bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimating the age of western grey kangaroos (Macropus fuliginosus ocydromus)
Authors: Mayberry Chris , Bencini Roberta , Mawson Peter R. , Maloney Shane K.
Published: November 2017

Scientific studies and population management may benefit from knowledge of the age structure of a target population. We evaluated traditional and newly developed methods of estimating the age of kangaroos with data from 336 western grey kangaroos (Macropus fuliginosus) culled from a wild population in south-western Australia. We compared their ages based on molar progression with data on head, leg, and foot length, a balanced sum of all three measures, dried eye-lens weight, and molar wear score, and derived formulae to estimate age from each variable. Molar wear score has a linear relationship to molar progression and therefore leads to similar estimations of age, but requires only one complete arcade of molars. Because the relationships between age and the lengths of head, foot and leg are curvilinear, these become less reliable indicators of age with increasing age but the accuracy can be improved by considering a combination of the lengths of head, foot, and leg. Estimation of age from dried lens weight is more accurate than estimation from morphometry. The use of morphometry to estimate the age of kangaroos older than two years is more reliable than previously thought and requisite data can be collected from live animals. Where lethal methods are needed to collect samples, a largely intact skull, a single arcade of molars, or the lens extracted from one eye can reliably be used to estimate age.
Thinking globally, acting locally
Authors: Baider Fabienne H.
Published: November 2017

The 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

The 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

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

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

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

Motivation

Planarians 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.

Results

We 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 implementation

The 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 information

Supplementary 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

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

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

Motivation

There 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.

Results

The 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 implementation

http://myriads.webs.uvigo.es

Supplementary information

Supplementary 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

Motivation

Proteins 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.

Results

The 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 implementation

MOCASSIN-prot, implemented in Perl and Matlab, is freely available at http://bioinfolab.unl.edu/emlab/MOCASSINprot.

Supplementary information

Supplementary 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

Motivation

Graphlets 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.

Results

We 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 implementation

An 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

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.
Promise and Challenges in Drug Development and Assessment for Cognitive Enhancers
Authors: Cummings Jeffrey , Zhong Kate
Published: November 2017

Cognitive disturbances are ubiquitous in neurologic and psychiatric disorders. Schizophrenia, depression, developmental disorders, acquired brain disorders (traumatic brain injury and stroke), and neurodegenerative disorders all have cognitive impairment as a manifestation. Cognitive enhancers can improve intellectual function and have been approved for Alzheimer’s dementia, dementia of Parkinson’s disease, and attention deficit hyperactivity disorder. Cognitive enhancers are being developed for other cognitive disorders. There are many advantages for development of symptomatic cognitive enhancers compared to disease-modifying agents. Cognitive enhancers typically modulate transmitter systems. Cross-disease phenotypes such as executive function impairment may represent a development strategy for cognitive enhancing agents. Life cycle management strategies for cognitive enhancers include expanding indications to disorders with related pathophysiology or to different stages of disease severity and development of alternate formulations. Cognitive enhancers can restore essential cognitive capability and are a critical element of optimal care of patients with neurologic and psychiatric disorders.
Cognitive Enhancement in Non-Alzheimer’s Dementias
Authors: Tousi Babak
Published: November 2017

Cognitive enhancement in non-Alzheimer’s dementias has not been studied as extensively as that in Alzheimer’s dementia. This chapter reviews the research on cognitive enhancement for three types of dementia: vascular dementia, dementia with Lewy bodies, and frontal lobe dementia. The chapter reviews both pharmacological and nonpharmacological approaches for treatment of dementia. The focus is on randomized controlled trials for currently available medications, specifically cholinesterase inhibitors and memantine. Major advances in physical and cognitive rehabilitation during the past decade have inspired clinicians and researchers to explore the role of potential cognitive enhancers in different types of dementias. This chapter also examines the effects of therapeutic interventions such as exercise, physical rehabilitation, cognitive rehabilitation, and electrical stimulation of the brain on cognition in non-Alzheimer’s dementias.
Cognitive Interventions in Parkinson’s Disease
Authors: Banks Sarah
Published: November 2017

People with Parkinson’s disease frequently demonstrate cognitive impairments, ranging from isolated cognitive impairments to frank dementia. Cognitive dysfunction in Parkinson’s disease has a clear impact on quality of life and independence; hence, there is a need to develop treatments that will reliably improve this important nonmotor symptom. Executive functions are the most frequently impacted cognitive domain, and they have been shown in other populations to be amenable to cognitive interventions. This chapter reviews the literature on cognitive interventions in Parkinson’s disease, and it places the literature into the context of cognitive impairment in Parkinson’s disease. It also reviews studies of cognitive interventions for other conditions. Current gaps in our understanding are highlighted, and proposals for future directions of research in this field are provided.
Cognitive Enhancement in Traumatic Brain Injury
Authors: Hart Tessa
Published: November 2017

Traumatic brain injury (TBI) is a prevalent source of disability. This chapter reviews the major approaches to remediation of cognitive dysfunction following TBI, in both the early and post-acute phases of recovery. Pharmacologic and behavioral treatments are discussed, focusing on the three major areas of cognition affected by TBI: attention, memory, and executive function. Trials of pharmacologic treatments, especially neuroprotective agents, have resulted in few treatment guidelines, probably due to the heterogeneous pathophysiology of TBI. Among behavioral treatments, both restorative and compensatory approaches are presented. Most of the available evidence favors compensatory treatments, in which patients are taught alternative strategies and/or changes are made in the social/physical environments to facilitate everyday functioning. Despite methodologic challenges and limitations in treatment definition that make comparisons across studies difficult, cognitive rehabilitation for TBI is increasingly viewed as a vital component of the effort to restore maximal independence at home and in society.
Cognitive Enhancement in Bipolar Disorder
Authors: Mahon Katie , Russo Manuela , Perez-Rodriguez M. Mercedes
Published: November 2017

Neurocognitive deficits are acknowledged as integral features of bipolar disorder (BD) and are known to contribute to the compromised level of functioning in individuals with BD. This chapter provides an overview of the current state of cognitive enhancement in BD. Few pharmacological agents have been investigated with regard to their potential for pro-cognitive effects in BD. Dopaminergic agents (pramipexole) and stimulants (modafinil, armodafinil, and amphetamine) as adjunctive treatment in BD appear to be promising cognitive enhancers, and there are few ongoing randomized clinical trials targeting both cognitive dysfunctions and clinical symptomatology in BD. Glutamatergic agents (d-cycloserine) may hold promise as potential cognitive enhancing agents in BD; however, as for dopaminergic agents and stimulants, no conclusive data exist. Larger samples and longer follow-up are needed to obtain a deep understanding of the efficacy and safety of these compounds and their role in the neurobiological mechanisms underpinning cognition in BD.
Pharmacologic Neuroprotection
Authors: Stocchetti Nino , Carbonara Marco
Published: November 2017

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

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

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

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

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.
Neuroprotection in Sepsis and Acute Respiratory Distress Syndrome
Authors: Dangayach Neha S. , Francoeur Charles L , Mayer Stephan A. , Sharshar Tarek
Published: November 2017

Diffuse cerebral dysfunction in sepsis and acute respiratory distress syndrome (ARDS) patients is highly prevalent. Delirium and alterations in level of consciousness in septic patients are symptoms that constitute sepsis-associated encephalopathy (SAE), which is distinct from hypoxic encephalopathy. SAE is associated with substantial mortality and long-term cognitive impairment. The underlying pathophysiology of SAE is complex and poorly understood. The pathophysiology of SAE includes neuroinflammation, microglial activation, microcirculatory failure, autoregulation impairment, blood–brain barrier disruption, apoptosis, and development of microinfarcts and microhemorrhages. Apart from standard resuscitation techniques targeted at maintaining adequate cerebral perfusion and oxygenation, specific neuroprotective interventions are not currently available. Given the vast unmet need for improving functional outcome among survivors of SAE, it is a priority for the critical care community to better define, understand, and prevent this common and devastating form of neurological injury.
Neuroprotection for Valvular and Coronary Artery Bypass Grafting Surgery
Authors: Bartels Karsten , Mackensen G. Burkhard
Published: November 2017

Major cardiac surgery represents a unique biologic stimulus leading to profound perturbations in inflammatory, hemostatic, and oxidative stress pathways, all of which are implicated in the pathogenesis of perioperative cerebral injury. Despite significant advances in surgical, anesthetic, and neuroprotective strategies, these adverse cerebral outcomes have profound personal, clinical, and financial implications. Preventing or treating these adverse outcomes remains difficult because the underlying mechanisms remain incompletely understood, and most neuroprotective strategies generated in experimental disease models of cardiac surgery have not successfully translated to humans. The nonpharmacological strategies that can be recommended on the basis of current evidence include optimal temperature management and ultrasound-guided assessment of the (potentially) atheromatous ascending aorta, with appropriate modification of aortic cannulation, clamping, or anastomotic technique. This chapter reviews past, present, and future directions in the field of neuroprotection in cardiac surgery.
Neuroprotection for Aortic Surgery and Stenting
Authors: Feinman Jared W. , Augoustides John G.
Published: November 2017

Despite recent advances, aortic surgery and stenting for an array of diseases still pose a significant risk of permanent and severe injury to the brain and/or spinal cord. These neurological risks are best understood in terms of the primary disease pathology, the extent of aortic involvement, mechanisms and risk factors, the role of neuromonitoring modalities, and the surgical techniques required for repair. This chapter will present an overview of perioperative practice in aortic surgery and stenting based on this framework and the latest guidelines and trials in order to describe best practices and promising options for neuroprotection in this challenging clinical setting.
Neuroprotection for Carotid Endarterectomy and Carotid Artery Stenting
Authors: Anastasian Zirka H. , Heyer Eric J.
Published: November 2017

Carotid endarterectomy (CEA) and carotid artery stenting (CAS) pose risks of cerebral injury and adverse neurological outcomes consisting of perioperative stroke and cognitive decline. This chapter examines the mechanisms of and risks for neurological injury associated with these procedures and the various strategies that are employed to protect the brain and minimize the risk of stroke and cognitive decline, including surgical and anesthetic techniques, blood pressure management, and statin administration. During CEA, neuromonitoring is used to guide surgical technique in order to prevent ischemic stroke due to hypoperfusion during carotid artery cross-clamping and embolic stroke during unclamping. For CAS, cerebral protective devices are the primary neuroprotection technique, with the focus on preventing embolic stroke during manipulation of wires, angioplasty, and stenting.
Optimization
Authors: Basu Sanjay
Published: November 2017

This chapter seeks to determine how can we best allocate limited resources among many different programs. Given a budget to run a program that must be distributed among many different alternative projects (e.g., within a public health department, we might allocate some resources to a vaccination program, another set of resources to a diabetes prevention program, and yet another set of resources to an air pollution reduction program), how can we try to maximize the chances that we allocate limited resources fairly, ensuring that each program has at least the minimal resources that it needs while also ensuring that the distribution of resources maximizes overall public health? This chapter uses computational tools to solve such problems, focusing on how we can make smart decisions to maximize the potential effectiveness or cost-effectiveness of any particular program we’re interested in supporting—a goal known as optimization.
Modeling in R
Authors: Basu Sanjay
Published: November 2017

Spreadsheet are straightforward to work with and do not require extensive knowledge of programming; they are easy to communicate with among people with varying levels of expertise; are convenient for optimization problems, given the availability of prepackaged Solver algorithms; and are commonly used for modeling in business management, nonprofit organization budgeting, consulting, and academia. But spreadsheets have their limitations, particularly when modeling large populations, long time periods, or complex situations with many states or conditions and equations. For larger scale models that need more flexibility than can be offered by a spreadsheet, the free statistical program R provides a straightforward approach to modeling and has the advantages of being free, fast, available on any operating system, commonly used, and widely supported by an online community. This chapter provides a detailed introduction to R that will be useful for the more advanced modeling methods introduced in Chapters 8 through 11.
Microsimulation
Authors: Basu Sanjay
Published: November 2017

In previous chapters, the author used Markov models to estimate the burden of disease and the potential impact of interventions. One of the key limitations to Markov models is that they don’t take into account a person’s unique individual characteristics: Markov models are designed to efficiently simulate the average outcome for an entire population. For many public health and healthcare system problems, however, we need to consider heterogeneity within a population, or differences in risk and differences in benefit from our programs. For that purpose, microsimulation models, which take into account unique characteristics of individuals and the correlations between these characteristics, can be more useful. This chapter details the construction and use of microsimulation models, using examples related to diabetes prevention and treatment.
Modeling Large-Scale Epidemics
Authors: Basu Sanjay
Published: November 2017

Previous chapters ignored a critical aspect of modeling some major diseases: the infectious nature of many diseases. For infectious diseases, the risk of getting the disease is related to how many people are infectious at a given time: the more infectious people in the area, the higher the risk of infection among susceptible people. In a typical Markov model, we can’t account for this basic feature of infectious diseases because the risk of moving from one state (healthy) to another state (diseased) is assumed to be constant. In this chapter, the author introduces a simulation modeling framework that has been used for decades to simulate infectious disease epidemics.
Good Modeling Practices
Authors: Basu Sanjay
Published: November 2017

Throughout this book, the author has focused on the practices of constructing models or using standard modeling templates and strategies to solve common public health and healthcare system problems. But inherent to the task of using models is the challenge of being a good consumer of models. Often, the planner is faced with the task of reading and interpreting models produced by others and determining whether they “believe” the model results and can make use of the model implementation to help make decisions. In this chapter, the author addresses the issue of how we might become better consumers of modeling studies.
What Are Learning Disabilities?
Authors: Franz Carleen , Ascherman Lee , Shaftel Julia
Published: November 2017

Definitions of learning disabilities from several sources reveal the heterogeneity of learning disabilities and the many terms used in different settings. Early warning signs of future educational challenges are listed. Case studies illustrate the presentation of learning disabilities of different types. Learning Disorders from DSM-5 are contrasted with Specific Learning Disabilities in the Individuals With Disabilities Education Act of 2004 (IDEA), which governs diagnosis and treatment in the school setting. The IDEA process of diagnosis and qualification is described for clinicians to clarify inconsistencies between clinical and school procedures and outcomes. Discontinuities between clinical and school assumptions, terms, and processes often lead to misunderstanding on the part of parents and clinicians.
Learning Disabilities in Written Expression
Authors: Franz Carleen , Ascherman Lee , Shaftel Julia
Published: November 2017

Writing disabilities have many potential origins, including oral language deficits, motor coordination problems, and reading disabilities. Multiple potential sources of written language problems are described, along with the integrative aspects of the writing process that make it one of the most demanding academic tasks. Remedial interventions vary according to the identified cause of the problem based on the results of the psychoeducational evaluation. Remediation targeting the individual and modifications to classroom instruction may be required. Case studies illustrate three different underlying causes of writing problems. Key among these are motor and spatial skills, general language ability, and comorbid behavioral or reading disorders.
Nonverbal Learning Disabilities
Authors: Franz Carleen , Ascherman Lee , Shaftel Julia
Published: November 2017

Nonverbal learning disabilities (NVLDs) occur when average or above-average verbal abilities contrast with weak visual-spatial, motor, and social communication skills. Students with NVLD often have delayed gross and fine motor skills, interpersonal skills deficits in nonverbal communication and pragmatic language, and problems with visual and spatial memory. The severity of NVLD varies from relatively mild social impairment or delays in gross motor skills, such as riding a bike or throwing a ball, to serious academic problems, often in mathematics. These students often demonstrate good comprehension and memory for rote information with weak figurative language and social communication skills. Case studies and remedial strategies are included to illustrate NVLD.
The Psychoeducational Evaluation
Authors: Franz Carleen , Ascherman Lee , Shaftel Julia
Published: November 2017

This chapter describes the content and procedures of a comprehensive psychoeducational evaluation. Components include the referral question, review of records, history, observation, and assessment. Rating scales, standardized tests, and interviews make up the assessment portion of the evaluation process. The entire process must use multiple measures and assess multiple viewpoints and settings. Cognitive, academic, behavioral, social skills, and executive functions may be included in the assessment. A thorough integration of the findings from multiple sources must be accomplished to reach meaningful diagnostic conclusions and determine relevant recommendations. IDEA requirements for school-based evaluation processes are explained and contrasted with independent evaluation methods.
Intellectual Assessment
Authors: Franz Carleen , Ascherman Lee , Shaftel Julia
Published: November 2017

Intellectual assessment includes the broad range of cognitive skills and processes as measured by major intelligence tests. Intelligence testing is an integral part of the assessment process; however, it is often misunderstood. A great deal of weight is assigned to the scores, and decisions are often made that are not justified by the results. It is important for the clinician to understand the nature of the process, the types and interpretations of the scores, and the limitations, to avoid common fallacies. Two of the predominant tests, the Wechsler Intelligence Scale for Children-V and the Woodcock-Johnson IV Tests of Cognitive Abilities, are described. Some misconceptions about IQ are explained, and interpretation of intelligence test results is carefully spelled out for the clinician unfamiliar with these tools. The various scores derived from the results of intelligence tests are clarified.
Interpretation of Assessment Results
Authors: Franz Carleen , Ascherman Lee , Shaftel Julia
Published: November 2017

Tests used in a comprehensive psychoeducational evaluation produce a myriad of scores, which can be confusing for the clinician and easily misinterpreted, even by experienced examiners. Standardized scores, raw scores, percentile ranks, age and grade equivalents, and other score types are explained and contrasted. Recommended scores are described so that the clinician will know what to look for and how to evaluate a report. In addition to test scores, verbal range descriptors such as “below average” or “superior” convey student performance in an accessible and user-friendly manner. Qualitative information can enrich the understanding of the student’s performance and provide crucial information for intervention planning.
Transition From School to College and Career
Authors: Franz Carleen , Ascherman Lee , Shaftel Julia
Published: November 2017

The transition period from adolescence to young adulthood is the final phase of special education supports and services, which end with high school completion. The IDEA requirements for transition services are spelled out for the benefit of clinicians and parents who are not familiar with these features of the Individualized Education Program for students 16 years and older. Measurable postsecondary goals for education, employment, and, if needed, independent living are based on student strengths, preferences, and needs. Additional steps include the identification of necessary transition assessments to define progress toward those goals, development of a course of study, and the involvement of external agencies as desired to assist the student and family to attain future goals. Challenges in transition planning are discussed along with an array of potential positive and negative outcomes for youth with disabilities. A case study is included as a model of best practices in transition planning.
Paediatric Electromyography
Authors: Pitt Matthew
Published: November 2017

Paediatric Electromyography is a single-author textbook which covers the full range of applications of the techniques of nerve conduction and electromyography (EMG) in children from the neonatal period to the late teenage years. It comprises five sections. Section 1 in its first chapter, gives a detailed introduction to the different skills that are needed to effect successful interventions in paediatric EMG. The emphasis here is that paediatric EMG is not simply adult EMG applied to younger subjects. Its second chapter is an introduction to the basic physiology which is common to any practice of nerve and muscle study. The next three sections (2–4), each comprised of three chapters, are structured anatomically covering in order, nerves, muscles, and neuromuscular junctions. All follow a similar pattern with the first chapter of the section dedicated to the underlying physiology needed for interpretation of the techniques used in the investigation of that particular part of the nervous system. The second chapter gives the pathophysiological associations and the final chapter covers any aspect not covered in the previous two chapters. In section 5 the techniques needed to deal with the more unusual clinical requests, such as investigation of facial palsy, swallowing abnormalities, brachial plexus injuries, and diaphragmatic problems are brought together in a final chapter. The book is concluded with three appendices. Appendix 1 describes protocols devised to cover the differing clinical request sent to any laboratory. Appendix 2 gives a comprehensive database of normative data, often derived from e-norm methodology, and intending to cover every measure recorded. Appendix 3 is an illustrated description of electrode placements for all the common nerve studies.
Introduction
Authors: Pitt Matthew
Published: November 2017

This chapter opens with a discussion of how paediatric electromyography (EMG) is materially different from that performed in adults. In this chapter, the recognition that EMG is considered a painful experience is acknowledged. The techniques to reduce this discomfort and the associated anxiety are described, including preparation of the children, both prior to the test and during the clinic appointment itself. The order of testing is another important factor along with the need for every intervention having a clear reason for its use. In other parts of the world, sedation is considered an essential accompaniment and the advantages and disadvantages of such an approach are itemized
Basic physiology
Authors: Pitt Matthew
Published: November 2017

The basic physiology common to all neurophysiological testing is covered in this chapter. It describes the process of the production of a transmembrane gradient by the sodium pump to the generation of an action potential, the influence of refractory periods, unidirectional propagation, and the influence of volume conduction on the appearance of the action potential when recorded on the skin surface. The practicalities of recording the signals are discussed, including the importance of bipolar stimulation and the practical limitations of what can be recorded and measured in nerve conduction studies. Finally, the technique of electrical stimulation is highlighted.
Pathophysiological correlations in neuropathies
Authors: Pitt Matthew
Published: November 2017

This chapter begins with an explanation of the pathophysiological correlations between the recorded changes and the underlying diagnosis which allow classification into demyelinating and axonal neuropathy. Demyelinating neuropathies are discussed first. The extensive and ever expanding literature in hereditary neuropathies is highlighted. The different variants of the acute inflammatory demyelinating polyneuropathy encountered in children are discussed along with the electrodiagnostic criteria for the diagnosis. Chronic inflammatory demyelinating polyneuropathy is then covered, both in its clinical presentation and electrodiagnosis. Other causes such as MNGIE and Lyme disease are highlighted. In the section on axonal neuropathy, division into hereditary and acquired is made. The diagnosis of sensorimotor hereditary neuropathies is discussed along with primarily sensory neuropathies including ataxia telangiectasia, Friedreich’s ataxia, and abetalipoproteinaemia, finishing with discussion of the hereditary sensory and autonomic neuropathies. The many different causes of acquired axonal neuropathy are listed and discussed including neoplasia, endocrine disturbances, metabolic conditions, infective agents, autoimmune conditions, mitochondrial disease, drugs, and vitamin deficiency, finishing with critical illness neuromyopathy.