Deep Learning Technology: Sebastian Arnold, Betty van Aken, Paul Grundmann, Felix A. Gers and Alexander Löser. Learning Contextualized Document Representations for Healthcare Answer Retrieval. The Web Conference 2020 (WWW'20)
Funded by The Federal Ministry for Economic Affairs and Energy; Grant: 01MD19013D, Smart-MD Project, Digital Technologies
Coughing and rattling are common, most severe in young, such as broilers, and rapidly spreading in chickens confined or at proximity. Morbidity is 100% in non-vaccinated flocks. Mortality varies according to the virus strain (up to 60% in non-vaccinated flocks). Respiratory signs will subdue within two weeks. However, for some strains, a kidney infection may follow, causing mortality by toxemia. Younger chickens may die of tracheal occlusion by mucus (lower end) or by kidney failure. The infection may prolong in the cecal tonsils.
In laying hens, there can be transient respiratory signs, but mortality may be negligible. However, egg production drops sharply. A great percentage of produced eggs are misshapen and discolored. Many laid eggs have a thin or soft shell and poor albumen (watery), and are not marketable or proper for incubation. Normally-colored eggs, indicative of normal shells for instance in brown chickens, have a normal hatchability.
Egg yield curve may never return to normal. Milder strains may allow normal production after around eight weeks.
Symptoms of viral pneumonia include fever, non-productive cough, runny nose, and systemic symptoms (e.g. myalgia, headache). Different viruses cause different symptoms.
Avian infectious bronchitis (IB) is an acute and highly contagious respiratory disease of chickens. The disease is caused by avian infectious bronchitis virus (IBV), a coronavirus, and characterized by respiratory signs including gasping, coughing, sneezing, tracheal rales, and nasal discharge. In young chickens, severe respiratory distress may occur. In layers, respiratory distress, nephritis, decrease in egg production, and loss of internal (watery egg white) and external (fragile, soft, irregular or rough shells, shell-less) egg quality are reported.
The incubation period is 5–7 days (with a range of 3–10). Symptoms can include a harsh, dry cough, retching, sneezing, snorting, gagging or vomiting in response to light pressing of the trachea or after excitement or exercise. The presence of a fever varies from case to case.
Initial symptoms are flu-like and may include fever, myalgia, lethargy symptoms, cough, sore throat, and other nonspecific symptoms. The only symptom common to all patients appears to be a fever above . SARS may eventually lead to shortness of breath and/or pneumonia; either direct viral pneumonia or first bacterial pneumonia.
Viral pneumonia is a pneumonia caused by a virus.
Viruses are one of the two major causes of pneumonia, the other being bacteria; less common causes are fungi and parasites. Viruses are the most common cause of pneumonia in children, while in adults bacteria are a more common cause.
Usually the atypical causes also involve atypical symptoms:
- No response to common antibiotics such as sulfonamide and beta-lactams like penicillin.
- No signs and symptoms of lobar consolidation, meaning that the infection is restricted to small areas, rather than involving a whole lobe. As the disease progresses, however, the look can tend to lobar pneumonia.
- Absence of leukocytosis.
- Extrapulmonary symptoms, related to the causing organism.
- Moderate amount of sputum, or no sputum at all (i.e. non-productive).
- Lack of alveolar exudate.
- Despite general symptoms and problems with the upper respiratory tract (such as high fever, headache, a dry irritating cough followed later by a productive cough with radiographs showing consolidation), there are in general few physical signs. The patient looks better than the symptoms suggest.
Kennel cough (also known as canine infectious tracheobronchitis) is an upper respiratory infection affecting dogs. There are multiple causative agents, the most common being the bacterium "Bordetella bronchiseptica" (found in 78.7% of cases in Southern Germany), followed by canine parainfluenza virus (37.7% of cases), and to a lesser extent canine coronavirus (9.8% of cases). It is highly contagious; however adult dogs may display immunity to reinfection even under constant exposure. Kennel cough is so named because the infection can spread quickly among dogs in the close quarters of a kennel or animal shelter.
Viral and bacterial causes of canine cough are spread through airborne droplets produced by sneezing and coughing. These agents also spread through contact with contaminated surfaces. Symptoms begin after a several day incubation period post-exposure, and in most cases will clear up on their own. However, in young puppies or immunocompromised animals, mixed or secondary infections can progress to lower respiratory infections such as pneumonia.
"Pharyngoconjunctival fever" is a specific presentation of adenovirus infection, manifested as:
- high fever that lasts 4–5 days
- pharyngitis (sore throat)
- conjunctivitis (inflamed eyes, usually without pus formation like pink eye)
- enlargement of the lymph nodes of the neck
- headache, malaise, and weakness
- Incubation period of 5–9 days
It usually occurs in the age group 5–18. It is often found in summer camps and during the spring and fall in schools. In Japan, the illness is commonly referred to as "pool fever" as it is often spread via public swimming pools.
In a typical case, an infant under two years of age develops cough, wheeze, and shortness of breath over one or two days. Crackles or wheeze are typical findings on listening to the chest with a stethoscope. The infant may be breathless for several days. After the acute illness, it is common for the airways to remain sensitive for several weeks, leading to recurrent cough and wheeze.
Some signs of severe disease include:
- poor feeding (less than half of usual fluid intake in preceding 24 hours)
- significantly decreased activity
- history of stopping breathing
- respiratory rate >70/min
- presence of nasal flaring and/or grunting
- severe chest wall recession (Hoover's sign)
- bluish skin
Chest radiographs (X-ray photographs) often show a pulmonary infection before physical signs of atypical pneumonia are observable at all.
This is occult pneumonia. In general, occult pneumonia is rather often present in patients with pneumonia and can also be caused by "Streptococcus pneumoniae", as the decrease of occult pneumonia after vaccination of children with a pneumococcal vaccine suggests.
Infiltration commonly begins in the perihilar region (where the bronchus begins) and spreads in a wedge- or fan-shaped fashion toward the periphery of the lung field. The process most often involves the lower lobe, but may affect any lobe or combination of lobes.
Apart from respiratory involvement, illnesses and presentations of adenovirus include gastroenteritis, conjunctivitis, cystitis, and rash illness. Symptoms of respiratory illness caused by adenovirus infection range from the common cold syndrome to pneumonia, croup, and bronchitis. Patients with compromised immune systems are especially susceptible to severe complications of adenovirus infection. Acute respiratory disease (ARD), first recognized among military recruits during World War II, can be caused by adenovirus infections during conditions of crowding and stress.
Lower respiratory tract infection (LRTI), while often used as a synonym for pneumonia, can also be applied to other types of infection including lung abscess and acute bronchitis. Symptoms include shortness of breath, weakness, fever, coughing and fatigue.
There are a number of symptoms that are characteristic of lower respiratory tract infections. The two most common are bronchitis and edema. Influenza affects both the upper and lower respiratory tracts.
Antibiotics are the first line treatment for pneumonia; however, they are not effective or indicated for parasitic or viral infections. Acute bronchitis typically resolves on its own with time.
In 2015 there were about 291 million cases. These resulted in 2.74 million deaths down from 3.4 million deaths in 1990. This was 4.8% of all deaths in 2013.
Bronchitis describes the swelling or inflammation of the bronchial tubes. Additionally, bronchitis is described as either acute or chronic depending on its presentation and is also further described by the causative agent. Acute bronchitis can be defined as acute bacterial or viral infection of the larger airways in healthy patients with no history of recurrent disease. It affects over 40 adults per 1000 each year and consists of transient inflammation of the major bronchi and trachea. Most often it is caused by viral infection and hence antibiotic therapy is not indicated in immunocompetent individuals. Viral bronchitis can sometimes be treated using antiviral medications depending on the virus causing the infection, and medications such as anti-inflammatory drugs and expectorants can help mitigate the symptoms. Treatment of acute bronchitis with antibiotics is common but controversial as their use has only moderate benefit weighted against potential side effects (nausea and vomiting), increased resistance, and cost of treatment in a self-limiting condition. Beta2 agonists are sometimes used to relieve the cough associated with acute bronchitis. In a recent systematic review it was found there was no evidence to support their use.
SARS may be "suspected" in a patient who has:
- Any of the symptoms, including a fever of or higher, and
- Either a history of:
1. Contact (sexual or casual) with someone with a diagnosis of SARS within the last 10 days OR
2. Travel to any of the regions identified by the World Health Organization (WHO) as areas with recent local transmission of SARS (affected regions as of 10 May 2003 were parts of China, Hong Kong, Singapore and the town of Geraldton, Ontario, Canada).
For a case to be considered "probable," a chest X-ray must be positive for atypical pneumonia or respiratory distress syndrome.
The World Health Organization (WHO) has added the category of "laboratory confirmed SARS" for patients who would otherwise be considered ""probable"" but who have not yet had a positive chest X-ray changes, but have tested positive for SARS based on one of the approved tests (ELISA, immunofluorescence or PCR).
When it comes to the chest X-ray the appearance of SARS is not always uniform but generally appears as an abnormality with patchy infiltrates.
Those infected with the virus may be asymptomatic or develop flu-like symptoms such as fever, cough, fatigue, and shortness of breath. Emergency symptoms include difficulty breathing, persistent chest pain or pressure, confusion, difficulty waking, and bluish face or lips; immediate medical attention is advised if these symptoms are present. Less commonly, upper respiratory symptoms such as sneezing, runny nose or sore throat may be seen. Gastrointestinal symptoms such as nausea, vomiting and diarrhoea have been observed in varying percentages. Some cases in China initially presented only with chest tightness and palpitations. In some, the disease may progress to pneumonia, multi-organ failure, and death. In those who develop severe symptoms, time from symptom onset to needing mechanical ventilation is typically eight days.
Loss of smell was identified as a common early symptom of COVID-19 in March 2020, although not as common as initially reported.
As is common with infections, there is a delay between the moment when a person is infected with the virus and the time when they develop symptoms. This is called the incubation period. The incubation period for COVID-19 is typically five to six days but may range from two to 14 days. 97.5% of people who develop symptoms will do so within 11.5 days of infection.
Reports indicate that not all who are infected develop symptoms. The role of these asymptomatic carriers in transmission is not yet fully known; however, preliminary evidence suggests that they may contribute to the spread of the disease. The proportion of infected people who do not display symptoms is currently unknown and being studied, with the Korea Centers for Disease Control and Prevention (KCDC) reporting that 20% of all confirmed cases remained asymptomatic during their hospital stay. China's National Health Commission began including asymptomatic cases in its daily cases on 1 April; of the 166 infections on that day, 130 (78%) were asymptomatic at the time of testing.
People with infectious pneumonia often have a productive cough, fever accompanied by shaking chills, shortness of breath, sharp or stabbing chest pain during deep breaths, and an increased rate of breathing. In the elderly, confusion may be the most prominent sign.
The typical signs and symptoms in children under five are fever, cough, and fast or difficult breathing. Fever is not very specific, as it occurs in many other common illnesses, may be absent in those with severe disease, malnutrition or in the elderly. In addition, a cough is frequently absent in children less than 2 months old. More severe signs and symptoms in children may include blue-tinged skin, unwillingness to drink, convulsions, ongoing vomiting, extremes of temperature, or a decreased level of consciousness.
Bacterial and viral cases of pneumonia usually present with similar symptoms. Some causes are associated with classic, but non-specific, clinical characteristics. Pneumonia caused by "Legionella" may occur with abdominal pain, diarrhea, or confusion, while pneumonia caused by "Streptococcus pneumoniae" is associated with rusty colored sputum, and pneumonia caused by "Klebsiella" may have bloody sputum often described as "currant jelly". Bloody sputum (known as hemoptysis) may also occur with tuberculosis, Gram-negative pneumonia, and lung abscesses as well as more commonly with acute bronchitis. "Mycoplasma" pneumonia may occur in association with swelling of the lymph nodes in the neck, joint pain, or a middle ear infection. Viral pneumonia presents more commonly with wheezing than does bacterial pneumonia. Pneumonia was historically divided into "typical" and "atypical" based on the belief that the presentation predicted the underlying cause. However, evidence has not supported this distinction, thus it is no longer emphasized.
Pneumonia occurs in a variety of situations and treatment must vary according to the situation. It is classified as either community or hospital acquired depending on where the patient contracted the infection. It is life-threatening in the elderly or those who are immunocompromised. The most common treatment is antibiotics and these vary in their adverse effects and their effectiveness. Pneumonia is also the leading cause of death in children less than five years of age in low income countries. The most common cause of pneumonia is pneumococcal bacteria, "Streptococcus pneumoniae" accounts for 2/3 of bacteremic pneumonias. This is a dangerous type of lung infection with a mortality rate of around 25%.
For optimal management of a pneumonia patient, the following must be assessed: pneumonia severity (including treatment location, e.g., home, hospital or intensive care), identification of causative organism, analgesia of chest pain, the need for supplemental oxygen, physiotherapy, hydration, bronchodilators and possible complications of emphysema or lung abscess.
Bronchiolitis is blockage of the small airway in the lungs due to a viral infection. It usually only occurs in children less than two years of age. Symptoms may include fever, cough, runny nose, wheezing, and breathing problems. More severe cases may be associated with nasal flaring, grunting, or the skin between the ribs pulling in with breathing. If the child has not been able to feed properly, signs of dehydration may be present.
Bronchiolitis is usually the result of infection by respiratory syncytial virus (72% of cases) or human rhinovirus (26% of cases). Diagnosis is generally based on symptoms. Tests such as a chest X-ray or viral testing are not routinely needed. Urine testing may be considered in those with a fever.
There is no specific treatment. Supportive care at home is generally sufficient. Occasionally hospital admission for oxygen, support with feeding, or intravenous fluids is required. Evidence for antibiotics, antivirals, bronchodilators, or nebulized hypertonic saline or epinephrine is either unclear or not supportive.
About 10% to 30% of children under the age of two years are affected by bronchiolitis at some point in time. It more commonly occurs in the winter in the Northern hemisphere. The risk of death among those who are admitted to hospital is about 1%. Outbreaks of the condition were first described in the 1940s.
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease was first identified in December 2019 in Wuhan, the capital of China's Hubei province, and has since spread globally, resulting in the ongoing 2019–20 coronavirus pandemic. Common symptoms include fever, cough, and shortness of breath. Other symptoms may include fatigue, muscle pain, diarrhea, sore throat, loss of smell, and abdominal pain. The time from exposure to onset of symptoms is typically around five days but may range from two to fourteen days. While the majority of cases result in mild symptoms, some progress to viral pneumonia and multi-organ failure. As of 17 April 2020, more than 2.23 million cases have been reported across 210 countries and territories, resulting in more than 153,000 deaths. More than 567,000 people have recovered.
The virus is primarily spread between people during close contact, often via small droplets produced by coughing, sneezing, or talking. While these droplets are produced when breathing out, they usually fall to the ground or onto surfaces rather than being infectious over long distances. People may also become infected by touching a contaminated surface and then touching their eyes, nose, or mouth. The virus can survive on surfaces up to 72 hours. It is most contagious during the first three days after the onset of symptoms, although spread may be possible before symptoms appear and in later stages of the disease.
The standard method of diagnosis is by real-time reverse transcription polymerase chain reaction (rRT-PCR) from a nasopharyngeal swab. Chest CT imaging may also be helpful for diagnosis in individuals where there is a high suspicion of infection based on symptoms and risk factors; however, it is not recommended for routine screening.
Recommended measures to prevent infection include frequent hand washing, maintaining physical distance from others (especially from those with symptoms), covering coughs and sneezes with a tissue or inner elbow, and keeping unwashed hands away from the face. The use of masks is recommended for those who suspect they have the virus and their caregivers. Recommendations for mask use by the general public vary, with some authorities recommending against their use, some recommending their use, and others requiring their use. Currently, there is no vaccine or specific antiviral treatment for COVID-19. Management involves treatment of symptoms, supportive care, isolation, and experimental measures.
The World Health Organization (WHO) declared the 2019–20 coronavirus outbreak a Public Health Emergency of International Concern (PHEIC) on 30 January 2020 and a pandemic on 11 March 2020. Local transmission of the disease has been recorded in most countries across all six WHO regions.
New or progressive infiltrate on the chest X-ray with one of the following:
- Fever > 37.8 °C (100 °F)
- Purulent sputum
- Leukocytosis > 10,000 cells/μl
In an elderly person, the first sign of hospital-acquired pneumonia may be mental changes or confusion.
Other symptoms may include:
- A cough with greenish or pus-like phlegm (sputum)
- Fever and chills
- General discomfort, uneasiness, or ill feeling (malaise)
- Loss of appetite
- Nausea and vomiting
- Sharp chest pain that gets worse with deep breathing or coughing
- Shortness of breath
- Decreased blood pressure and fast heart rate
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus strain that causes coronavirus disease 2019 (COVID-19), a respiratory illness. It is colloquially known as the coronavirus, and was previously referred to by its provisional name 2019 novel coronavirus (2019-nCoV). SARS-CoV-2 is a positive-sense single-stranded RNA virus. It is contagious in humans, and the World Health Organization (WHO) has designated the ongoing pandemic of COVID-19 a Public Health Emergency of International Concern. Because the strain was first discovered in Wuhan, China, it is sometimes referred to as "Wuhan virus" or "Wuhan coronavirus". Since the WHO discourages the use of names based on locations such as MERS, and to avoid confusion with the disease SARS, it sometimes refers to SARS-CoV-2 as "the COVID-19 virus" in public health communications. The general public frequently calls both SARS-CoV-2 and the disease it causes "coronavirus", but scientists typically use more precise terminology.
Taxonomically, SARS-CoV-2 is a strain of Severe acute respiratory syndrome-related coronavirus (SARSr-CoV). It is believed to have zoonotic origins and has close genetic similarity to bat coronaviruses, suggesting it emerged from a bat-borne virus. An intermediate animal reservoir such as a pangolin is also thought to be involved in its introduction to humans. The virus shows little genetic diversity, indicating that the spillover event introducing SARS-CoV-2 to humans is likely to have occurred in late 2019.
Epidemiological studies estimate each infection results in 1.4 to 3.9 new ones when no members of the community are immune and no preventive measures taken. The virus is primarily spread between people through close contact and via respiratory droplets produced from coughs or sneezes. It mainly enters human cells by binding to the receptor angiotensin converting enzyme 2 (ACE2).
The length of time between exposure to the bacteria and the appearance of symptoms is generally two to ten days, but can rarely extend to as much as 20 days. For the general population, among those exposed between 0.1 and 5% develop disease, while among those in hospital between 0.4 and 14% develop disease.
Those with Legionnaires' disease usually have fever, chills, and a cough, which may be dry or may produce sputum. Almost all with Legionnaires' experience fever, while approximately half have cough with sputum, and one third cough up blood or bloody sputum. Some also have muscle aches, headache, tiredness, loss of appetite, loss of coordination (ataxia), chest pain, or diarrhea and vomiting. Up to half of those with Legionnaires' have gastrointestinal symptoms, and almost half have neurological symptoms, including confusion and impaired cognition. "Relative bradycardia" may also be present, which is low or low-normal heart rate despite the presence of a fever.
Laboratory tests may show that kidney functions, liver functions and electrolyte levels are abnormal, which may include low sodium in the blood. Chest X-rays often show pneumonia with consolidation in the bottom portion of both lungs. It is difficult to distinguish Legionnaires' disease from other types of pneumonia by symptoms or radiologic findings alone; other tests are required for definitive diagnosis.
Persons with Pontiac fever experience fever and muscle aches without pneumonia. They generally recover in two to five days without treatment. For Pontiac fever the time between exposure and symptoms is generally a few hours to two days.
Early reports compared the virus to severe acute respiratory syndrome (SARS), and it has been referred to as Saudi Arabia's SARS-like virus. The first person, in June 2012, had a "seven-day history of fever, cough, expectoration, and shortness of breath." One review of 47 laboratory confirmed cases in Saudi Arabia gave the most common presenting symptoms as fever in 98%, cough in 83%, shortness of breath in 72% and myalgia in 32% of people. There were also frequent gastrointestinal symptoms with diarrhea in 26%, vomiting in 21%, abdominal pain in 17% of people. 72% of people required mechanical ventilation. There were also 3.3 males for every female. One study of a hospital-based outbreak of MERS had an estimated incubation period of 5.5 days (95% confidence interval 1.9 to 14.7 days). MERS can range from asymptomatic disease to severe pneumonia leading to acute respiratory distress syndrome (ARDS). Kidney failure, disseminated intravascular coagulation (DIC), and pericarditis have also been reported.
Pneumonia is typically diagnosed based on a combination of physical signs and a chest X-ray. However, the underlying cause can be difficult to confirm, as there is no definitive test able to distinguish between bacterial and non-bacterial origin.
The World Health Organization has defined pneumonia in children clinically based on either a cough or difficulty breathing and a rapid respiratory rate, chest indrawing, or a decreased level of consciousness. A rapid respiratory rate is defined as greater than 60 breaths per minute in children under 2 months old, greater than 50 breaths per minute in children 2 months to 1 year old, or greater than 40 breaths per minute in children 1 to 5 years old. In children, low oxygen levels and lower chest indrawing are more sensitive than hearing chest crackles with a stethoscope or increased respiratory rate. Grunting and nasal flaring may be other useful signs in children less than five years old.
In general, in adults, investigations are not needed in mild cases. There is a very low risk of pneumonia if all vital signs and auscultation are normal. In persons requiring hospitalization, pulse oximetry, chest radiography and blood tests—including a complete blood count, serum electrolytes, C-reactive protein level, and possibly liver function tests—are recommended. Procalcitonin may help determine the cause and support who should receive antibiotics.
The diagnosis of influenza-like illness can be made based on the signs and symptoms; however, confirmation of an influenza infection requires testing. Thus, treatment is frequently based on the presence of influenza in the community or a rapid influenza test.
Signs and symptoms of PCP include fever, non-productive cough (because sputum is too viscous to become productive), shortness of breath (especially on exertion), weight loss, and night sweats. There is usually not a large amount of sputum with PCP unless the patient has an additional bacterial infection. The fungus can invade other visceral organs (such as the liver, spleen, and kidney), but only in a minority of cases.
Pneumothorax is a well-known complication of PCP. An acute history of chest pain with breathlessness and diminished breath sounds is typical of pneumothorax.