bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Limbic System
Authors: Flemming Kelly D. , Benarroch Eduardo E. 
Published: July 2015

Abstract
The limbic “lobe” is not a well-defined lobe like other areas of the cortex. The term limbic system is also a misnomer because the “system” involves several cortical and subcortical structures. The cortical areas include the insular cortex, the cingulate gyrus, the parahippocampal gyrus, and the hippocampus. The subcortical structures include the amygdala, the nucleus accumbens (ventral or “limbic” striatum), the septal nuclei, the dorsomedial and anterior nuclei of the thalamus, and the hypothalamus. Brainstem components include the periaqueductal gray matter and the monoaminergic nuclei (in particular, dopaminergic neurons of the ventral tegmental area).
Cerebellum
Authors: Graff-Radford Jonathan , Hassan Anhar , Benarroch Eduardo E. 
Published: July 2015

Abstract
The cerebellum is crucial for planning, executing, terminating, and learning movements. The cerebellum compares actual motor performance with intended motor performance; thus, it is important in the adaptation of movement and posture as well. In addition, the cerebellum contributes to cognition and behavior. The main functions of the cerebellum appear to be the timing of motor functions and other functions. This chapter reviews the anatomy and circuitry of the cerebellum.
Cortex
Authors: Flemming Kelly D. 
Published: July 2015

Abstract
The cerebral cortex consists of 2 hemispheres, the left and the right. These are divided by the falx cerebri, a dural-derived structure. The cerebral cortex receives input from a wide variety of subcortical structures, often connecting via the thalamus and from other areas of the cortex via association fibers. The cortex then projects back to wide regions of the central nervous system, including the cortex, thalamus, basal nuclei, cerebellum, brainstem, and spinal cord. The types of fibers connecting areas of the central nervous system are designated based on the regions they connect. This chapter reviews the gross anatomy of the cerebral cortex.
Focal Cognitive Syndromes
Authors: Caselli Richard J. 
Published: July 2015

Abstract
The neurologic results of cortical lesions reflect the structural properties of the affected region. Lesions affecting primary sensorimotor cortices result in primary sensorimotor deficits that are qualitatively all-or-nothing, such as blindness (hemianopia) and paralysis (hemiparesis). Quantitatively, though, the severity of the deficit depends on the extent of the lesion (so that a hemiparetic patient may not be completely paralyzed but simply weak). Lesions affecting modality-specific association regions result in conceptually more complex disorders that are confined to a single modality, such as nonfluent aphasia or prosopagnosia. This chapter reviews clinical cortical syndromes.
Cellular Signaling
Authors: Staff Nathan P. 
Published: July 2015

Abstract
Cell communication in the nervous system is finely tuned to respond rapidly to external stimuli, learn from those stimuli, and produce more effective responses in the future. The physical basis for this cell communication is the manipulation of ion gradients via ion pumps and channels, chemical neurotransmission, and synaptic plasticity, all of which are discussed in this chapter.
Cellular Processes
Authors: Staff Nathan P. 
Published: July 2015

Abstract
Although cells in the nervous system contain all the cellular machinery that exists in other cells throughout the body, nervous system cells have many specialized functions that present unique challenges in the maintenance of cell functionality and homeostasis. The unique morphology of neurons demands elaborate cytoarchitecture, energy production, and cellular processing machinery that are unparalleled in other parts of the body. In this chapter, a broad overview of cellular processes related to cytoskeleton, axonal transport, protein processing, and energy metabolism within the nervous system are discussed. Foreshadowing subsequent chapters, many diseases of the nervous system are due to breakdowns of the intricate processes that are outlined in this chapter.
Nerve Conduction Studies and Needle Electromyography
Authors: Crum Brian A. 
Published: July 2015

Abstract
Nerve conduction studies (NCSs) and needle electromyography (EMG) should be considered extensions of the neurologic history and examination of the peripheral sensory and motor systems. NCSs assess large, myelinated sensory and motor nerve fibers. EMG assesses primarily type 1 muscle fibers. Because of the limitations of NCSs and EMG, small-fiber function (ie, small-fiber neuropathies) and, to an extent, type 2 muscle-fiber diseases (ie, steroid myopathy) cannot be excluded with these studies. The main goal of NCSs and EMG is to obtain objective evidence of disease within the peripheral nervous system and to assist with localization of the problem.
Evoked Potentials
Authors: Watson James C. 
Published: July 2015

Abstract
Evoked potentials provide a noninvasive, sensitive, and quantitative way to assess the functional integrity of the somatosensory, auditory, and visual pathways. The basic principle of evoked potentials is to apply a stimulus (sensory, auditory, or visual) in a controlled manner to create a volley of depolarization and repolarization. The role of somatosensory and brainstem auditory evoked potentials in the outpatient setting has declined in the past decades with the improved quality and availability of neuroimaging; however, their use has had a resurgence in electrophysiologic monitoring of surgical cases of the spine and posterior fossa, for which they are now a part of the standard of care.
Mood Disorders
Authors: Kung Simon 
Published: July 2015

Abstract
Mood disorders (depression and bipolar disorders) are the second most common set of psychiatric disorders, behind anxiety disorders. The lifetime prevalence of any mood disorder in US adults is approximately 20%, and the 12-month prevalence is approximately 10%. Common mood disorders and their treatment are discussed below. Additional information on pharmacologic therapy and electroconvulsive therapy is covered elsewhere.
Pharmacologic Treatment of Psychiatric Disorders
Authors: Abulseoud Osama A. 
Published: July 2015

Abstract
Human behaviors, including thinking, feeling, and action, can be viewed as products of the interactions between brain circuits, neurotransmitters, and oscillations that are influenced to a certain extent by inherited genes, acquired values, and social norms. A psychiatric disorder reflects a dysfunctional brain, and one way to treat such a disorder is through the use of pharmacologic compounds that can help restore order in disorderly brains. This chapter reviews the 4 main classes of drugs used to treat major mental illnesses: antidepressants, mood stabilizers, sedative hypnotics, and antipsychotics, followed by brief comments on a few drugs used to treat alcohol, opiate, and nicotine dependence. A short account on the use of electroconvulsive therapy (ECT) for difficult-to-treat conditions concludes the chapter.
Non-small cell lung cancer and superior vena cava obstruction
Authors: Beaton Laura , Wong Swee-Ling , Mulatero Clive 
Published: July 2015

Abstract
Non-small cell lung cancer (NSCLC) accounts for approximately 85% of all lung cancers. Patients frequently present with a variety of non-specific symptoms including cough and dyspnoea and more rarely with symptoms such as haemoptysis or the signs of superior vena cava obstruction (SVCO), as illustrated in this case. Treatment strategies in early and recurrent disease are discussed including the role of tyrosine kinase inhibitors against tumours with epidermal growth factor receptor (EGFR) sensitising mutations.
Advanced pancreatic cancer
Authors: Basu Bristi , Doherty Gary , Corrie Pippa 
Published: July 2015

Abstract
Improving outcomes in pancreatic adenocarcinoma remains a key challenge, and few advances have yet impacted significantly on life expectancy; the overall 5-year survival rate remains less than 5%, even including patients undergoing surgical resection. This case history illustrates the difficulties in diagnosis and the complexity of this disease. Most patients present too late for curative surgery, and symptom palliation involves multidisciplinary approaches to relieve common problems associated with obstructive jaundice, pain, cachexia, and ascites. Venous thromboembolism is also common, and its management discussed here. Although responses to chemotherapy and radiotherapy are poor, systemic therapy has been established as an effective adjuvant for those patients identified early enough to undergo surgery, whilst, in advanced disease, recent approaches to combination chemotherapy may offer modest improvements in life expectancy. However, drug-induced toxicity limits patients &lt;tolerance of treatment. Considerable hope lies in a better understanding of the molecular characteristics of this disease, which may yield novel targets for therapeutic intervention.
Colorectal liver metastases
Authors: Maisey Nick , Khan Khurum 
Published: July 2015

Abstract
Colorectal cancer (CRC) remains the second commonest cause of cancer-related mortality in the world. There have been significant advances in the treatment of metastatic CRC, particularly in the management of CRC with liver metastases. These advances are primarily driven by the development of active targeted agents for use in both the neoadjuvant and metastatic setting; however, these drugs work best when combined with conventional chemotherapy agents. Despite these advances, there remains a paucity of predictive biomarkers to inform us about the most effective management of these patients. It is therefore imperative to select carefully the patients, with comprehensive multidisciplinary team (MDT) input, in order to optimize the management of these patients. This chapter describes a case of colorectal liver metastases and its management within the MDT and the toxicities associated with systemic therapy. Specifically discussed are the management of capecitabine-induced diarrhoea, cetuximab-associated rash, and neuropathy with oxaliplatin.
Metastatic renal cell cancer and hypercalcaemia
Authors: Wheater Matthew , Chitnis Meenali 
Published: July 2015

Abstract
The standard of care in the treatment of renal cancer has changed dramatically in recent years. This chapter highlights the major advances that have been made, with a focus on the evidence base for the use of vascular endothelial growth factor (VEGF)-targeted tyrosine kinase inhibitors (TKIs) and mTOR inhibitors in renal cancer. The case highlights the typical presentation of metastatic renal cancer and the treatment options available. The common side effects of VEGF-targeted therapies are outlined. This chapter also summarizes current therapeutic uncertainties and challenges in the management of renal cancer, including the role and timing of palliative nephrectomy, optimal sequencing of targeted agents, and emergence of resistance to targeted therapies. The case also discusses the management of hypercalcaemia, common in many malignancies. Lastly, potential future areas for development in the field of renal cancer are discussed.
Transformed follicular lymphoma
Authors: Davies Andrew , Lee Chern Siang 
Published: July 2015

Abstract
Follicular lymphoma is the commonest subtype of indolent non-Hodgkin’s lymphoma (NHL), with a steady rise in incidence over the last 40 years. It has a long clinical course, characterized by a progressing and regressing pattern in response to treatment, and is usually considered incurable. There is no consensus on optimal therapy, but the management strategy incorporates consideration of tumour characteristics and patient-related factors. The quality and duration of response typically decline with repeated treatments. This is particularly in the event of histological transformation to a more aggressive subtype of NHL such as diffuse large B-cell lymphoma. This case study illustrates the clinical approach to lymphoma in general and discusses in detail the management paradigm for indolent and transformed NHL.
Metastatic germ cell cancer
Authors: Shamash Jonathan , Bradbury Jennifer 
Published: July 2015

Abstract
This is a case of a patient presenting with extensive metastatic non-seminoma who remains in remission. The classification and prognosis for non-seminoma and the management options for stage I disease are discussed. The chemotherapy options for advanced disease at presentation and for relapsed disease are explored. Issues surrounding acute treatment-related toxicity are considered, particularly lung injury secondary to bleomycin. Given the improvements that have been made, in terms of prognosis, for patients with germ cell cancers, it is essential to consider the potential late effects of treatment. The risk of cardiovascular complications and secondary malignancy are discussed in this context. Some of the current challenges and controversies in advanced disease, such as the management of residual metastatic disease in multiple sites and brain metastases, are also explored.
Osteosarcoma and the use of high-dose chemotherapy
Authors: Strauss Sandra , Shiu Kai-Keen 
Published: July 2015

Abstract
Primary bone malignancies are rare, and it is unlikely that an oncology trainee, or even a consultant, will have been involved closely in the care of a patient with this diagnosis, unless they have worked within a specialist sarcoma unit. However, due to the centralization of specialist care, patients may present to local non-specialist hospitals with complications of treatment or progression of disease. The principles of management of these rare tumours require timely, but safe, delivery of intensive, combination chemotherapy, specialist orthopaedic surgery, and a potentially aggressive approach to resection of metastatic disease. Furthermore, the majority of patients are young and should be managed within specialist services with age-appropriate care facilities. As management involves high doses of potentially toxic therapies, the complications of high-dose methotrexate and ifosfamide are discussed in this chapter. These are usually, but not always, managed within a specialist centre, so all involved in their care should be aware of, and be able to, act upon/seek appropriate specialist advice.
Laryngeal cancer and oral mucositis
Authors: Sibtain Amen , Eminowicz Gemma 
Published: July 2015

Abstract
Hoarseness or voice change can be a presenting feature of laryngeal carcinomas. Diagnosis is confirmed with nasendoscopy, staging imaging, and biopsy. Laryngeal cancer is the commonest of all head and neck tumours, and treatment depends upon the stage of disease. Localized disease may be treated with surgical procedures, e.g. laser resection or partial laryngectomy, or radiotherapy which may preserve voice function more successfully. More advanced disease may be treated with total laryngectomy and/or chemoradiotherapy. Before chemoradiotherapy is started, the dental, nutritional, and SALT status must be assessed and optimized. Careful monitoring of the nutritional status and SALT throughout treatment is essential. Patients should stop smoking; nutritional support should continue, and mucositis be managed carefully throughout chemoradiotherapy. The case history discussed here highlights all of these important issues in laryngeal carcinoma.
Neuroendocrine tumours and treatment complications
Authors: Valle Juan , Lamarca Angela 
Published: July 2015

Abstract
Neuroendocrine tumours (NETs) are epithelial neoplasms with predominant neuroendocrine differentiation which can arise in most organs of the body; gastroenteropancreatic (GEP)-NETs are those arising from the digestive tract. NETs vary considerably with respect to the functionality (evidenced by excessive hormone secretion) and the clinical and biological behaviour. Updates in the terminology, classification, and advances in therapy options for these tumours have changed their management. The important aspects of diagnosis, clinical presentation, and treatment options are reviewed in this case, with a special focus on available therapies for metastatic GEP-NETs, including somatostatin analogues, radionuclide therapies, interferon (IFN), and chemotherapy, as well as novel targeted therapies, namely everolimus and sunitinib, reviewing the most relevant data.
Late cardiovascular complications of cancer treatment
Authors: Plummer Chris , El-Khouly Fatima 
Published: July 2015

Abstract
The use of adjuvant therapies in early breast cancer has improved prognosis and reduced recurrence rates. The acute effects of chemotherapy are well established and are important considerations in each patient’s management. The long-term effects of chemotherapy require further research to predict risks, identify early signs of toxicity, and treat these effectively to prevent long-term morbidity and mortality. The use of drugs which can affect the cardiovascular system in the short and long term requires an understanding of these risks and the use of appropriate monitoring. This chapter uses a case history to explore the factors contributing to heart failure and other potential late effects of chemotherapy.
Acid Rather Than Nonacid Reflux Burden Is a Predictor of Tooth Erosion
Authors: Ganesh Meenakshi , Hertzberg Anne , Nurko Samuel , Needleman Howard , Rosen Rachel 
Published: July 2015

ABSTRACTObjectives:The relation between tooth erosion (TE) and gastroesophageal reflux in children has not been clearly established, and there are no studies to determine the relation with refluxate height, nonacid reflux, and erosions. The aim of this study was to determine the relation between TE and acid and nonacid gastroesophageal refluxes measured using combined pH and multichannel intraluminal impedance (pH‐MII).Methods:We conducted a prospective cohort study of children presenting for pH‐MII testing. Once informed consent was obtained, patients completed questionnaires about their reflux symptoms and diet, and then underwent pH‐MII catheter placement and a dental examination. The Keels‐Coffield erosion index was used to score the extent and severity of TE. Reflux parameters of patients with and without TE were compared using Student t test and correlations were performed using Spearman correlations.Results:A total of 27 patients participated in the study, all of whom were on acid suppression at the time of pH‐MII testing. Of the 27 patients, 10 (37%) had TE. There were significant positive correlations between acid reflux episodes (r = 0.44, P = 0.02), the percentage of time that acid reflux was present in the distal esophagus (r = 0.44, P = 0.02), and reflux index (r = 0.54, P = 0.004) with the number of TE in a given patient. The percentage of time that acid reflux was present in the proximal esophagus was positively correlated with the number of teeth erosions per patient with borderline significance (r = 0.38, P = 0.05).Conclusions:There was a positive correlation between acid reflux parameters and TE. Acid, rather than nonacid reflux, seems to have a significant role in the pathogenesis of TE.
Notification that new names of prokaryotes, new combinations and new taxonomic opinions have appeared in volume 65, part 4, of the IJSEM
Authors: Oren Aharon , Garrity George M. 
Published: July 2015

This listing of names of prokaryotes published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41(1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles).
The following taxonomic opinions (i.e. the emendation of circumscriptions or the creation of synonyms) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part III: Algorithm for first approximation
Authors: Ezawa Kiyoshi , Graur Dan , Landan Giddy 
Published: August 2015

AbstractBackgroundInsertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enables us to reliably calculate the probability of the sequence evolution through indel processes. In a separate paper (Ezawa, Graur and Landan 2015a), we established anab initioperturbative formulation of a continuous-time Markov model of the evolution of anentiresequence via insertions and deletions. And we showed that, under a certain set of conditions, theab initioprobability of an alignment can be factorized into the product of an overall factor and contributions from regions (or local alignments) separated by gapless columns. Moreover, in another separate paper (Ezawa, Graur and Landan 2015b), we performed concrete perturbation analyses on all types of local pairwise alignments (PWAs) and some typical types of local multiple sequence alignments (MSAs). The analyses indicated that even the fewest-indel terms alone can quite accurately approximate the probabilities of local alignments, as long as the segments and the branches in the tree are of modest lengths.ResultsTo examine whether or not the fewest-indel terms alone can well approximate the alignment probabilities of more general types of local MSAs as well, and as a first step toward the automatic application of ourab initioperturbative formulation, we developed an algorithm that calculates the first approximation of the probability of a given MSA under a given parameter setting including a phylogenetic tree. The algorithm first chops the MSA into gapped and gapless segments, second enumerates all parsimonious indel histories potentially responsible for each gapped segment, and finally calculates their contributions to the MSA probability. We performed validation analyses using more than ten million local MSAs. The results indicated that even the first approximation can quite accurately estimate the probability of each local MSA, as long as the gaps and tree branches are at most moderately long.ConclusionsThe newly developed algorithm, called LOLIPOG, brought ourab initioperturbation formulation at least one step closer to a practically useful method to quite accurately calculate the probability of a MSA under a given biologically realistic parameter setting.[This paper and three other papers (Ezawa, Graur and Landan 2015a,b,c) describe a series of our efforts to develop, apply, and extend theab initioperturbative formulation of a general continuous-time Markov model of indels.]List of abbreviationsHMMhidden Markov modelindelinsertion/deletionLHSlocal history setMSAmultiple sequence alignmentPASpreserved ancestral sitePWApairwise alignment