bluuebunny/crossref_metadata_2025 huggingface dataset:
Onset of Melanophore Patterns in the Head Region of Chinook Salmon: A Natural Marker for the Reidentification of Individual Fish
Authors: Merz Joseph E. , Skvorc Paul , Sogard Susan M. , Watry Clark , Blankenship Scott M. , Van Nieuwenhuyse Erwin E.
Published: July 2012

We used pattern recognition algorithms and image processing to identify individual Chinook salmon Oncorhynchus tshawytscha. Using melanophore spot patterns located on the dorsal head region, algorithms ranked all database images against each other. We coupled this technology with a graphical user interface to visually confirm or reject top-ranked algorithm results and tested this process on 295 juvenile Chinook salmon in seven photo sessions over a 251-d period. Juveniles began developing spots, identifiable in photo images, between 167 and 197 d after conception (52.7-mm fork length [FL]). Unique spot patterns appeared 197–232 d from conception, beginning at approximately 104-mm FL. Of 254 fish surviving the experimental period, 106 (42%) demonstrated identifiable patterns, 102 (40%) developed spots but patterns were insufficient for identification, and 46 (18%) exhibited a complete lack of spots. Spot patterns continued developing on individual fish by study end. On average, fish that developed recognizable spot patterns did so at approximately 140-mm FL. Once they did, reidentification was 100% correct in up to four subsequent trials. Patterns remained identifiable even after a 25–32% size increase over a 55-d period and as juveniles went through smoltification. Although patterns occurred at sizes typically larger than salmon observed at some California Central Valley monitoring locations, this technique provides a potentially valuable, noninvasive method of identifying individual salmon during emigration. Improved image collection techniques and use of body areas exhibiting identifiable patterns at earlier developmental stages may increase fish available for pattern identification. These results demonstrate the indexing of a large database using pattern recognition algorithms for Chinook salmon. The utility of such an approach may be valuable for addressing specific biological questions associated with mass-produced (wild and hatchery), migratory salmonids, especially as individuals develop, grow, and move through the various habitats available to them.

Received November 21, 2011; accepted March 22, 2012
Cricket team selection using data envelopment analysis
Authors: Amin Gholam R. , Sharma Sujeet kumar
Published: July 2012

This paper suggests a new method for cricket team selection using data envelopment analysis (DEA). We propose a DEA formulation for evaluation of cricket players in different capabilities using multiple outputs. This evaluation determines efficient and inefficient cricket players and ranks them on the basis of DEA scores. The ranking can be used to choose the required number of players for a cricket team in each cricketing capability. A real dataset, Indian Premier League 4 (IPL 2011), cricket players having various capabilities is used to choose the best cricket team. The proposed method has the advantage of considering multiple factors related to the performance of players in multiple capabilities collected from IPL 4 and aggregates their scores using a linear programming DEA model. This DEA Aggregation gives the scores of players objectively instead of using subjective computations. The proposed DEA method can be used to form a national cricket team from several clubs or a team of top cricketers.
Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data
Authors: Su Xiaoquan , Xu Jian , Ning Kang
Published: July 2012

Background: It has long been intriguing scientists to effectively compare different microbial communities (also referred as ‘metagenomic samples’ here) in a large scale: given a set of unknown samples, find similar metagenomic samples from a large repository and examine how similar these samples are. With the current metagenomic samples accumulated, it is possible to build a database of metagenomic samples of interests. Any metagenomic samples could then be searched against this database to find the most similar metagenomic sample(s). However, on one hand, current databases with a large number of metagenomic samples mostly serve as data repositories that offer few functionalities for analysis; and on the other hand, methods to measure the similarity of metagenomic data work well only for small set of samples by pairwise comparison. It is not yet clear, how to efficiently search for metagenomic samples against a large metagenomic database.

Results: In this study, we have proposed a novel method, Meta-Storms, that could systematically and efficiently organize and search metagenomic data. It includes the following components: (i) creating a database of metagenomic samples based on their taxonomical annotations, (ii) efficient indexing of samples in the database based on a hierarchical taxonomy indexing strategy, (iii) searching for a metagenomic sample against the database by a fast scoring function based on quantitative phylogeny and (iv) managing database by index export, index import, data insertion, data deletion and database merging. We have collected more than 1300 metagenomic data from the public domain and in-house facilities, and tested the Meta-Storms method on these datasets. Our experimental results show that Meta-Storms is capable of database creation and effective searching for a large number of metagenomic samples, and it could achieve similar accuracies compared with the current popular significance testing-based methods.

Conclusion: Meta-Storms method would serve as a suitable database management and search system to quickly identify similar metagenomic samples from a large pool of samples.

Contact:  ningkang@qibebt.ac.cn

Supplementary information: Supplementary data are available at Bioinformatics online.
Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood
Authors: Lee S.H. , Yang J. , Goddard M.E. , Visscher P.M. , Wray N.R.
Published: July 2012

Summary: Genetic correlations are the genome-wide aggregate effects of causal variants affecting multiple traits. Traditionally, genetic correlations between complex traits are estimated from pedigree studies, but such estimates can be confounded by shared environmental factors. Moreover, for diseases, low prevalence rates imply that even if the true genetic correlation between disorders was high, co-aggregation of disorders in families might not occur or could not be distinguished from chance. We have developed and implemented statistical methods based on linear mixed models to obtain unbiased estimates of the genetic correlation between pairs of quantitative traits or pairs of binary traits of complex diseases using population-based case–control studies with genome-wide single-nucleotide polymorphism data. The method is validated in a simulation study and applied to estimate genetic correlation between various diseases from Wellcome Trust Case Control Consortium data in a series of bivariate analyses. We estimate a significant positive genetic correlation between risk of Type 2 diabetes and hypertension of ~0.31 (SE 0.14, P = 0.024).

Availability: Our methods, appropriate for both quantitative and binary traits, are implemented in the freely available software GCTA (http://www.complextraitgenomics.com/software/gcta/reml_bivar.html).

Contact:  hong.lee@uq.edu.au

Supplementary Information: Supplementary data are available at Bioinformatics online.
Is spawning time of marine fish imprinted in the genes? A two-generation experiment on local Atlantic cod (Gadus morhua L.) populations from different geographical regions
Authors: Otterå H. , Agnalt A-L. , Thorsen A. , Kjesbu O.S. , Dahle G. , Jørstad K.
Published: July 2012

Otterå*, H., Agnalt, A-L., Thorsen, A., Kjesbu, O.S., Dahle, G., and Jørstad, K. 2012. Is spawning time of marine fish imprinted in the genes? A two-generation experiment on local Atlantic cod (Gadus morhua L.) populations from different geographical regions. – ICES Journal of Marine Science, 69: 1722–1728.

Spawning time (onset of spawning) in Atlantic cod (Gadus morhua L.) was monitored in an experimental setup and combined with modelled spawning time estimates from the wild. The experiment broodstock were collected from several geographical areas and kept in a common environment. Their spawning times in 2004 were compared with the spawning times of their daughters in 2009 and 2010. Daughter spawning time was highly correlated with that of the mother, indicating genetic regulation of spawning time. However, large individual variation in spawning time was observed. The modelling data suggests a north-south gradient in onset of spawning along the Norwegian coast, driven by differences in temperature, i.e. later dates of spawning in the north.
Literature & Theology: The First Decade
Authors: Jay Elisabeth
Published: July 2012

This essay offers reflections on the origins and ethos of the early years of the Journal, tracing the transatlantic editorial teams’ navigation of swiftly changing cultural conditions through and beyond the change in title—Literature and Theology: An International Journal of Theory, Criticism and Culture.
Ageing
Authors: Bowker Lesley K , Price James D , Smith Sarah C
Published: July 2012

The ageing person 2

Theories of ageing 3

Demographics: life expectancy 4

Demographics: population age structure 6

Demographics: ageing and illness 8

Illness in older people 10

There are many differences between old and young people. In only some cases are these changes due to true ageing, ie due to changes in the characteristic(s) compared with when the person was young....
Neurology
Authors: Bowker Lesley K , Price James D , Smith Sarah C
Published: July 2012

The ageing brain and nervous system 152

Tremor 154

Neuropathic pain/neuralgia 156

HOW TO . . . Treat neuralgia 157

Parkinson's disease: presentation 158

Parkinson's disease: management 160

HOW TO . . . Manage a patient with Parkinson's disease who cannot take oral medication 161

HOW TO . . . Treat challenging symptoms in Parkinson's disease ...
Stroke
Authors: Bowker Lesley K , Price James D , Smith Sarah C
Published: July 2012

Definition and classification 180

Predisposing factors 182

Acute assessment 184

HOW TO . . . Assess for inattention 185

Investigations 186

Acute management 188

HOW TO . . . Manage swallow after stroke 189

Stroke units 190

HOW TO . . . Estimate prognosis after stroke 191

Thrombolysis 192

Ongoing management 194

HOW TO . . . Protect your patient from another stroke ...
Pressure injuries
Authors: Bowker Lesley K , Price James D , Smith Sarah C
Published: July 2012

Pressure sores 502

Compression mononeuropathy 504

Rhabdomyolysis 505

Areas of skin necrosis due to pressure-induced ischaemia found on sacrum, heels, over greater trochanters, shoulders, etc. Also known as decubitus ulcers or bedsores. Incidence higher in hospital (new sores form during acute illness) but prevalence higher in long-stay community settings (healing takes months/years). Average hospital prevalence 5–10% despite drives to improve education and preventative strategies. The financial and staffing resource burden of pressure sores is huge....
Genitourinary medicine
Authors: Bowker Lesley K , Price James D , Smith Sarah C
Published: July 2012

The ageing genitourinary system 508

HOW TO . . . Examine the older female genital system 509

Benign prostatic hyperplasia: presentation 510

Benign prostatic hyperplasia: treatment 512

Prostatic cancer: presentation 514

Prostate-specific antigen 516

Prostatic cancer: treatment 518

Postmenopausal vaginal bleeding 520

Vaginal prolapse 522

HOW TO . . . Care for a vaginal pessary ...
Ethics
Authors: Bowker Lesley K , Price James D , Smith Sarah C
Published: July 2012

Capacity 654

HOW TO . . . Assess capacity 655

The Mental Capacity Act 2005 656

Deprivation of Liberty Safeguards 657

Making financial decisions 658

Making medical decisions 660

Making social decisions 662

HOW TO . . . Manage a patient insisting on returning home against advice 663

Advance directives 664...
Environmental emergencies
Authors: Wyatt Jonathan P. , Illingworth Robin N. , Graham Colin A. , Hogg Kerstin , Clancy Michael J. , Robertson Colin E.
Published: July 2012

Hypothermia 254

Frostbite and non-freezing cold injury 257

Drowning and near drowning 258

Diving emergencies 260

Heat illness 264

Electrical injuries 266

Radiation incidents 268

Hypothermia exists when the core temperature (T°)<35°C.

Infants and the elderly are at particular risk. In young adults hypothermia is usually due to environmental exposure (eg hill-walking or cold water immersion), or to immobility and impaired conscious level from alcohol or drugs. In the elderly, it is more often a prolonged state of multifactorial origin: common precipitants include unsatisfactory housing, poverty, immobility, lack of cold awareness (autonomic neuropathy, dementia), drugs (sedatives, antidepressants), alcohol, acute confusion, hypothyroidism and infections....
Wounds, fractures, orthopaedics
Authors: Wyatt Jonathan P. , Illingworth Robin N. , Graham Colin A. , Hogg Kerstin , Clancy Michael J. , Robertson Colin E.
Published: July 2012

The approach to wounds 402

Further assessment of skin wounds 404

Wound management 406

Tetanus prophylaxis 410

Antibiotic prophylaxis 411

Wound aftercare 412

Infected wounds and cellulitis 413

Bite wounds 414

Specific bites and stings 416

Needlestick injury 418

Puncture wounds 419

How to describe a fracture ...
Obstetrics and gynaecology
Authors: Wyatt Jonathan P. , Illingworth Robin N. , Graham Colin A. , Hogg Kerstin , Clancy Michael J. , Robertson Colin E.
Published: July 2012

Gynaecological problems 564

Vaginal discharge 566

Contraceptive problems 568

Genital injury and assault 570

Gynaecological pain 572

Vaginal bleeding 574

The pregnant patient 576

Emergency normal delivery 578

Difficulties in normal delivery 580

Vaginal bleeding in pregnancy 582

Spontaneous abortion 584

Ectopic pregnancy 586

Vaginal bleeding in later pregnancy ...
Paediatric emergencies
Authors: Wyatt Jonathan P. , Illingworth Robin N. , Graham Colin A. , Hogg Kerstin , Clancy Michael J. , Robertson Colin E.
Published: July 2012

Paediatric problems also covered elsewhere in this book:

Consent 28

Poisoning 179

Incubation periods of infectious diseases 220

Childhood infectious diseases 222

Meningitis 224

Gastroenteritis/food poisoning 226

Infestations 230

Analgesia in specific situations 280

Nasal diamorphine 281

Local anaesthesia in children 287

Sedation 309

Instructions after minor head injury ...
Hepatobiliary pathology
Authors: Carton James
Published: July 2012

Acute viral hepatitis 116

Chronic viral hepatitis 117

Alcoholic liver disease 118

Non-alcoholic fatty liver disease 119

Autoimmune hepatitis 120

Primary biliary cirrhosis 121

Primary sclerosing cholangitis 122

Wilson's disease 123

Hereditary haemochromatosis 124

Cirrhosis 125

Benign liver lesions 126

Hepatocellular carcinoma 127

Intrahepatic cholangiocarcinoma ...
Urological pathology
Authors: Carton James
Published: July 2012

Genitourinary malformations 158

Urinary tract infection 160

Urinary tract obstruction 162

Urinary calculi 164

Cystic renal diseases 165

Benign renal tumours 166

Renal cell carcinoma 168

Childhood renal tumours 170

Urothelial carcinomas 172

Benign prostatic hyperplasia 174

Prostate carcinoma 176

Testicular germ cell tumours 178...
Haematopathology
Authors: Carton James
Published: July 2012

Iron deficiency anaemia 256

Anaemia of chronic disease 257

Megaloblastic anaemias 258

Hereditary spherocytosis 259

Glucose-6-phosphate dehydrogenase deficiency 260

Thalassaemias 261

Sickle cell disorders 262

Idiopathic thrombocytopenic purpura 264

Thrombotic thrombocytopenic purpura 265

von Willebrand disease 266

Haemophilia 267

Thrombophilia 268

Acute B-lymphoblastic leukaemia 269...
Neuropathology
Authors: Carton James
Published: July 2012

Nervous system malformations 322

Epilepsy 323

Head injury 324

Cerebral infarction 325

Intracerebral haemorrhage 326

Subarachnoid haemorrhage 328

Meningitis 330

Cerebral infections 331

Multiple sclerosis 332

Alzheimer's disease 333

Dementia with Lewy bodies 334

Parkinson's disease 335

Huntington's disease 336

Motor neurone disease 337

Creutzfeldt–Jacob disease ...
Multisystem diseases
Authors: Carton James
Published: July 2012

Systemic lupus erythematosus 346

Systemic sclerosis 348

Sarcoidosis 349

Vasculitis 350

• A multisystem autoimmune disease characterized by
autoantibody production against a number of nuclear and cytoplasmic
autoantigens.

• Incidence of 4 per 100,000 people per year.

• Most cases occur in women of childbearing age....
Spirituality and meaning for children, families, and clinicians
Authors: Macauley Robert , Rushton Cynda Hylton
Published: July 2012

Spirituality is undeniably an integral dimension of good-quality paediatric palliative care. The first step towards being able to more fully integrate the spiritual lives of patients and families into clinical care requires that clinicians explore and embrace their own spirituality. Through an exploration of their own spirituality, clinicians may come to realize that rather than seeking relief from the constant pressures of unattainable perfection and the anxiety caused by the certainty of death, there is another way of being that sees opportunities for growth and deeper meaning in what emerges from life. Although the death of a child is painful for all involved, the amount of associated suffering is directly proportional to the resistance invoked (e.g. ‘This cannot be happening’). Once it is truly understood that the goal of clinicians is to change what can be changed and to accept that which is — as it is — spirituality allows clinicians to refocus their energy in constructive ways that benefit the patient, family members, and the interdisciplinary team.
Symptoms in life-threatening illness: overview and assessment
Authors: Rajapakse Dilini , Comac Maggie
Published: July 2012

The aims of this chapter are to discuss the reasons why accurate symptom assessment is important, the prevalence of symptoms in paediatric palliative care, the principles of symptom assessment as part of symptom management, the challenges to symptom assessment, and the tools available for symptom assessment, and to examine the areas where knowledge and expertise are lacking, and the reasons for this. We then discuss areas for future study and identify the resources available for symptom assessment.
Pharmacological approaches to pain. 2: Simple analgesics and opioids
Authors: Drake Ross , Friedrichsdorf Stefan J. , Hain Richard D. W.
Published: July 2012

This chapter will consider the pharmacological management of pain in children with life-limiting conditions, and wherever possible will draw on the pool of knowledge obtained from studies of children. The choice of analgesic drug(s) (see Figure 21.1 ) is made on the basis of assessment of pain severity. The World Health Organization (WHO) approach was based on the assumption that, for most children with cancer, pain will gradually increase as their illness progresses, and that this increase in pain intensity should be matched by the stepwise introduction of progressively stronger analgesics. Fairly rapid escalation of pain is usual for children with cancer, but is typically slower and less consistent for those with pain of non-malignant origin. One aim of this model was to avoid cycling through alternative medications of the same potency rather than selecting a stronger class of drug. Thus if a step 1 non-opioid analgesic is no longer effective, a minor opioid in step 2 should be added. Severe pain requires step 3, namely a strong opioid in the same class as morphine. Of course a child with severe pain should not be condemned to slow progress up the ladder — a strong opioid should be commenced immediately.
Respiratory symptoms
Authors: Brook Lynda , Twigg Emma , Venables Amanda , Shaw Claire
Published: July 2012

Respiratory symptoms are extremely important in paediatric palliative care. Breathing is one of the activities of daily living, and the cessation of breathing is probably the most immediate outward sign that death has occurred. It is therefore perhaps not surprising that the symptom burden related to problems with breathing and breathlessness is complex and multidimensional. Respiratory symptoms, particularly dyspnoea and cough, are invariably listed in the top ten most prevalent and distressing symptoms in paediatric palliative care for both cancer and non-cancer patients. The significance of dyspnoea and other breathing problems in paediatric palliative care is increasingly recognized. The options for management of respiratory symptoms in paediatric palliative care are also increasing. This chapter will consider in detail the aetiology, pathophysiology, and assessment of respiratory symptoms, including differences between different diagnostic groups in terms of prevalence of specific symptoms, symptom aetiology, and impact on quality of life. We shall consider in detail the options for managing dyspnoea, including pharmacological and non-pharmacological approaches. We shall also consider the role of mechanical respiratory support and the potential benefi ts and harms of such an approach at different stages of the child’s illness journey, the potential benefits of physiotherapy and psychological approaches, and other important respiratory symptoms, such as cough, haemoptysis, and retained respiratory secretions at the end of life (‘death rattle’).
Place of care
Authors: Vickers Jan , Chrastek Jody
Published: July 2012

Palliative care for children and young people can now span a period ranging from hours and days to months and years, with many young people with life-limiting illness making the transition to adult services. Greatly improved supportive care and advances in medical technology have underpinned this, but have also given rise to additional and increasing challenges to providing effective support in all care settings for children with often complex health and technology needs. The primary objective of palliative care is to support the child and family, to allow them to maintain resilience and to cope from the time of diagnosis, through periods of stability and times of crisis, through to the end of life and bereavement. Parents or carers will need support and empowerment with all aspects of palliative care, including symptom management, complex nursing skills, practical support, and psychosocial and spiritual care, at different times and to different extents, in order to achieve the best quality of life for their child. This support must also be extended to the wider family and the siblings in particular, who often receive less attention because the needs of the ill child are so great. The care provided should be tailored to the needs and wishes of the child and their family, and also reflect their individual cultural needs, but inevitably must be delivered within the constraints of the available healthcare staff, facilities, and resources. Ideally, care will be delivered with minimal disruption to normal everyday life (i.e. at home or in school). However, at times care in a hospital, hospice, or other facility will be necessary. To ensure effective care across all care settings, it is essential that the provision of all care and support is coordinated and flexible enough to meet the range of needs, with an emphasis on prompt and effective inter-professional communication and teamwork. This chapter is based upon the models of care in thee UK and the USA, but the principles will be widely applicable in the context of different healthcare systems. We consider the key dimensions for care in all care settings, as well as how needs are determined, including the wishes of the child and their family and assessment by members of the multidisciplinary team. We then explore how these needs are best met by examining models of care in the different care settings, and consider how we can ensure equity in choice and care provision across care settings.
Healthcare providers’ responses to the death of a child
Authors: Papadatou Danai
Published: July 2012

One of the current challenges in paediatric palliative services is to improve the quality of care. However, improvement requires a review and better understanding of our relationships with children and their families, as these relationships are the main source of their dissatisfaction at the end of life. We need to shift the restricted focus of our attention from the assessment and management of patient and family needs, to the reciprocal influence among those who seek and those who provide paediatric palliative care services. This ‘relationship-centred’ approach illuminates how the quality of care is determined by what transpires in a large network of relationships which are affected by the reality of childhood death. It is concerned with the establishment of relationships that are potentially enriching and rewarding for both care seekers and care providers. Through this process it seeks to understand not only the subjective views, needs, and experiences of the patient and their family, but also the subjectivity of the professionals, the teams, and the organization. One of the benefits of the relationship-centred approach is that it sheds light on the private worlds of care providers, and incites them to seek a balance between their personal and professional life and practice by engaging in what Renzenbrink has described as ‘relentless self-care.’ Relentless self-care must always be associated with relentless team care — a responsibility assumed by the service or organization to which we belong. If the work setting does not recognize the challenging and demanding nature of paediatric palliative care, and has no policies in place for adequate staff support, then our personal efforts for self-care will remain limited. By contrast, if the culture of the organization fosters collaboration, solidarity, and mutual support, along with regular feedback and supervision, then an ethos of genuine care will permeate all relationships. Self-care is not — and should not — be an individual affair, but rather it should be a collective pursuit, which promotes mutual support in times of distress, and the sharing of rewarding experiences that derive from our encounters with children and their families.
Perioperative Positioning Injuries
Authors: Warner Mark A.
Published: July 2012

Positioning-related injuries such as central and peripheral neuropathies, compartment syndromes, and soft-tissue injury can be reduced by considering preoperative and intraoperative factors. Preoperative considerations include normal joint range of motion, body habitus, and health status. Intraoperative considerations include compression by table attachments, duration of surgery, airway management, and use of pads and supports.
Intravenous Regional Anesthesia
Authors: Frie Edward D.
Published: July 2012

The intravenous injection of local anesthetic into an exsanguinated limb provides anesthesia by diffusion of the drug to peripheral nerves supplied by small vessels. Intravenous regional anesthesia is most commonly used for procedures on the hand, wrist, and digits; however, it may also be effective for minor surgery on the foot and ankle. The following aspects of the procedure are reviewed: clinical applications, relevant anatomy, patient position, technique (including neural localization techniques, needle insertion site, and needle redirection cues), and side effects and complications.
Femoral Nerve Blockade
Authors: Wynd Kimberly P. , Smith Hugh M.
Published: July 2012

Blockade of the femoral nerve provides surgical anesthesia and postoperative analgesia to the anterior aspect of the thigh and knee. The following aspects of the procedure are reviewed: clinical applications, relevant anatomy, patient position, technique (including neural localization techniques, needle insertion site, and needle redirection cues), and side effects and complications. A discussion of ultrasound guidance and peripheral nerve catheters completes the chapter
Ischemic Heart Disease
Authors: Prasad Abhiram
Published: July 2012

Ischemic heart disease, principally myocardial infarction, causes approximately 1 of 3 deaths in the United States, or nearly 800,000 deaths annually. The substantial decrease in the death rate from acute myocardial infarction that has occurred since 1970 is attributed to efforts in primary prevention and new interventions in the treatment of myocardial infarction. The variable presentation of patients with coronary heart disease includes patients who are asymptomatic (with or without silent ischemia), patients who have stable or unstable angina or myocardial infarction, and patients with sudden death.
Heart Failure and Cardiomyopathies
Authors: Karon Barry L. , Pereira Naveen L.
Published: July 2012

Heart failure is a clinical syndrome characterized by the inability of the heart to maintain adequate cardiac output to meet the metabolic demands of the body while still maintaining normal or near-normal ventricular filling pressures. Heart failure may be present at rest, but often it is present only during exertion as a result of the dynamic nature of cardiac demands. For correct treatment of heart failure, the mechanism, underlying cause, and any reversible precipitating factors must be identified. Typical manifestations of heart failure are dyspnea and fatigue that limit activity tolerance and fluid retention leading to pulmonary or peripheral edema. The most recent proposed categorization divided the cardiomyopathies into primary and secondary cardiomyopathies, and the primary disorders are further subdivided as genetic, acquired, or mixed. Although this proposal takes into account our progressive understanding of this heterogeneous group of disorders, the previous phenotypic classification of dilated, hypertrophic, and restrictive diseases still provides utility in day-to-day understanding and management of these disorders.
HIV Infection
Authors: Temesgen Zelalem , Kasten Mary J.
Published: July 2012

Testing for HIV became available in the United States in 1985. Amazing gains in the understanding and treatment of HIV have been made during the past 25 years. HIV and other retroviruses cause a frequently symptomatic primary infection followed by a relatively asymptomatic period lasting months to years and a final stage of overt disease in most people. There are 2 types of HIV: HIV-1 and HIV-2. Most reported cases of HIV disease around the world are caused by HIV-1. HIV-2 is found predominantly in western Africa. Although HIV-1 and HIV-2 are clinically indistinguishable and have identical modes of transmission, HIV-2 appears to be less easily transmitted than HIV-1 and slower to progress to AIDS. Epidemiology, diagnosis, and treatment of HIV are also reviewed.
Hospital Medicine
Authors: Newman James S. , Rosenman David J.
Published: July 2012

Technologic advancements and other innovative efforts to improve the quality of hospital-based care have resulted in large and complicated networks of personnel, information systems, devices, medications, and countless other resources. In parallel with these changes, the medical acuity of the typical hospitalized patient has increased. The field of hospital medicine emerged in response to this combination of increasing hospital complexity, patient acuity, and professional demands. This chapter highlights several topics that may be unique to the hospital and are not discussed elsewhere in this textbook. They include interfaces among settings and people in the hospital, medication reconciliation, dismissal from the hospital, information systems, nutritional assessment and provision, geriatric assessment, complications of hospitalization, hospital-acquired infections, complications of surgery, the quality and safety movements, bioterrorism, and risks to health care workers.
Men’s Health
Authors: Beckman Thomas J. , Abu-Lebdeh Haitham S.
Published: July 2012

Benign prostatic hyperplasia (BPH) and erectile dysfunction are among the commonest diagnoses in a men's health practice. BPH is common among older men. The prostate is the size of a walnut (20 cm3) in men younger than 30 years and it gradually increases in size, leading to BPH in most men older than 60 years. BPH results from epithelial and stromal cell growth, which begins in the transitional zone of the prostate and causes urinary outflow resistance. Over time, this resistance leads to detrusor muscle dysfunction, urinary retention, and lower urinary tract symptoms (LUTS). Male sexual dysfunction includes erectile dysfunction (ED), decreased libido, anatomical abnormalities (eg, Peyronie disease), and ejaculatory dysfunction. ED, defined as the inability to achieve erections firm enough for vaginal penetration, affects millions of men in the United States.
Diagnosis of Neurologic Disorders
Authors: Crum Brian A. , Benarroch Eduardo E. , Brown Robert D.
Published: July 2012

Primary care physicians need a good working knowledge of common and emergency neurologic disorders since they are often encountered in general clinical practice (about 10% of patients of primary care physicians in the United States have neurologic disorders, and about 25% of inpatients have a neurologic disorder as a primary or secondary problem). In the aging population, cerebrovascular disorders, dementias, and Parkinson disease are becoming more prevalent. Understanding a patient with neurologic disease depends on localizing the problem on the basis of the medical history and examination findings, considering a differential diagnosis, and correlating the clinical findings with abnormalities found on appropriate diagnostic testing.
Diagnosis and Common Disorders
Authors: Park John G.
Published: July 2012

Common symptoms of pulmonary disease include cough, sputum, hemoptysis, dyspnea, chest pain, cyanosis, and clubbing. A thorough history and physical examination, including palpation, auscultation, and percussion, are key to accurate diagnosis. The radiologic tests performed in the diagnosis of chest diseases include plain CXR, CT, magnetic resonance imaging, pulmonary angiography, and bronchial angiography. Simple microscopy with a "wet" slide preparation of sputum is helpful in assessing the degree of sputum eosinophilia and detecting the presence of Charcot-Leyden crystals. The major indication for pulmonary function tests (PFTs) is dyspnea. PFT results do not diagnose lung disease, but they are used to assess the mechanical function of the respiratory system and to quantify the loss of lung function. Obstructive, restrictive, and occupational lung diseases are reviewed.
Vascular Diseases
Authors: Spittell Peter C.
Published: July 2012

Peripheral vascular diseases, such as aneurysmal disease, intermittent claudication, acute arterial occlusion, and thromboangiitis, are prevalent in current medical practice. Vasospastic disorders, another class of vascular disease, are characterized by episodic color changes of the skin resulting from intermittent spasm of the small arteries and arterioles of the skin and digits. Vasospastic disorders are important because they frequently are a clue to another underlying disorder, such as arterial occlusive disease, connective tissue disorders, neurologic disorders, or endocrine disease. Characteristic clinical features, accurate diagnostic techniques, and improved treatment of peripheral vascular disease further emphasize the need for increased awareness of this group of disorders.
Infective Endocarditis: Diagnosis and Treatment
Authors: Wilson John W. , Estes Lynn L.
Published: July 2012

• Viridans streptococci

•Staphylococcus aureus

• Enterococci

• HACEK organisms

• Same as native valves, plus

• Coagulase-negative staphylococci

• Fungi

• Gram-negative rods (early postoperative period)

The diagnosis of infective endocarditis (IE) rests on demonstrated evidence of cardiac involvement and persistent bacteremia due to microorganisms that typically cause endocarditis. Establishing a microbiologic diagnosis is critical to therapeutic decisions. Every effort should be made to identify the causative organism....
Intra-Abdominal Infections
Authors: Wilson John W. , Estes Lynn L.
Published: July 2012

• Peritoneal infection without an obvious source

• Adult patients with cirrhosis and ascites (higher risk: gastrointestinal [GI] bleeding, previous spontaneous bacterial peritonitis [SBP], or low protein concentration in ascitic fluid) or, occasionally, congestive heart failure, malignancy, or connective tissue disease

• Pediatric patients with postnecrotic cirrhosis, nephrotic syndrome, or urinary tract infections...
Vaccination Schedules
Authors: Wilson John W. , Estes Lynn L.
Published: July 2012

The recommended immunization schedule for those 0–6 years is presented in Figure 5. For those who fall behind in the immunization schedule or start late, see the catch-up schedule available on the CDC Web site: http://www.cdc.gov/vaccines/recs/schedules/downloads/child/catchup-schedule-pr

aHepatitis B (HepB) vaccine. (Minimum age: Birth.)

•...
The Two Doctors Fick
Authors: Munis James R.
Published: July 2012

We often confuse the ‘Fick principle’ with ‘Fick's law of diffusion.’ They are not the same. Ironically, Fick borrowed heavily from already known physical laws when he first described both his law of diffusion and his principle. Borrowing from Ohm's law of electricity, Fick applied concepts of diffusion and transfer across a resistance to formulate a law of diffusion that could be applied to gas or solute transfer across a membrane. Whether we are talking about transfer across the alveolar-capillary membrane or across a dialysis membrane, the concept is the same. The concept is similar to electricity—you have a transfer rate, resistance, and a gradient. Now let's consider the Fick principle. On the basis of another physical law he understood that, in the steady state, the difference between the amount of oxygen going into a tissue bed minus that leaving the tissue bed must be equal to the oxygen consumed. With a little reworking, this became the Fick principle: Cardiac output = O2 consumption / (arterial O2 - venous O2).
Diffusion Limitation—Montana Style
Authors: Munis James R.
Published: July 2012

The pathway of oxygen through the body consists of the diffusion of oxygen across the alveolar-capillary membrane and then the peripheral tissue membranes, followed by the convective transport of oxygen in the blood. Any transport process will have its choke points and limitations. In the case of oxygen, the constraints can take 1 of 2 forms, perfusion limitation or diffusion limitation.
Select Viruses in Adults
Authors: Walker Randall C.
Published: July 2012

The following types of viral infections are discussed in this chapter: viral infections that have the capacity for multiorgan or systemic disease; infections that affect adults who may be otherwise healthy or at least not in special populations such as herpes simplex virus (HSV) type 1, varicella-zoster virus (VZV), Epstein-Barr virus, adenovirus, mumps virus, human parvovirus B19, and coxsackievirus. Reviews of these viruses focus on differentiating clinical features, diagnostic tools and treatment, and salient microbiologic and epidemiologic factors.
Cryptococcus neoformans
Authors: Kusne Shimon , McCullough Ann E
Published: July 2012

Cryptococcosis is caused by 2 varieties of Cryptococcus neoformans: Cryptococcus neoformans var neoformans (serotypes A and D) and Cryptococcus neoformans var gatti (serotypes B and C). Serotypes A and D are found worldwide, mostly in avian droppings. Serotypes B and C are found in tropical and subtropical countries in association with eucalyptus trees. Infection can cause pneumonia, meningitis, or meningoencephalitis. It can also cause headache, fever, and unstable gait, especially in patients with AIDS. Diagnosis and treatment are also reviewed.
Parasitic Infections
Authors: Rosenblatt Jon E. , Pritt Bobbi S.
Published: July 2012

This chapter covers protozoa, helminths, and arthropods. 1. Protozoa are single-celled, microscopic eukaryotic organisms like amebae and Giardia. Helminths are parasitic worms including nematodes (roundworms), cestodes (tapeworms), and trematodes (flukes). Arthropods, like ticks and mites, are generally considered parasites. Specific organisms reviewed include Giardia lamblia, Cyclospora cayetanensis, Blastocystis hominis, Entamoeba histolytica, Plasmodium falciparum, Babesia microti, and Toxoplasma gondii. Diagnosis and treatment of different types of infection are also reviewed.
Urinary Tract Infections
Authors: Hellinger Walter C
Published: July 2012

There are several terms important to a discussion of urinary tract infection (UTI). Bacteriuria is bacteria in the urine. Significant bacteriuria is at least 105 bacteria/mL of voided urine. Asymptomatic bacteriuria is bacteria in the urine without symptoms associated with urinary tract infection. Urinary tract infection is bacteriuria (or funguria) and symptoms associated with upper UTI or lower UTI (or both). UTI s are sometimes characterized as asymptomatic or symptomatic, in which case asymptomatic UTI is synonymous with asymptomatic significant bacteriuria.
Uncomplicated UTI is infection of a physiologically and anatomically normal urinary tract. Complicated UTI is infection of a physiologically or anatomically abnormal urinary tract. Cystitis is lower UTI typically associated with urinary frequency, dysuria, or urgency. Acute pyelonephritis is upper UTI of recent onset with renal involvement, often associated with fever, chills, flank pain, or nausea. Diagnosis and treatment of specific infections are also reviewed.
Sepsis Syndrome
Authors: Badley Andrew D
Published: July 2012

Systemic inflammatory response syndrome (SIRS) is the specific host systemic response that may be elicited by various stimuli, including infection, burns, pancreatitis, ischemia, trauma, hemorrhage, immune-mediated tissue injury, and exogenous stimuli. 2. Sepsis is SIRS resulting from infection. Sepsis syndrome is sepsis with altered tissue perfusion of vital organs (resulting in oliguria, hypoxemia, elevated levels of lactate, or altered mentation or any combination of these conditions) When a patient has SIRS, the objective is to define its cause. If SIRS is caused by infection, appropriate antibiotics must be administered and supportive care guided by the patient's history and physical examination.
Infectious Diarrhea
Authors: Orenstein Robert
Published: July 2012

Acute diarrhea is usually defined as increased volume or looser consistency of stool. Specifically, more than 3 loose stools daily for less than 14 days. The majority of cases are self-limited. There are typically 4 causes for acute infectious diarrhea: noroviruses, diarrheogenic E coli, Clostridium difficile, or other toxins or parasites. Diagnosis and treatment of specific causes are reviewed.
Viral Hepatitis
Authors: Rizza Stacey A
Published: July 2012

Many viruses can cause multisystem disease in humans. There are 5 hepatotropic viruses that primarily infect the human liver and cause hepatitis: A, B, C, D, and E. In 1996 a sixth virus, hepatitis G virus, was described, but its role in human disease remains uncertain. According to the Centers for Disease Control and Prevention, approximately 10 cases of viral hepatitis per 100,000 people are reported each year in the United States. The causes, diagnosis, and treatment of each virus are reviewed.
Osteomyelitis, Infectious Arthritis, and Orthopedic Device Infection
Authors: Berbari Elie F , Osmon Douglas R
Published: July 2012

Infections involving the bones and joints (osteomyelitis, infectious arthritis, and prosthetic joint infections) are covered in this chapter. Two major mechanisms by which osteomyelitis occur are contiguous inoculation and direct inoculation. Contiguous inoculation occurs when microorganisms contaminate the bone directly through an ulcer adjacent to the bone, trauma, or surgery on the bone. Most cases of infectious arthritis due to bacteria are the consequence of hematogenous seeding from an infection elsewhere in the body. Direct inoculation of the joint occurs through surgical procedures, such as arthroscopy or therapeutic injections. Infectious arthritis can cause irreversible cartilage damage and irreversible dysfunction of the joint from recruitment of leukocytes that release enzymes that destroy cartilage. Prosthetic joints are used to treat painful arthritides, to relieve pain in patients with spinal stenosis, and to fix fractures in patients with long bone fractures Results are often excellent, but infection is a major complication of the procedures.
HIV-Associated Opportunistic Infections and Conditions
Authors: Meehan Anne M , Poeschla Eric M
Published: July 2012

Opportunistic infections (OIs) accounted for most of the morbidity and mortality associated with HIV infection in the early era of the pandemic. Introduction of effective primary and secondary antimicrobial prophylaxis regimens markedly decreased their incidence. Later in the HIV/AIDS pandemic, the introduction of effective highly active antiretroviral therapy (HAART) further reduced OI mortality independently of antimicrobial prophylaxis. HIV-associated OIs still occur when HIV is newly diagnosed and the course of care is in its early stages or when HAART therapy fails or antimicrobial prophylaxis is stopped prematurely. Immune status of the patient is the critical factor in determining whether a specific OI occurs. Management of specific OIs, such as pneumocystis pneumonia, encephalitis, cryptococcosis, and tuberculosis, is also reviewed.
Health Care–Associated Infections
Authors: Thompson Rodney L , Sampathkumar Priya
Published: July 2012

Health care–associated infection (HAI) is an infection that occurs in hospitals, nursing homes, clinics, or home health care programs. Infection control departments have been constituted to prevent and control infectious complications in health care settings. Prevention and control require combinations of education and training, procedures and policies, surveillance and reporting, and interventions that include isolation and teamwork. Common HAIs (nosocomial infections) include urinary tract infections, surgical site infections, bloodstream infections, and ventilator-associated pneumonia. Diagnosis and treatment of each type of infection are reviewed.
Viruses and Virus Diseases of Rubus
Authors: Martin Robert R. , MacFarlane Stuart , Sabanadzovic Sead , Quito Diego , Poudel Bindu , Tzanetakis Ioannis E.
Published: July 2012

Blackberry and raspberry are members of the family Rosaceae. They are classified in the genus Rubus, which comprises hundreds of species and has a center of origin in the Far East. Rubus is divided into 15 subgenera with blackberries classified in the Rubus (formerly Eubatus) and raspberries in the Idaeobatus subgenera. Rubus species are propagated vegetatively and are subject to infection by viruses during development, propagation, and fruit production stages. Reports of initial detection and symptoms of more than 30 viruses, virus-like diseases, and phytoplasmas affecting Rubus spp. were reviewed more than 20 years ago. Since the last review on Rubus viruses, significant progress has been made in the molecular characterization of many of the viruses that infect Rubus spp. Currently, reverse transcription–polymerase chain reaction detection methods are available for most of the viruses known to infect Rubus. The goals of this article are to update the knowledge on previously characterized viruses of Rubus, highlight recently described viruses, review the virus-induced symptoms, describe the advances made in their detection, and discuss our knowledge about several virus complexes that cause serious diseases in Rubus. Virus complexes have been identified recently as the major cause of diseases in blackberries and raspberries.