Persius/hicric huggingface dataset:
Roderic D.M. Page
Professor Roderic Dugald Morton Page (born 1962) is an evolutionary biologist at the University of Glasgow, Scotland, and the author of several books. He is currently professor at the University of Glasgow and the editor of the journal Systematic Biology. His main interests are in phylogenetics, evolutionary biology and bioinformatics. He is known for his work on cospeciation and in particular the development of bioinformatic software such as TreeMap, RadCon, and TreeView.

# Bibliography
- Page, R.D.M. (1990). Panbiogeography : a cladistic approach. Thesis (PhD in Zoology) University of Auckland.
- Page, R.D.M. and Holmes, E. C. (1998). Molecular Evolution: A phylogenetic approach. Blackwell Scientific, Oxford. ISBN 0865428891
- Page, R.D.M. ed. (2002). Tangled trees: phylogeny, cospeciation and coevolution. University of Chicago Press. ISBN 0-226-64467-7
Round atelectasis

# Overview
The pathogenesis of round atelectasis is not certain, but it is thought to be due to an inflammatory reaction and fibrosis in the superficial layer of the pleura. As the fibrous tissue matures, it contracts, causing pleura to fold into the lung, which in turn causes atelectasis. Round atelectasis is almost always asymptomatic and is detected on chest radiographs obtained for other reasons. A history of asbestos exposure is frequently (in 70% of cases) present. Asbestos-related round atelectasis is also known as asbestos pseudotumor or Blesovsky syndrome. Conditions such as congestive heart failure], pulmonary infarction], Dressler syndrome, parapneumonic effusion, tuberculous effusion, and nonspecific pleurisy can precede round atelectsis formation. Lung cancer] is the main differential diagnosis. After diagnosis, a follow-up CT should be obtained to exclude lung cancer.

## Chest X-ray
- The typical chest radiographic appearance is of a rounded peripheral "mass" with or without lung distortion.
- Pleural thickening is usually seen.

## CT
- The CT features are:
- A round or oval mass that abuts the pleura
Has sharp lung borders
Has a fuzzy border which projects to the hila (Origin of Comet tail sign)
a "comet tail" of bronchovascular structures going into the mass (Comet tail sign).
Thickening of the adjacent pleura.
- A round or oval mass that abuts the pleura
- Has sharp lung borders
- Has a fuzzy border which projects to the hila (Origin of Comet tail sign)
- a "comet tail" of bronchovascular structures going into the mass (Comet tail sign).
- Thickening of the adjacent pleura.
- Volume loss is often, but not invariably, apparent.
Rubrospinal tract

# Overview
The rubrospinal tract is a part of the nervous system. It is a part of the indirect extra-pyramidal tract

# Function
It is an alternative route for the mediation of voluntary movement.  It is responsible for large muscle movement such as the arms and the legs as well as for fine motor control. It facilitates the extension and inhibits the flexion in the upper extremities.
It is small and rudimentary in humans.  In some other primates, however, experiments have shown that over time, the rubrospinal tract can assume almost all the duties of the corticospinal tract when the corticospinal tract is lesioned.

# Path
In the midbrain, it originates in the red nucleus, crosses to the other side of the midbrain, and descends in the lateral part of the brainstem tegmentum.
In the spinal cord, it travels through the lateral funiculus of the spinal cord in the company with the lateral corticospinal tract.
Safety in numbers
Safety in numbers is the hypothesis that, by being part of a large physical group or mass, an individual is proportionally less likely to be the victim of a mishap, accident, or other bad event.
Evidence often advanced for this position includes the flocking of birds and shoaling of fish. In both of these instances, by being part of a large group, individuals face less risk of falling victim to predators than they would if traveling alone.
Safety in numbers is also used to describe the theory that a motorist is less likely to collide with a pedestrian or bicyclist if more people walk or bicycle. A Public Health Consultant has concluded that the theory is correct, based on statistical analysis of collision data. A Cycling Transportation Engineer has disputed that conclusion, writing that the data used is insufficient to demonstrate that there is  a cause-and-effect relationship.
After cycling was promoted in Finland, the number of trips increased by 72% and there was a 75% drop in cyclists deaths. Motor vehicle traffic decreased by 16%, bicycle use increased by 28% and cyclist injuries decreased by 20% after the London Congestion Charge began. 
While such data shows a degree of  correlation, conclusions of causality may very well be based on a statistically spurious relationship.
Sandbox/equations

# Equations

### Nephrology
- Anion gap = ( + )  ( + )
we can simplify it to: Na-(Cl+HCO3)
(Typically= 122mEq)
- Delta-delta() = anion gap(calculated anion gap-expected)/HCO3(24-measured HCO3)
- Urine anion gap = Urine anion gap is calculated by subtracting the urine concentration of chloride (anions) from the concentrations of sodium plus potassium (cations)= Na+ + K+  Cl
- Calculated osmoles = 2 + /18 + /2.8 ,where  and  are measured in mg/dL.
- Calculated osmolarity= 2 Na + Glucose + Urea (all in mmol/L)
- Osmolal gap= measured osmoles - calculated osmoles
- Estimated creatinine clearance =
- Glomerular filtration rate (GFR) = Urine concentrationUrine flow/Plasma concentration
- Fractional Excretion of sodium =
- Corrected sodium in hyperglycemia = measured Na + 2.4
- Total body water =  0.60  IBW(ideal body weight) ( 0.85 if female and  0.85 if elderly)
- Free water deficit = 0.6 x weight (kg) x 
- Trans-tubular potassium gradient (TTKG) =

### Cardiology
- Mean arterial pressure (MAP) =  + Central venous pressure(CVP)
Or
in mmHg
- Cardiac Index (CI) = Cardiac output(CO)/ Body surface area(BSA)
Or 
(Stroke volumeHeart rate)/Body surface area
in L/min/m2
- Stroke volume (SV) = Cardiac output(CO)/Heart rate(HR)
in mL/contraction
- Stroke volume index (SVI) = Cardiac index (CI)/ Heart rate (HR)
in mL/contraction/m2
- Systemic vascular resistance (SVR) =
in dynessec/cm5
- Pulmonary vascular resistance (PVR) =
in dynessec/cm5
- Cardiac output = Oxygen consumption/
13.6 is equal to (arterial oxygen saturation - mixed venous oxygen)
in L/min
Sandbox/guillermo

# Principles of Eradication Therapy for Helicobacter pylori infection
- Indications for diagnosis and treatment, established:
Active peptic ulcer disease.
Confirmed history of peptic ulcer disease not previously treated for H. pylori.
Gastric MALT lymphoma.
After endoscopic resection of early gastric cancer.
Uninvestigated dyspepsia (review H. pylori prevalence).
- Active peptic ulcer disease.
- Confirmed history of peptic ulcer disease not previously treated for H. pylori.
- Gastric MALT lymphoma.
- After endoscopic resection of early gastric cancer.
- Uninvestigated dyspepsia (review H. pylori prevalence).
- Low clarithromycin resistance areas (<15%):
In areas of low resistance the PPI-clarithromycin-containing triple therapy is recommended as the first-line treatment as well as bismuth-containing quadruple therapy.
In areas of low resistance after failure of a PPI-clarithromycin-containing treatment, either a bismuth-containing quadruple therapy or levofloxacin-containing triple therapy is recommended.
- In areas of low resistance the PPI-clarithromycin-containing triple therapy is recommended as the first-line treatment as well as bismuth-containing quadruple therapy.
- In areas of low resistance after failure of a PPI-clarithromycin-containing treatment, either a bismuth-containing quadruple therapy or levofloxacin-containing triple therapy is recommended.
- High clarithromycin resistance areas (15%):
In areas of high resistance, bismuth-containing quadruple therapy are recommended for first-line treatment.
In areas of high resistance after failure of bismuth containing quadruple therapy, levofloxacin containing triple therapy is recommended.
- In areas of high resistance, bismuth-containing quadruple therapy are recommended for first-line treatment.
- In areas of high resistance after failure of bismuth containing quadruple therapy, levofloxacin containing triple therapy is recommended.
- After failure of second-line treatment, treatment should be guided by antimicrobial susceptibility testing.
- FDA approved first line regimens duration:
Triple therapy: 7 days (10 days if rabeprazole).
Quadruple therapy: 4 weeks.
- Triple therapy: 7 days (10 days if rabeprazole).
- Quadruple therapy: 4 weeks.
- Confirm the eradication of H. pylori infection in patients who have had an H. pylori-associated ulcer or gastric MALT lymphoma or who have undergone resection for early gastric cancer.
- The urea breathing test is the most reliable nonendoscopic test to document eradication of H. pylori infection.
- Testing to prove H. pylori eradication is most accurate if performed at 4 weeks after the completion of eradication therapy.
 There is a reported prevalence of 15% in the Northeast of the US.

# Helicobacter pylori Eradication Therapies
 Click on the following categories to expand treatment regimens.
Sandbox: Maria 15
Synonyms and keywords: HFpEF; Heart Failure with Preserved Ejection Fraction; HFnEF; Heart Failure with a Normal Ejection Fraction; DHF; Diastolic Heart Failure

# Overview

# Historical Perspective
- Heart failure with preserved ejection fraction was first discovered by

# Classification

# Pathophysiology

# Causes
- To see a comprehensive list of all causes of heart failure, please click here

# Epidemiology and Demographics

## Age

## Gender

## Race

# Risk Factors
- Common risk factors in the development of

# Natural History, Complications and Prognosis
- The majority of patients with leukocytosis are initially symptomatic.
- Early clinical features, include:
- Common complications of leukocytosis, include:

# Diagnosis

## Symptoms

## Laboratory Findings
- Laboratory findings consistent with the diagnosis of HFpEF, include:

# Treatment

## Medical Therapy
Sandbox:screening

# Overview

# Screening
- There is insufficient evidence to recommend routine screening for .
OR
- According to the , screening for  is not recommended.
OR
- According to the , screening for  by  is recommended every  among patients with , , and .
Sandbox:skorjian4
- Brain: Pontine Glioma: Gross; fixed tissue, anterior view of brain stem and cerebellum with bosselated tumor adjacent to basilar artery
- Brain: Pontine Glioma: Gross; fixed tissue, sagittal section brain stem and cerebellum
- Brain: Glioma: Gross; fixed tissue, horizontal section brain stem and cerebellum with obvious gelatinous appearing neoplasm a pontine glioma
- Brain: Oligodendroglioma: Gross; natural color, large, well circumscribed lesion in left frontal lobe
- Brain: Glioma: Gross; fixed tissue, horizontal sections brain stem and cerebellum showing large pontine glioma
- Brain: Pontine Glioma and Diffuse Meningeal Gliomatosis: Gross; fixed tissue, view of cerebral hemispheres from inferior with brain stem and cerebellum removed. Pontine asymmetry is easily seen due to low grade astrocytoma and meningeal gliomatosis is easily seen over frontal lobes
- Brain: Pontine Glioma and Diffuse Meningeal Gliomatosis in 7 yo boy: Gross; fixed tissue, view of cerebral hemispheres from vertex meningeal gliomatosis.
- Brain: Pontine Glioma and Diffuse Meningeal Gliomatosis: Gross; in situ dural nodule
Sandbox MEN 2 epi
__NOTOC_

# Overview

# Prevalence
- Worldwide, the prevalence of multiple endocrine neoplasia type 2 is 2.5 per 100,000 persons in 2010.
In United States the prevalence of multiple endocrine neoplasia type 2 is 1 in 30,000 to 50,000 person.
MEN2 has been reported in approximately 500 to 1000 families worldwide.
70-80% of all multiple endocrine neoplasia type 2 cases are MEN type 2A.
- Worldwide, the prevalence of multiple endocrine neoplasia type 2 is 2.5 per 100,000 persons in 2010.
- In United States the prevalence of multiple endocrine neoplasia type 2 is 1 in 30,000 to 50,000 person.
- MEN2 has been reported in approximately 500 to 1000 families worldwide.
- 70-80% of all multiple endocrine neoplasia type 2 cases are MEN type 2A.

# Incidence
- In developed countries, the incidence of (insert disease state here) is _____ per 100,000 persons.
- In developed countries, the incidence of (insert disease state here) is _____ per 100,000 persons.

# Age
- It can be found in all ages.
- MEN 2B manifest in early infancy while MEN 2A and familial medullary thyroid carcinoma is found in adulthood.

# Gender
- The prevalence and incidence of multiple endocrine neoplasia type 2 does not vary by gender.

# Race
- The prevalence of multiple endocrine neoplasia type 2 does not vary by race.

# Developed Countries
- In United States the prevalence of multiple endocrine neoplasia type 2 is 1 in 30,000 to 50,000 person..
Sandbox bookshelf

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Sandbox parminder
- Absence of exocrine tissue with the loss of normal pancreatic architecture
Patients with insulinomas usually develop neuroglycopenic symptoms.  These include recurrent headache, lethargy, diplopia, and blurred vision, particularly with exercise or fasting.  Severe hypoglycemia may result in seizures, coma, and permanent neurological damage.  Symptoms resulting from the catecholaminergic response to hypoglycemia (i.e. tremulousness, palpitations, tachycardia, sweating, hunger, anxiety, nausea) are not as common.  Sudden weight gain (the patient can become massively obese) is sometimes seen. A neater list of symptoms would include:
- Anxiety
- Behavior changes
- Blurred vision
- Confusion
- Convulsions
- Dizziness
- Headache
- Hunger
- Loss of consciousness
- Rapid heart rate
- Sweating
- Tremor
- Weight gain
-  Padidela, R.; Fiest, M.; Arya, V.; Smith, V. V.; Ashworth, M.; Rampling, D.; Newbould, M.; Batra, G.; James, J.; Wright, N. B.; Dunne, M. J.; Clayton, P. E.; Banerjee, I.; Hussain, K. (2014). "Insulinoma in childhood: clinical, radiological, molecular and histological aspects of nine patients". European Journal of Endocrinology. 170 (5): 741747. doi:10.1530/EJE-13-1008. ISSN 0804-4643..mw-parser-output cite.citation{font-style:inherit}.mw-parser-output q{quotes:"\"""\"""'""'"}.mw-parser-output code.cs1-code{color:inherit;background:inherit;border:inherit;padding:inherit}.mw-parser-output .cs1-lock-free a{background:url("")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-lock-limited a,.mw-parser-output .cs1-lock-registration a{background:url("")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-lock-subscription a{background:url("")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration{color:#555}.mw-parser-output .cs1-subscription span,.mw-parser-output .cs1-registration span{border-bottom:1px dotted;cursor:help}.mw-parser-output .cs1-hidden-error{display:none;font-size:100%}.mw-parser-output .cs1-visible-error{display:none;font-size:100%}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration,.mw-parser-output .cs1-format{font-size:95%}.mw-parser-output .cs1-kern-left,.mw-parser-output .cs1-kern-wl-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right,.mw-parser-output .cs1-kern-wl-right{padding-right:0.2em}
-  "Proceedings of the 1991 International Congress of Rhinology. Tokyo, Japan". Rhinol Suppl. 14: 1273. 1992. PMID 1356383.
Sandifer syndrome
Synonyms and keywords: Sandifer's syndrome

# Overview
Sandifer syndrome is a pediatric medical disorder, characterized by gastrointestinal symptoms and associated neurological features. There is a significant correlation between the syndrome and gastro-esophageal reflux disease (GERD); however, it is estimated to occur in less than 1% of children with reflux.  Diagnosis is made on the basis of the association of gastro-esophageal reflux with the characteristic movement disorder.  Early diagnosis is critical, as treatment is simple and leads to prompt resolution of the movement disorder.

# Differential Diagnosis
- Benign infantile spasms
- Epileptic seizures

# Natural History, Complications and Prognosis
Onset is usually confined to infancy and early childhood, with peak prevalence at 1836 months. In rare cases, particularly where the child is severely mentally impaired, onset may extend to adolescence.
Spasms may last for 13 minutes and may occur up to 10 times a day. Ingestion of food is often associated with occurrence of symptoms; this may result in reluctance to feed. Associated symptoms, such as epigastric discomfort, vomiting (which may involve blood) and abnormal eye movements have been reported. Clinical signs may also include anemia.
Sandifer syndrome is not typically life-threatening and the prognosis is typically good.

# Diagnosis

## Symptoms
- Spasmodic torticollis
- Dystonia
- Nodding and rotation of the head
- Neck extension
- Gurgling
- Writhing movements of the limbs
- Severe hypotonia

## Physical Examination
Neurological examination is usually normal.

# Treatment
Successful treatment of the associated underlying disorder, such as GERD or hiatal hernia, may provide relief.
Santalum spicatum
Santalum spicatum, a species known as Australian sandalwood, is a tree native to semi-arid areas of southern and western Australia.  It is traded as sandalwood and its valuable oil has been used as an aromatic, a medicine and a food source. S. spicatum is one of four high value Santalum species occurring in Australia.

# Description
It belongs to the family Santalaceae and is one of four species to occur in Western Australia. It has a similar distribution to quandong (Santalum acuminatum)and is a hemi-parasite requiring macro-nutrients from roots of hosts. It has a shrubby to small tree habit, but can grow to 6 metres and is tolerant of drought and salt.  The  foliage is grey green in colour.   The fruit of S. spicatum is spherical, about 3 cm in diameter and is orange. An edible kernel with a hard shell forms the bulk of the fruit; the shell is smoother than S. acuminatum's deeply pitted surface. Germination occurs during warm and moist conditions. The impact of over cultivation and land clearing for agriculture, since the 1880s, has greatly reduced the range of the species. The oils produced by the tree contain a greater complexity of chemicals, many of which have antimicrobial qualities.

# Commercial use
The harvest and export of S. spicatum has been an important part of the west australian economy, at one time forming more than half of the states revenue. Settlement of the Wheatbelt area was accelerated by the funds generated by 'Sandalwood' found there. Distribution and population of the endemic stands were significantly affected during periods of rural development and  economic downturn.
Research by the Forestry Products Commission (Western Australia), State universities and private industry is being undertaken into the cultivation of the tree and the properties of its wood and nuts.    Replanting has occurred at some properties as a land restoration strategy, a food crop and in the long term for harvest.  Oil valued at $1 000(Au) per kilogram is produced at Mount Romance in Albany, Western Australia.
The area of commercial plantations has risen from 7 to 70 km2 between 2000 and 2006. The export of 2 000 tonnes of sandalwood a year is primarily sourced from plantations.  The harvest of naturally occurring trees is reduced when compared to the industry of the nineteenth century. Exports of over 50 000 tonnes in the last decade were related to agricultural expansion by increased access and harvesters.

## Cultivation
Germination is difficult and may depend on the El Nino cycle. Success has been reported by placing the kernels in moist vermiculite in sealed plastic bags at room temperature. Once germinated, it should be planted next to a (preferably Australian native) seedling, and watered adequately.
Scholars workbook

# Current Project
Category: Oncology
Topics:
- Breast cancer (microchaptered)
- Colorectal cancer (microchaptered)
- Small cell carcinoma of the lung (microchaptered)
- Lung cancer (microchaptered)
- Skin cancer (microchaptered)
- Cervical cancer (microchaptered)
- Prostate cancer (microchaptered)
- Pancreatic cancer (microchaptered)
- Brain cancer  (microchaptered)
- Liver cancer  (microchaptered)
- Leukemia  (microchaptered)
AML
CML
ALL
CLL
HCL
- AML
- CML
- ALL
- CLL
- HCL
- Melanoma (microchaptered)
- Ovarian cancer (microchaptered)
Guidelines Resources:
- American Academy of Family Physicians
- American College of Obstetricians and Gyencologists
- American College of Physicians
- American Society of Internal Medicine
- American Cancer Society
- American Gastroenterological Association
- American Geriatrics Society
- American Medical Association
- American Urological Association
- Canadian Task for Preventative Health Care
- National Institutes of Health
- U.S. Preventative Services Task Force
- Centers for Disease Control
- National Comprehensive Cancer Network

# Plan
- Develop microchapters for each topic.
- We will assess oncology topics by prevalence and hazard ratios.
- Starting with the most prevalent forms, we will pull all current and historically important guidelines documents.
- From there, we will begin with creating a structure for the screening chapter. The purpose of the screening chapter is to describe methods used to search for early asymptomatic disease.
- Why screen? To favorably modify the natural history of the disease, to improve morbidity, to reduce mortality (it is not usually a primary prevention but more often, a secondary prevention)
- What disease are appropriate for screening? Diseases that have serious consequences, diseases that respond better when treatment is given before symptom onset, prevalence of detectable preclinical phase of disease is high in population to be screened
- How do we assess whether a screening test is suitable?
- How do we assess whether a screening program works?
- What is the value of screening for those screened?
Secondary task: Find major clinical trials related to the cancer of interest. Isolate the appendix that contains the participating centers. Create a database of the centers and contact information. Solicit the participation of these centers for authorship on WikiDoc.

# Previous/Completed Projects