Published: November 2017

Abstract
The evidence base for neuroprotection in critical care and perioperative medicine rests on outcomes research, a critical component of which is the quantitative assessment of the functional effects of neurological injury. Outcomes assessment is conceptualized hierarchically in terms of global outcome, impairment, disability, handicap, and health-related quality of life. This chapter describes the different classes of outcome measures and the instruments within each class that are most commonly used in clinical neuroprotection research. Desirable characteristics of outcome measures are described, as well as considerations for statistical analysis of ordinal scale data. The authors describe several resources for clinicians and clinical researchers to aid in choosing or evaluating outcome measures for clinical neuroprotection trials.
Neuroprotection for Mechanical Circulatory Support
Authors: Dunn Lauren E , Willey Joshua Z , Lazar Ronald M 
Published: November 2017

Abstract
This chapter examines the adverse neurological events associated with mechanical circulatory support (MCS), which includes left ventricular assist devices (LVAD) and percutaneous devices for cardiac disease. The most frequently encountered neurological events are ischemic and hemorrhagic stroke, as well as intracerebral hemorrhage (ICH), heart failure and cardiovascular disease. The management of acute cerebrovascular conditions in this population poses unique challenges, given concomitant anticoagulation usage, hemodynamically unstable patients, and lack of randomized controlled trials investigating these clinical scenarios. Other acute neurological events include cerebral hyperperfusion and cerebral air embolism. This chapter describes these complications and their risk factors, and the available evidence-based and institutional management strategies.