bluuebunny/crossref_metadata_2025 huggingface dataset:
Price Explosiveness, Speculation, and Grain Futures Prices
Authors: Etienne Xiaoli L. , Irwin Scott H. , Garcia Philip
Published: August 2014

A recently developed testing procedure is used to detect and date‐stamp explosive episodes (“bubbles”) in corn, soybean, and wheat futures markets during 2004–2013. We find that the markets experienced price explosiveness only approximately two percent of the time and, when bubbles do occur, they are generally short‐lived and small in magnitude. The correspondence between observed price spikes and bubbles is rather low, with a large portion of the price explosiveness occurring during downward price movements. Commodity index trader positions do not significantly affect the probability of a positive bubble occurring in grain futures markets, which directly contradicts the argument (the “Masters Hypothesis”) that waves of index investment distorted underlying supply‐and‐demand relationships and led to a series of massive bubbles in agricultural futures markets. In addition, commodity index trader positions tend to reduce negative bubble occurrence, while general speculative activity as measured by Working's T reduces the probability of a positive bubble. There is some evidence that the positions of noncommercial traders have a direct effect on positive bubble occurrence, but the effect declines when accounting for the composition of other traders in the market. Overall, speculation has little effect or negative effects on price explosiveness. Finally, positive bubbles are more likely to occur in the presence of low inventories, strong exports, a weak U.S. dollar, and booming economic growth, whereas negative bubbles are more likely to occur with large inventories, weak exports, and stagnant economic growth.
Cell population identification using fluorescence-minus-one controls with a one-class classifying algorithm
Authors: Feher Kristen , Kirsch Jenny , Radbruch Andreas , Chang Hyun-Dong , Kaiser Toralf
Published: August 2014

Motivation: The tried and true approach of flow cytometry data analysis is to manually gate on each biomarker separately, which is feasible for a small number of biomarkers, e.g. less than five. However, this rapidly becomes confusing as the number of biomarker increases. Furthermore, multivariate structure is not taken into account. Recently, automated gating algorithms have been implemented, all of which rely on unsupervised learning methodology. However, all unsupervised learning outputs suffer the same difficulties in validation in the absence of external knowledge, regardless of application domain.

Results: We present a new semi-automated algorithm for population discovery that is based on comparison to fluorescence-minus-one controls, thus transferring the problem into that of one-class classification, as opposed to being an unsupervised learning problem. The novel one-class classification algorithm is based on common principal components and can accommodate complex mixtures of multivariate densities. Computational time is short, and the simple nature of the calculations means the algorithm can easily be adapted to process large numbers of cells (106). Furthermore, we are able to find rare cell populations as well as populations with low biomarker concentration, both of which are inherently hard to do in an unsupervised learning context without prior knowledge of the samples’ composition.

Availability and implementation: R scripts are available via https://fccf.mpiib-berlin.mpg.de/daten/drfz/bioinformatics/with{username,password}={bioinformatics,Sar=Gac4}.

Contact:  kristen.feher@drfz.de or kaiser@drfz.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
RVboost: RNA-seq variants prioritization using a boosting method
Authors: Wang Chen , Davila Jaime I. , Baheti Saurabh , Bhagwate Aditya V. , Wang Xue , Kocher Jean-Pierre A. , Slager Susan L. , Feldman Andrew L. , Novak Anne J. , Cerhan James R. , Thompson E. Aubrey , Asmann Yan W.
Published: August 2014

Motivation: RNA-seq has become the method of choice to quantify genes and exons, discover novel transcripts and detect fusion genes. However, reliable variant identification from RNA-seq data remains challenging because of the complexities of the transcriptome, the challenges of accurately mapping exon boundary spanning reads and the bias introduced during the sequencing library preparation.

Method: We developed RVboost, a novel method specific for RNA variant prioritization. RVboost uses several attributes unique in the process of RNA library preparation, sequencing and RNA-seq data analyses. It uses a boosting method to train a model of ‘good quality’ variants using common variants from HapMap, and prioritizes and calls the RNA variants based on the trained model. We packaged RVboost in a comprehensive workflow, which integrates tools of variant calling, annotation and filtering.

Results: RVboost consistently outperforms the variant quality score recalibration from the Genome Analysis Tool Kit and the RNA-seq variant-calling pipeline SNPiR in 12 RNA-seq samples using ground-truth variants from paired exome sequencing data. Several RNA-seq–specific attributes were identified as critical to differentiate true and false variants, including the distance of the variant positions to exon boundaries, and the percent of the reads supporting the variant in the first six base pairs. The latter identifies false variants introduced by the random hexamer priming during the library construction.

Availability and implementation: The RVboost package is implemented to readily run in Mac or Linux environments. The software and user manual are available at http://bioinformaticstools.mayo.edu/research/rvboost/.

Supplementary information:  Supplementary data are available at Bioinformatics online.
Breathlessness
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

This chapter covers the broad topic of the symptom of breathlessness and the multiplicity of causes for this. A description of the physiological mechanisms causing the sensation of dyspnoea is given. There is a discussion of factors to consider in the clinical assessment of someone with breathlessness such as exacerbating factors, associated symptoms, family history. Particular reference to presenting features of bilateral diaphragmatic weakness, laryngeal stridor, and Cheyne-Stokes respiration is made, along with symptoms of orthopnoea and trepopnoea. Appropriate investigations are described, which clearly cover a broad range of possible differential diagnoses. A table of possible causes of breathlessness divides them by speed of onset: from instantaneous to acute, subacute, and chronic. Breathlessness with a normal chest radiograph is highlighted, along with episodic breathlessness. The often difficult clinical area of distinguishing between respiratory and cardiac causes of breathlessness is discussed, with appropriate investigations and how the results may help discriminate between the two.
Pleural effusion
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

Pleural effusion is common, in association with a range of different conditions, most commonly cardiac failure, pneumonia, malignancy, and pulmonary embolism. This chapter provides an approach to the assessment of the patient with a pleural effusion: history, examination, CXR, pleural ultrasound, along with guidance on which patients should undergo diagnostic or therapeutic thoracentesis and/or chest drain insertion. Tests to perform on the pleural fluid to help elicit the underlying cause are listed. Causes of transudative and exudative effusion are discussed, along with hints about differentiating between the two. Further investigations to consider, if the diagnosis remains unclear, are considered.
Pulmonary disease in the immunocompromised (HIV)
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

Respiratory disease remains common in the setting of HIV infection, despite advances in therapy with antiretroviral therapy and antimicrobial prophylaxis. An approach to the patient with respiratory symptoms and HIV infection is discussed, including clinical assessment, investigations, including CXR, blood and sputum cultures, CD4 count, CT chest, bronchoscopy, lavage, lung biopsy. Immune reconstitution inflammatory syndrome (IRIS) is described. A list of causes of respiratory diseases in the setting of immunocompromise due to HIV infection is provided, along with guidance for treatment.
Unexplained ventilatory failure
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

The conventional definitions of type I and type II ventilatory failure are discussed; this chapter predominantly concentrates on a discussion of the pathophysiology and possible causes of type II ventilatory failure with a raised carbon dioxide. A comprehensive list of possible causes is provided, with indicators of which are the most common possibilities. The list is divided helpfully into the underlying pathological defect: failure of drive (including different brainstem abnormalities or suppression of drive) or pump failure (including neurological causes, chest wall causes, airway obstruction). Possible clinical presentations are discussed, with the clinical features associated with slow onset and those with apparent rapid onset. A clinical approach to the investigation and management of people with ventilatory failure is provided, including consideration of non-invasive ventilation, physiotherapy, and cough assist devices.
Cystic fibrosis
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

Cystic fibrosis is the commonest genetic condition, and 1 in 25 of Caucasians are carriers of a CF gene, producing the disease in 1 in 2,500 births. The CFTR (cystic fibrosis transmembrane conductance regulator), a complex chloride channel, is now recognized to have over 1,800 different genetic abnormalities. The different ways they interfere with CFTR function are covered, and this understanding has led to some recent developments in small molecule drug therapies. Advances in other therapies have led to improvements in life expectancy. These therapies are discussed in detail, including: antibiotics (including home IV therapy), long-term macrolides, DNase, hypertonic saline, mannitol, ivacaftor, steroids, immunotherapy, physiotherapy, nutrition, NIV, lung transplant. Management of specific complications, including pneumothorax, haemoptysis, bronchopulmonary aspergillosis, asthma-like syndromes, pancreatic insufficiency, CF-related diabetes, intestinal obstruction, liver disease, osteoporosis, fertility, is covered. Difficult issues, including care of the dying CF patient, are considered.
Gastrointestinal disease and the lung
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

Hepatic hydrothorax, hepatopulmonary syndrome, and porto-pulmonary hypertension are all seen in patients with pre-existing liver disease. The chest physician may be asked to be involved with these patients. This chapter discusses the specifics of diagnosis and management, including physiological tests to look for right-to-left shunting, echocardiography, right heart catheterization. Inflammatory bowel disease (Crohn’s and ulcerative colitis), coeliac disease, and pancreatitis have specific respiratory complications which are described, along with appropriate management.
Idiopathic interstitial pneumonias
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

The complicated area of idiopathic interstitial pneumonias is systematically discussed. Recent expert consensus has split these conditions into more clearly defined histological and radiological entities, and these are described in detail, particularly their very different prognoses. They include: idiopathic pulmonary fibrosis (IPF), non-specific interstitial pneumonia (NSIP), cryptogenic organizing pneumonia (COP), acute interstitial pneumonia (AIP), respiratory bronchiolitis-associated interstitial lung disease (RB-ILD), desquamative interstitial pneumonia (DIP), lymphoid interstitial pneumonia (LIP). The role of specific blood markers, high-resolution CT scanning, bronchoalveolar lavage, and the more invasive diagnostic tests, such as open lung biopsy, are debated. The PANTHER-IPF trial’s recent results are discussed, and the use of pirfenidone for idiopathic pulmonary fibrosis is considered.
Respiratory infection—fungal
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

Many fungi can affect the lung through direct invasion or immunological mechanisms. This chapter covers the range of fungi and the mechanisms by which they can cause damage, as well as the factors provoking invasion, such as immunosuppression, HIV, infection, bone marrow suppression, and use of biological therapies like infliximab. Aspergillus is the most common and covered in detail, including simple allergic asthma, allergic bronchopulmonary aspergillosis, invasive Aspergillus disease, aspergilloma, and hypersensitivity pneumonitis due to Aspergillus. The role of steroids and antifungal agents is explored. Pneumocystis pneumonia (PCP) is also covered in detail, particularly its treatment in different settings. The endemic mycoses (histoplasmosis, blastomycosis, coccidioidomycosis and paracoccidioidomycosis), cryptococcosis, and candidal pneumonia are all discussed, with sections on their presentation, diagnosis, and treatment.
Sarcoidosis
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

Sarcoidosis remains an enigma within respiratory medicine, although recent developments have begun to clarify the pathophysiology. The immunological basis behind the typical features of this disease is explored. The different clinical presentations and evolution of the different types of sarcoid are covered, with advice on different management strategies, particularly the use of steroids, as this remains a vexed question. Second-line therapies, including methotrexate, azathioprine, hydroxychloroquine, and other immunosuppressants, are detailed. The value of the many diagnostic tests available is reviewed, including serum ACE, high-resolution CT, bronchoscopy, biopsy, mediastinoscopy, attenuated Mantoux test, and pulmonary function tests. Non-pulmonary complications, including cardiac, renal, neurological, musculoskeletal, gastrointestinal, and haematological involvement, are covered.
Unusual lung diseases
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

It is often said that rare diseases together occur commonly because there are so many of them. However, knowledge of the many individual oddities that present to a respiratory physician will often be first acquired from reading about them. This chapter covers 12 of the rare and exotic conditions likely to be met during the career of a respiratory physician, for example, amyloidosis, haemosiderosis, haemorrhagic telangiectasia, histiocytosis, lymphangioleiomyomatosis, ciliary dyskinesia, arteriovenous malformations, to name some of them.
Upper airway diseases
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

Upper airway problems are sometimes encountered by the respiratory physician and may be missed due to unfamiliarity. This chapter covers several areas. Acute upper airway obstruction can be due to a number of causes, including anaphylaxis. It can be life-threatening, and the potential causes and the principles of management need to be understood. The various upper airway infections that can occur, in isolation or with lower respiratory tract infections, are covered.
Intensive care unit (ICU)—when to involve
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

A close relationship should exist between the respiratory service and the ITU. The respiratory unit will need ITU expertise when patients deteriorate and need close monitoring or invasive ventilation; conversely, ITU will call upon the respiratory services when patients take longer to wean from invasive ventilation, usually via tracheostomy. This short chapter provides guidance on liaising with the ITU for help and details the use of the recent National Early Warning Score for assessing if patients need high dependency, or intensive care, involvement.
Oxygen therapy
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

Oxygen therapy is viewed by many as a harmless treatment, requiring little knowledge. However, respiratory physicians know that it should be treated like any other drug, capable of both great benefit and great harm. Recent BTS audits have highlighted the prevalent misuse of oxygen, a drug that should be prescribed. The use of oxygen, both acutely and in the home, is discussed in this chapter. The specific indications for high concentrations of oxygen and the very different place of controlled oxygen therapy are fully covered. The importance of monitoring the SaO2 to determine the concentration of oxygen used is emphasized and explained. The devices available for delivering different concentrations of oxygen are detailed. An example alert card for patients who are likely to go into worse ventilatory failure with uncontrolled oxygen is included. The recent current guidance (BTS), regulations, and practicalities concerning the prescription of home oxygen are fully covered, including long-term oxygen (LTOT), ambulatory oxygen, and short-burst oxygen (SBOT).
Pulmonary rehabilitation
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

The provision of pulmonary rehabilitation services has greatly increased in recent years, due to its efficacy and it being one of the few treatments that can significantly improve quality of life in patients with COPD and other chronic dyspnoea-inducing respiratory diseases. This chapter discusses the specific aims of a rehabilitation programme, the evidence behind them, the outcome measures, patient selection and assessment, and its components (physical training, disease education, psychological interventions, and nutritional advice).
Cricothyroidotomy
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

Cricothyroidotomy may save a life when the upper airway is compromised and cannot be cleared. This short chapter and diagram give a clear description and guidance on performing a cricothyroidotomy in an emergency.
Miscellaneous diagnostic tests
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

This chapter covers three diagnostic tests in common use that are not described elsewhere in this Handbook. Skin prick tests are still used, although some units have replaced them with the more expensive RAST tests for specific IgE. A full description of how to do and read them is included. The simple technique of induced sputum for TB and PCP is less frequently used although likely to increase in use as specific new biomarkers of disease are identified in sputum. Bronchoprovocation testing to measure bronchial reactivity is also done by many units to help in the diagnosis of asthma, and a full description of the various techniques is included in this chapter.
Pleurodesis
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

Pleurodesis is a standard procedure in respiratory medicine that can be done in a number of ways, from minimally invasive through to a full surgical operation. This chapter concentrates on the medical procedure of chemical pleurodesis using sclerosing agents. The indications (usually malignant pleural effusions) and complications are discussed, and a clear description of ‘how to do it’ is included.
Thoracentesis
Authors: Chapman Stephen , Robinson Grace , Stradling John , West Sophie , Wrightson John
Published: August 2014

Thoracentesis may be required for diagnostic or therapeutic purposes. Various techniques exist for extracting fluid from the pleural space, and this chapter discusses the indications and recommended techniques, for both diagnosis and relief of symptoms.
The Psychiatric Interview
Authors: Desai Anand , Rosnick Lyle
Published: August 2014

This chapter focuses on how to conduct a psychiatric interview. While adhering to the basic medical model, the psychiatric interview has four additional essential and distinguishing features: a psychological perspective, empathic listening, particular attention to the physician’s emotional responses, and a focus on the interview process. Two relatively common challenges to history taking are the disorganized patient and the difficult-to-engage patient. It is particularly important that physicians conducting psychiatric interviews maintain a professional stance that is empathic, respectful, and curious..
Mood Disorders
Authors: Ganança Licínia , Kahn David A. , Oquendo Maria A.
Published: August 2014

This chapter discusses the mood disorders. Major depressive disorder is characterized by neurovegetative changes, anhedonia, and suicidal ideation. Persistent depressive disorder is a milder form of depression, lasting for at least 2 years, with little or no remission during that time... Psychotic features can occur in both depressive and manic episodes. Premenstrual dysphoric disorder is diagnosed through use of a prospective daily symptom ratings log showing a cyclical pattern over at least 2 consecutive months. Patients with mood episodes with mixed features have a high risk of suicide. Some patients with bipolar disorder and major depressive disorder may develop catatonic features characterized by marked psychomotor disturbance. Selective serotonin reuptake inhibitors (SSRIs) are the usual first-line medication treatment for patients with major depressive disorder. For patients with bipolar disorder the mainstays of somatic therapy are lithium and the anticonvulsants valproate and carbamazepine.
Neurocognitive Disorders and Mental Disorders Due to Another Medical Condition
Authors: Rucci Jennifer M. , Feinstein Robert E.
Published: August 2014

The defining feature of neurocognitive disorders is a decline in cognitive functioning. Patients suffering from delirium experience an acute change in mental status, fluctuating levels of consciousness, and an inability to acquire new information. Patients with major neurocognitive disorder experience significant cognitive decline in complex attention, executive function, learning and memory, language, perceptual-motor, and social cognition. The chapter also discusses mental disorders due to another medical condition. These patients can experience psychotic, mood, or anxious symptoms or a personality change; their intellectual functioning usually remains intact. A patient presenting with a first episode of psychiatric symptoms and no prior psychiatric history should be evaluated for an acute medical etiology causing the psychiatric symptoms, particularly if he or she is over 40 years of age. Anticholinesterase inhibitors (donepezil, galantamine, and rivastigmine) may slow the rate of cognitive decline in Alzheimer’s disease, and the combination of an anticholinesterase inhibitor and memantine may be more effective than either medication alone.
Somatic Symptom and Related Disorders
Authors: Harding Kelli Jane K. , Fallon Brian A.
Published: August 2014

This chapter discusses the somatic symptom disorders, which are a heterogeneous group unified by physical symptoms or concerns that are associated with prominent distress or impairment. Somatic symptom disorders are estimated to account for 1 in 10 primary care patient visits. The relative prominence of somatic symptoms is essential to the difference between illness anxiety disorder, which is an example of the obsessional/cognitive subtype (not prominent) and somatic symptom disorder,, in which the somatic symptoms are prominent. Patients with body dysmorphic disorder, also an Obsessional/Cognitive subtype, are preoccupied with a perceived defect in physical appearance. Patients with conversion disorder (functional neurological symptom disorder) (dissociative sub-type) present with neurological symptoms that cannot be fully explained physiologically. Patients with factitious disorder consciously simulate illness for psychological purposes rather than practical gain.
Psychological Factors Affecting Medical Conditions
Authors: Nash Sara Siris , Hutner Lucy , Caligor Eve
Published: August 2014

This chapter deals with patients who have a psychological or behavioral factor that is adversely influencing their medical condition. These factors include psychological distress, interpersonal problems, coping styles, and maladaptive health behaviors. It is important to remember that regression is a nearly universal psychological reaction to being ill. Responses to a physical illness are affected by patients’ personality traits. The role of stress should be taken into account in the treatment of patients with medical conditions. Living with a chronic physical illness, including chronic pain, presents a psychological challenge for patients and their families. Secondary gain can interfere with motivation for recovery.
Suicide
Authors: Rothberg Brian , Feinstein Robert E.
Published: August 2014

All psychiatric assessments should include screening for recent suicidal ideation and past suicide behavior. The Columbia-Suicide Severity Rating Scale (C-SSRS) provides a reliable objective assessment of suicide risk. A history of past suicide attempts is a risk factor for future suicide, and risk is increased by more serious, more frequent, or more recent attempts. Over 90% of individuals who die by suicide have at least one psychiatric disorder. Patients with schizophrenia, alcohol and other substance use disorders, and borderline and antisocial personality disorders are at increased risk for suicide. Familial transmission of suicide risk appears to occur independent of the familial risk for psychiatric disorders; impulsivity seems to be an inherited trait that makes individuals more vulnerable to suicide. Hospitalization should be considered if suicidal ideation is present in a patient who is psychotic or who has a history of past attempts, particularly if near lethal, and may be the safest option in patients with other contributing medical conditions, limited family or social support, or lack of access to timely outpatient follow-up.
Violence
Authors: Feinstein Robert E. , Rothberg Brian
Published: August 2014

Potentially violent patients need immediate attention and evaluation to determine their risk of imminent violence. A past history of violence is the best predictor of future violent behavior, and individuals who have committed violent acts in the past and have been arrested for assaultive behavior represent the highest risk; people who carry weapons or have access to weapons are of relatively high risk. Individuals with violent impulses who are either intoxicated or are in withdrawal have the most extreme risk for imminent violence. The treatment of acute aggression or agitation involves the judicious use of sedative-anxiolytics or low doses of second-generation antipsychotics. SSRIs have been used to treat aggressive, impulsive, and violent symptoms, particularly in individuals with head injuries, and lithium carbonate can reduce impulsive aggression to extremely low levels in some aggressive patients. Two Tarasoff decisions have become national standards for clinical practice regarding “duty to warn” and “duty to protect” all potential victims of life-threatening danger from a homicidal patient.
Child, Adolescent, and Adult Development
Authors: Slater Jonathan A. , Stratigos Katharine A. , Cutler Janis L.
Published: August 2014

The development of children and adolescents is characterized by abrupt discontinuities as well as continuous aspects of behavior such as individual temperament. The crucial task of the first year of life is the development and solidification of the attachment between infant and caretaker. Toddlers and adolescents tend to experience intense conflicts around autonomy and control that become resolved as they progress in the process of separation-individuation. The tasks of middle childhood include developing a sustained sense of mastery and competence, morality, and stable self-esteem; as ego functions grow and consolidate, children become increasingly able to tolerate frustration and delays in the gratification of their wishes and desires. Adolescence begins with puberty, the period of sexual maturation in which the primary sex organs develop and become capable of reproduction and secondary sex characteristics appear. Although adolescents tend to engage in risk-taking behaviors, the majority of adolescents maintain normal academic and social functioning; an adolescent whose rebelliousness includes severe disturbances in conduct, mood, or drug abuse should be evaluated for possible psychopathology requiring treatment. The main social developmental tasks for adults take place in the realms of work and intimate relationships.
History and examination
Authors: Raine Tim , Dawson James , Sanders Stephan , Eccles Simon
Published: August 2014

Basic history

Basic examination

Recording your
clerking

Medicine

Cardiovascular

Respiratory

Gastrointestinal

Neurological

Endocrine

Skin

Oncological/haematological

Surgery

Breast

Eyes

Head and neck

Musculoskeletal

Urological

Other specialties

Female reproductive
system

Obstetric

Psychiatric

Neonatal
examination

Paediatric

Taking a thorough history is an essential skill
as a junior doctor and something you will become extremely practised at. These two
pages show the basic features of a history, with details of how to perform a basic
examination following after. The rest of the chapter shows how to adapt these basic
approaches for specific situations....
Respiratory
Authors: Raine Tim , Dawson James , Sanders Stephan , Eccles Simon
Published: August 2014

Breathlessness and low sats
emergency

Breathlessness and low
sats

Stridor in a conscious adult
patient

Cough

Call for senior help early if
patient deteriorating.

•Sit patient up

•15l/min O2 in all patients if acutely unwell

•Monitor pulse oximeter, BP, defibrillator’s ECG leads if unwell...
Neurology and psychiatry
Authors: Raine Tim , Dawson James , Sanders Stephan , Eccles Simon
Published: August 2014

Coma and reduced GCS
emergency

Coma and reduced GCS

Acute confusion

Dementia

Adult seizures
emergency

Paediatric seizures
emergency

Seizures

Neurodegenerative
disorders

Stroke/CVA/TIA
emergency

Stroke

Focal neurology

Back pain

Headache

Dizziness

Aggressive behaviour
emergency

Mood
disturbance/psychosis

Call for senior help early if
patient unwell or deteriorating....
Fluids and renals
Authors: Raine Tim , Dawson James , Sanders Stephan , Eccles Simon
Published: August 2014

Acute kidney injury

Chronic renal failure

Haematuria

Proteinuria

Glomerular disease

Urological disorders

Low urine output

IV fluids

Potassium
emergencies

Electrolyte
imbalance

Acute rise from baseline of serum urea and creatinine ±oliguria ( Table 12.1);1there are three basic mechanisms:

•Prerenal hypoperfusion of kidney due to eg ↓BP, hypovolaemia,
renal artery occlusion (mass, emboli)...
Haematology
Authors: Raine Tim , Dawson James , Sanders Stephan , Eccles Simon
Published: August 2014

Anaemia

Transfusion of blood
products

Clotting emergencies

Bleeding

Anticoagulation

Reduced red blood cell (RBC) mass, usually conveniently approximated as reduced
haemoglobin concentration (eg ♂ <130g/L, ♀ <115g/L1). Causes easily divide into 3 basic mechanisms (reduced RBC production,
increased RBC des-truction, RBC loss) with clues found in abnormalities of RBC
size and shape....
Emergency department
Authors: Raine Tim , Dawson James , Sanders Stephan , Eccles Simon
Published: August 2014

Trauma

Head injury

Neck injury

Falls and collapse

Acutely painful limb
emergency

Acute limb pain

Chronic limb pain

Limb swelling

Joint pain

Neck lumps

ENT

Groin lumps

Burns emergency

Burns

Anaphylaxis in
adults

Hypotension
emergency

Hypotension

Shock

Pyrexia

Overdose emergency

Overdose and deliberate
self-harm

Vaginal bleeding...
Principles of Palliative Care
Authors: Breitbart William S.
Published: August 2014

Palliative medicine refers to the medical discipline of palliative care. Modern palliative care has evolved from the hospice movement into a more expansive network of clinical care delivery systems with components of home care and hospital-based services. Palliative care begins with the onset of a life-threatening illness and proceeds past death to include bereavement interventions for family and others, with a mission to meet the physical, psychological, social, spiritual, and existential needs of the “whole patient.“ This chapter includes an overview of definitions of palliative care, the global need for palliative care, and ideal components of palliative care programs. A comprehensive review of the most recent research findings on impact of early palliative care on quality of life and survival is provided.
Depression in Palliative Care
Authors: Breitbart William S.
Published: August 2014

Depression is prevalent, but under-recognized, underdiagnosed, and undertreated in palliative care settings. Risk factors associated with depression in patients with advanced cancer are well defined and include a variety of medical and psychosocial factors. It is challenging to diagnose depression in palliative care settings because of the presence of overlapping physical symptoms specific to the cancer, such as fatigue and decreased appetite. Inclusive, exclusive, etiological, substitutive, and high-threshold approaches have been proposed to improve diagnosis of depression among medically ill patients. Management of depression in the palliative care settings comprises use of psychopharmacological agents and individual and group psychotherapies. The psycho-oncology clinician should take into consideration that antidepressants alone may not be adequate in patients with shortened life expectancies. Psychostimulants might be preferred in patients with less than a month to live. Cognitive behavioral interventions, supportive expressive group therapy, meaning-centered psychotherapy, dignity therapy, and mindfulness-based meditation therapy have emerged as effective psychotherapy modalities in decreasing depressive symptoms and suffering in advanced cancer patients.
Testing the neutrino annihilation model for launching GRB jets
Authors: Leng Mingbin , Giannios Dimitrios
Published: August 2014

The mechanism behind the launching of gamma-ray burst (GRB) jets remains debated resulting in large uncertainty over the jet composition. Both magnetohydrodynamical and neutrino annihilation models have been proposed for the energy extraction in a black hole/accretion-disc central engine. In particular, for the extreme accretion rates $\dot{M}\sim 0.1\hbox{--}1$ M⊙ s−1 expected for bursts of duration T ≲ 100 s, the disc can be an efficient neutrino emitter. Neutrino–antineutrino annihilation results in an energy deposition rate at the jet that can, in principle, account for the burst's energetics. Recent discoveries of X-ray flares hours after the burst and of ultra-long GRBs suggest that GRB activity can last for ∼104 s or longer. These long-lived events have fluence similar to that of classical GRBs. In view of these findings, we re-evaluate the neutrino annihilation model. We derive the maximum possible energy of a neutrino-powered jet as a function of the burst duration and show that the available energy drops fast for longer bursts. For a standard choice of the parameters, the model falls short by three to four orders of magnitude in explaining the observed energetics of events that last longer than ∼103 s.
Andromeda II as a merger remnant
Authors: Łokas Ewa L. , Ebrová Ivana , Pino Andrés del , Semczuk Marcin
Published: August 2014

Using N-body simulations, we study the origin of prolate rotation observed in the kinematic data for Andromeda II (And II), a dwarf spheroidal satellite of M31. We propose an evolutionary model for the origin of And II involving a merger between two discy dwarf galaxies with different disc scalelengths. The dwarfs are placed on a radial orbit towards each other with their angular momenta inclined by 90 deg. The merger remnant forms a stable triaxial galaxy with rotation only around the longest axis whose origin is naturally explained as due to the symmetry of the initial configuration and the conservation of angular momentum components along the direction of the merger. The stars originating from the two dwarfs show significantly different surface density profiles while having very similar kinematics as required by the data. We also study an alternative scenario for the formation of And II, via tidal stirring of a discy dwarf. While intrinsic rotation occurs naturally in this model as a remnant of the initial rotation of the disc, it is mostly around the shortest axis of the stellar component. We conclude that the velocity distribution in And II is much more naturally explained by a scenario involving a past merger.
Bayesian Multilevel MIMIC Modeling for Studying Measurement Invariance in Cross-group Comparisons
Authors: Bruyneel Luk , Li Baoyue , Squires Allison , Spotbeen Sara , Meuleman Bart , Lesaffre Emmanuel , Sermeus Walter
Published: August 2014

Background:

Recent methodological advancements should catalyze the evaluation of measurement invariance across groups, which is required for conducting meaningful cross-group comparisons.

Objective:

The aim of this study was to apply a state-of-the-art statistical method for comparing latent mean scores and evaluating measurement invariance across managers’ and frontline workers’ ratings of the organization of hospital care.

Methods:

On the 87 nursing units in a single institution, French-speaking and Dutch-speaking nursing unit managers’ and staff nurses’ ratings of their work environment were measured using the multidimensional 32-item practice environment scale of the nursing work index (PES-NWI). Measurement invariance and latent mean scores were evaluated in the form of a Bayesian 2-level multiple indicators multiple causes model with covariates at the individual nurse and nursing unit level. Role (manager, staff nurse) and language (French, Dutch) are of primary interest.

Results:

Language group membership accounted for 7 of 11 PES-NWI items showing measurement noninvariance. Cross-group comparisons also showed that covariates at both within-level and between-level had significant effects on PES-NWI latent mean scores. Most notably, nursing unit managers, when compared with staff nurses, hold more positive views of several PES-NWI dimensions.

Conclusions:

Using a widely used instrument for measuring nurses’ work environment, this study shows that precautions for the potential threat of measurement noninvariance are necessary in all stages of a study that relies on survey data to compare groups, particularly in multilingual settings. A Bayesian multilevel multiple indicators multiple causes approach can accommodate for detecting all possible instances of noninvariance for multiple covariates of interest at the within-level and between-level jointly.
Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales’ and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov.
Authors: Sen Arnab , Daubin Vincent , Abrouk Danis , Gifford Isaac , Berry Alison M. , Normand Philippe
Published: August 2014

The phylogeny of the class

Actinobacteria

remains controversial, essentially because it is very sensitive to the choice of dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses among candidate species phylogenies based on the number of lateral gene transfers (LGT) needed to explain the diversity of histories among gene trees for a set of genomes. We used 100 completely sequenced genomes representing 35 families and 17 orders of the class

Actinobacteria

and evaluated eight different hypotheses for their phylogeny, including one based on a concatenate of 54 conserved proteins present in single copy in all these genomes, trees based on 16S and 23S rRNA gene sequences or their concatenation, and a tree based on the concatenation of MLSA genes (encoding AtpI, GyrA, FtsZ, SecA and DnaK). We used Prunier to infer the number of LGT in 579 proteins (different from those used to build the concatenated tree) present in at least 70 species, using the different hypothetical species trees as references. The best tree, with the lowest number of lateral transfers, was the one based on the concatenation of 54 proteins. In that tree, the orders

Bifidobacteriales

,

Coriobacteriales

, ‘Coryneb
acteriales’, ‘Micromonosporales’, ‘Propionibacteriales’, ‘Pseudonocardiales’, Streptomycetales and ‘Streptosporangiales’ were recovered while the orders ‘Frankiales’ and

Micrococcales

were not. It is thus proposed that the order ‘Frankiales’, which has an effectively but not validly published name, be split into Frankiales ord. nov. (type family

Frankiaceae

), Geodermatophilales ord. nov. (

Geodermatophilaceae

), Acidothermales ord. nov. (

Acidothermaceae

) and Nakamurellales ord. nov. (

Nakamurellaceae

). The order

Micrococcales

should also be split into

Micrococcales

(genera

Kocuria

,

Rothia

,

Micrococcus

,

Arthrobacter

,

Tropheryma

,

Microbacterium

,

Leifsonia

and

Clavibacter

), Cellulomonales (

Beutenbergia

,

Cellulomonas

,

Xylanimonas

,

Jonesia

and

Sanguibacter

) and Brachybacteriales (

Brachybacterium

) but the formal proposal for this will have to wait until more genomes become available for a significant proportion of strains in this order.
W
ickerhamiella siamensis f.a., sp. nov., an endophytic and epiphytic yeast species isolated from sugar cane leaf
Authors: Khunnamwong Pannida , Surussawadee Janjira , Jindamorakot Sasitorn , Limtong Savitree
Published: August 2014

Six strains representing a novel yeast species were isolated from tissue (DMKU-SE106T, DMKU-SE110, DMKU-SE112 and DMKU-SE132) and the external surface (DMKU-SP335 and DMKU-SP406) of sugar cane leaves collected in Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and sequence analysis of the D1/D2 region of the LSU rRNA gene and the internal transcribed spacer (ITS) region, the six strains were found to represent a single novel species of the genus Wickerhamiella although the formation of ascospores was not observed. The sequences of the D1/D2 region of the LSU rRNA gene and ITS region of the six strains differed from each other by 0–2 and 2–3 nt substitutions, respectively. The novel species was related most closely to Candida infanticola but with 4.5–4.6 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene and 6.6–7.1 % nucleotide substitutions in the ITS region. The name Wickerhamiella siamensis f.a., sp. nov. is proposed. The type strain is DMKU-SE106T ( = BCC 61185T = NBRC 109697T = CBS 13331T).
Sphingobacterium
yanglingense sp. nov., isolated from the nodule surface of soybean
Authors: Peng Shi , Hong Dong Dan , Xin Yang Bing , Jun Li Ming , Hong Wei Ge
Published: August 2014

A Gram-staining-negative, non-motile, catalase- and oxidase-positive strain, designated CCNWSP36-1T, was isolated from the nodule surface of soybean [Glycine max (L.) Merrill] cultivar Zhonghuang 13. The 16S rRNA gene sequence analysis clearly showed that the isolate represented a member of the genus

Sphingobacterium

. On the basis of pairwise comparisons of 16S rRNA gene sequences, strain CCNWSP36-1T showed 96.8 % similarity to

Sphingobacterium nematocida

CCTCC AB 2010390T and less than 95.2 % similarity to other members of the genus

Sphingobacterium

. Growth of strain CCNWSP36-1T occurred at 10–40 °C and at pH 5.0–9.0. The NaCl range (w/v) for growth was 0–4 %. The predominant isoprenoid quinone was MK-7. The polar lipids were phosphatidylethanolamine and several unidentified polar lipids. Sphingolipid was present. The major fatty acids were iso-C15 : 0 and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). The G+C content of the genomic DNA was 41.1 mol%. As the physiological and biochemical characteristics of strain CCNWSP36-1T and the type strains of its closest phylogenetic neighbours showed clear differences, a novel species, Sphingobacterium yanglingense, is proposed. The type strain is CCNWSP36-1T ( = ACCC 19328T = JCM 30166T).
In vitro antifungal susceptibility of Malassezia furfur from bloodstream infections
Authors: Iatta Roberta , Figueredo Luciana A. , Montagna Maria Teresa , Otranto Domenico , Cafarchia Claudia
Published: August 2014

Fungaemia caused by Malassezia spp. in hospitalized patients requires prompt and appropriate therapy, but standard methods for the definition of the in vitro antifungal susceptibility have not been established yet. In this study, the in vitro susceptibility of Malassezia furfur from bloodstream infections (BSIs) to amphotericin B (AMB), fluconazole (FLC), itraconazole (ITC), posaconazole (POS) and voriconazole (VRC) was assessed using the broth microdilution (BMD) method of the Clinical and Laboratory Standards Institute (CLSI) with different media such as modified Sabouraud dextrose broth (SDB), RPMI and Christensen’s urea broth (CUB). Optimal broth media that allow sufficient growth of M. furfur, and produce reliable and reproducible MICs using the CLSI BMD protocol were assessed. Thirty-six M. furfur isolates collected from BSIs of patients before and during AMB therapy, and receiving FLC prophylaxis, were tested. A good growth of M. furfur was observed in RPMI, CUB and SDB at 32 °C for 48 and 72 h. No statistically significant differences were detected between the MIC values registered after 48 and 72 h incubation. ITC, POS and VRC displayed lower MICs than FLC and AMB. These last two antifungal drugs showed higher and lower MICs, respectively, when the isolates were tested in SDB. SDB is the only medium in which it is possible to detect isolates with high FLC MICs in patients receiving FLC prophylaxis. A large number of isolates showed high AMB MIC values regardless of the media used. In conclusion, SDB might be suitable to determine triazole susceptibility. However, the media, the drug formulation or the breakpoints herein applied might not be useful for assessing the AMB susceptibility of M. furfur from BSIs.