Persius/hicric huggingface dataset:
Sandbox: esophageal candida

# Overview
Esophageal candidiasis is an opportunistic infection of the esophagus by Candida albicans.  The disease occurs in patients in immunocompromised states, including post-chemotherapy and in AIDS.  It is also known as candidal esophagitis or monilial esophagitis

# Clinical presentation
Patients with esophageal candidiasis present with odynophagia, or painful swallowing.  Longstanding esophageal candidiasis can result in weight loss.  There is often concomittant thrush.
Some patients present with esophageal candidiasis as a first presentation of systemic candidiasis

# Diagnostic testing
Patients where esophageal candidiasis is suspected should undergo esophagogastroduodenoscopy if it is safe to do so.  Endoscopy often reveals classic diffuse raised plaques that characteristically can be removed from the mucosa by the endsocope.  Brushing or biopsy of the plaques shows hyphae that are characteristic of Candida species.

# Therapy
A variety of medications may be used to treat esophageal candidiasis.  They include:
- nystatin
- oral triazoles, such as fluconazole
- caspofungin, used in refractory or systemic cases
- amphotericin, used in refractory or systemic cases
Sandbox:diagnostic criteria

# Overview
- The diagnosis of  is made when at least  of the following  diagnostic criteria are met: , , , and .
- The diagnosis of  is based on the  criteria, which include , , and .
- The diagnosis of  is based on the  definition, which includes , , and .
OR
- There are no established criteria for the diagnosis of .

# Diagnostic Criteria
- The diagnosis of  is made when at least  of the following  diagnostic criteria are met:
- The diagnosis of  is based on the  criteria, which include
- The diagnosis of  is based on the  definition, which includes
OR
- There are no established criteria for the diagnosis of .
Sandbox:differential myxoma
The table below summarizes the findings that differentiate Cardiac Myxoma from other conditions that cause emboli and hemorrhage:
-  Papillary fibroelastoma of the heart  Accessed on November 24,2015
-  Papillary fibroelastoma Wikipedia. Accessed on November 24,2015
-   Lipoma.Radiopedia. Accessed on November 24, 2015
-   Rhabdomyoma. t Wikipedia. Accessed on November 24, 2015
-   Intracardiac thrombi. Radiopedia. Accessed on November 24, 2015
-   Secondary cardiac neoplasm.Radiopedia. Accessed on November 24, 2015
Sandbox ammu WNV blue boxes

# Overview
WNV infection is considered a clinical spectrum. Infection due to WNV may have any of 3 different clinical presentations: Asymptomatic (~70-80%), mild febrile syndrome termed West Nile fever (~20%), and neuroinvasive disease termed West Nile meningitis or encephalitis (<1%). Patients who are suspected to have WNV infection should specifically be inquired about recent mosquito bites.

# History
Patients who are suspected to have West Nile virus infection should be inquired about recent mosquito bites. In addition, important clues in the history include the time of the year, geographical location, recent travel, and outdoor activities. Patients should also be asked about virus-associated symptoms and their progression.

# Symptoms

## Asymptomatic
An asymptomatic course of the disease is observed among approximately 80% of individuals infected with WNV.

## West Nile fever

### Constitutional symptoms
- Fever
- Chills
- Body aches
- Fatigue
- Arthralgia
- Diaphoresis
- Drowsiness
- Anorexia
- Insomnia

### HEENT symptoms
- Headache
- Ocular pain
- Hearing impairment
- Cough

### Gastrointestinal symptoms
- Nausea
- Vomiting
- Diarrhea

### Genitourinary symptoms
- Bladder urgency
- Urinary incontinence

### Cutaneous manifestations
- Macular or papular skin rash on the trunk
- Lymphadenopathy

## Neuroinvasive disease
Neuroinvasive disease is the most severe form of WNV infection. Patients can present with fever associated with a wide range of neurological manifestations, such as flaccid paralysis, symptoms of meningitis or encephelatitis, or a combination of these conditions.

### Constitutional symptoms
- High fever
- Diffuse body aches

### Neurological symptoms
Shown below is a table of the most common neurological symptoms of neuroinvasive WNV disease with their corresponding frequencies.
- Headache
- Photophobia
- Neck stiffness
- Tremor
- Seizure
- Paralysis
- Rash
- Confusion
- Irritability
- Disorientation
- Tremor
- Ataxia
- Bulbar dysfunction
- Focal weakness
- Sensory loss
- Memory loss
- Diplopia
- Cranial nerve palsy
- Lower limb weakness

### Multiorgan involvement
- Chorioretinitis: Very specific for identifying WNV virus infection among patients with high pre-test probability
- Hepatitis
- Myocarditis
- Nephritis
- Pancreatitis
- Splenomegaly
Short stature homeobox gene
The short stature homeobox (SHOX) gene is a gene, located on both the X and Y chromosomes, which is associated with short stature in humans if mutated or present in only one copy (haploinsufficiency).

# Pathology
The gene was first found during a search for the cause of short stature in women with Turner syndrome, in which there is loss of genetic material from the X chromosome, classically by loss of one entire X chromosome.
Since its discovery, the SHOX gene has been found to play a role in idiopathic short stature (short stature of unknown cause without other symptoms), Leri-Weill dyschondrosteosis, and Langer mesomelic dysplasia.
Gene dosage effects of extra copies of SHOX may be a cause of the increased stature seen in other sex chromosome aneuploidy conditions such as 47,XXX, 47,XYY, 47,XXY, 48,XXYY, etc.

# Function
The SHOX gene is a homeobox gene, meaning that it helps regulate development. The SHOX gene is composed of 6 different exons and is located in the pseudoautosomal region (PAR1) of the X chromosome and Y chromosome. Experiments have found similar genes in a variety of animals and insects.
Signal recognition particle
The signal recognition particle (SRP) is an abundant, cytosolic, universally conserved ribonucleoprotein (protein-RNA complex) that recognizes and targets specific proteins to the endoplasmic reticulum in eukaryotes and the plasma membrane in prokaryotes.

# History
The function of SRP was discovered by the study of processed and unprocessed immunoglobulin light chains; newly synthesized proteins in eukaryotes carry N-terminal hydrophobic signal sequences, which are bound by SRP when they emerge from the ribosome.

# Mechanism
In eukaryotes, SRP binds to the signal sequence of a newly synthesized peptide as it emerges from the ribosome.  This binding leads to the slowing of protein synthesis known as "elongation arrest", a conserved function of SRP that facilitates the coupling of the protein translation and the protein translocation processes. SRP then targets this entire complex (the ribosome-nascent chain complex) to the protein-conducting channel, also known as the translocon, in the ER (Endoplasmic reticulum) membrane.  This occurs via the interaction and docking of SRP with its cognate SRP receptor that is located in close proximity to the translocon.
In eukaryotes there are three domains between SRP and its receptor that function in guanosine triphosphate (GTP) binding and hydrolysis.  These are located in two related subunits in the SRP receptor (SR and SR) and the SRP protein SRP54 (known as Ffh in bacteria).  The coordinated binding of GTP by SRP and the SRP receptor has been shown to be a prerequisite for the successful targeting of SRP to the SRP receptor.
Upon docking, the nascent peptide chain is inserted into the translocon channel where it enters into the ER.  Protein synthesis resumes as SRP is released from the ribosome. The SRP-SRP receptor complex dissociates via GTP hydrolysis and the cycle of SRP-mediated protein translocation continues.
Once inside the ER, the signal sequence is cleaved from the core protein by signal peptidase. Signal sequences are therefore not a part of mature proteins.

# Composition
Despite SRP function being analogous in all organisms, its composition varies greatly. The eukaryotic SRP is composed of six distinct polypeptides bound to an RNA molecule (the 7SL RNA), with GTPase activity. The components of the complex are:
- SRP9
- SRP14
- SRP19
- SRP54
- SRP68
- SRP72
- SRP RNA
The prokaryotic SRP is composed of one polypeptide bound to an RNA molecule (the 4.5S RNA), with GTPase activity. The components of the complex are:
- Ffh
- 4.5S RNA
Ffh is the structural and functional homolog of the SRP54 protein in eukaryotes.  The 4.5S RNA shares sequence and structural homology with one domain of the larger 7S RNA.
- SRP19-7S.S SRP RNA complex from M. jannaschii
SRP19-7S.S SRP RNA complex from M. jannaschii
- S-domain of human SRP
S-domain of human SRP

# Autoantibodies
Anti-signal recognition particle antibodies are mainly associated with, but are not very specific for, polymyositis. For individuals with polymyositis, the presence of anti-SRP antibodies are associated with more prominent muscle weakness and atrophy.
Skeletonization (forensics)

# Overview
In forensics, skeletonization refers to the complete decomposition of the non-bony tissues of a corpse, leading to a bare skeleton. In a temperate climate, it usually requires three months to several years for a body to completely decompose into a skeleton, depending on factors such as temperature, presence of insects, and submergence in a substrate such as water. In the tropics, skeletonization can occur in weeks, while in the Andes Mountains or tundra, skeletonization will never occur if subzero temperatures persist.
The rate of skeletonization and the present condition of the corpse can be used to determine the time of death.
After skeletonization has occurred, the skeleton of mid to large size mammals such as humans takes about twenty years under optimal conditions to be completely dissolved by acids in the soil leaving no trace of the organism. In neutral pH soil or sand, the skeleton will persist for at least several thousand years before it finally disintegrates. Infrequently, however, the skeleton can undergo fossilization, leaving an impression of the bone that can persist for millions of years.
Small Nucleolar RNA SNORD64
SNORD64 (also known as HBII-13)  is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifiying RNA is located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
SNORD64 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.
snoRNA HBII-13 is expressed mainly in the tissues of brain, but is also in the lungs, the kidneys and muscle  however HBII-13 has no identified target RNA . The HBII-13 gene is located in in a 460 kb intron of the large, paternally expressed, transcription unit (SNURF-SNRNP-UBE3A AS) along with several other snoRNAs HBII-436, HBII-437, HBII-438A/B and the clusters of HBII-85, HBII-52 
. This host gene is an antisense transcript to maternally expressed UBE3A gene.
Small nucleolar RNA SNORD15
SNORD15 (also known as U15)  is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
U15 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs. U15 is predicted to guide the 2'O-ribose methylation of 28S ribosomal RNA (rRNA) residue A3764 .
In humans there are two closely related copies of the U15 snoRNA (called SNORD15A and SNORD15B). They are both encoded in the introns of the ribosomal protein S3 . In Xenopus laevis it is located within the introns of ribosomal protein S1 
snoR75 from Arabidopsis thaliana and homologues in rice Oryza sativa and other plants are alternatively known as U15, and, despite a significantly shorter sequence length, appear to be related .
Small nucleolar RNA SNORD16
snoRNA U16 (also known as SNORD16)  is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifiying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
snoRNA U16 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.
U81 i spredicted to guide the 2'O-ribose methylation of 18S ribosomal RNA (rRNA) residue A484 and is encoded within an intron of the gene for ribosomal proteins L1 in animals .  This snoRNA was independently named MBII-98 in mouse .
Small nucleolar RNA SNORD18
SNORD18 (also known as U18)  is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifiying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
U18 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.
In humans and Xenopus laevis there three closely related copies of U18 (called U18A, U18B, U18C) which are encoded in introns of ribosomal protein L1. . In yeast U18 is located in the introns of Elongation Factor 1 beta (EF1-beta).  Related snoRNAs in Arabidopsis thaliana and rice Oryza sativa have been named R63 and Z106 respectively. Factors involved in the processing of the intronic snoRNA have recently been elucidated .
Small nucleolar RNA SNORD19
SNORD19 (also known as HBII-108)  is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifiying RNA is located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
SNORD19 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.
HBII-108 is the human orthologue of the mouse MBII-108 
 and is predicted to guide 2'O-ribose methylation of the small subunit (SSU) ribosomal RNA (rRNA),  18S, on position G683 . In the human genome snoRNA HBII-108 is located in the introns of the gene nucleostemin (NS), along with another snoRNA HBII-210.
Small nucleolar RNA SNORD22
snoRNA U22 (also known as SNORD22)  is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifiying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
U22 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs .
In the human genome snoRNA U22 is encoded along with seven other snoRNAs within the introns of the same gene (called UHG for U22 host gene) in mammals . U22 has has also been indentified in the amphibian Xenopus laevis U22 is predicted to guide the 2'-O-ribose methylation guide for ribosomal RNA
Small nucleolar RNA SNORD25
snoRNA U25 (also known as SNORD25) is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifiying RNA is located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
U25 is a member of the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.
U25 is found in gene clusters in plants  and within the U22 snoRNA host gene (UHG) in mammals .  U25 is thought to as a 2'-O-ribose methylation guide for ribosomal RNA   This RNA has also been named snoRNA R73 in some plants.
Small nucleolar RNA SNORD29
SNORD29 (also known as U29)  is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifiying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
U29 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.
In humans U29 and several other snoRNAs (U22 and U25-U31) are located in the introns of the same gene (called UHG for U22 host gene) . U29 is proposed to guide the 2'O-ribose methylation of 28S ribosomal RNA (rRNA) residue A4493  .
Small nucleolar RNA SNORD34
snoRNA U34 (also known as SNORD34)  is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifiying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
snoRNA U34 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.
snoRNA U34 was initially charcterised by a computational screen and in the human genome is encoded within intron 5 of the gene for ribosomal protein L13a . U34 is predicted to guide site-specific 2'-O-methylation of 25S rRNAs. Unusually for a snoRNA although the selection of the target nucleotide requires the antisense element and the conserved box D or D' of the snoRNA, in the case of U34 snoRNP the methyltransferase activity is thought to reside in one of the protein components.  U34 snoRNA has homologues in mouse, Arabidopsis (annotated as snoR4) and in several copies in rice (alternatively named snoZ181) .
Small nucleolar RNA SNORD36
snoRNA U36 (also known as SNORD36) is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifiying RNA is located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
snoRNA U36 is a member of the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.
U36 is encoded within the intron of ribosomal protein rpL7a, and has two regions of complementarity to 18S and 28S ribosomal RNA.  This complementarity suggests that U36 acts as a 2'-O-ribose methylation guide .  This snoRNA is also related to other snoRNAs (snoR47 and Z100) identified in the rice plant Oryza sativa .
Small nucleolar RNA SNORD37
SNORD37 (also known as U37)  is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifiying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
snoRNA U37 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.
This snoRNA was originally identified by computational screening of vertebrate genomes for conserved C/D box motifs within  intronic regions and expression experimentally verified by northern blotting . The mouse orthologue was identified .
SNORD37 is predicted to guide the 2'O-ribose methylation of the 28S ribosomal RNA (rRNA) at residue A3697 .
Small nucleolar RNA SNORD51
SNORD51 (also known as U51)  is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifiying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
U51 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.
This snoRNA was originally cloned from HeLa cells and expression verified by northern blotting. It is predicted to guide 2'O-ribose methylation of ribosomal RNA (rRNA) 28S residue A1511. In the human genome it is located in the introns of the same gene as the H/ACA box snoRNA ACA41.
Small nucleolar RNA SNORD66
SNORD66 (also known as HBII-142)  is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifiying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
HBII-142 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.
HBII-142 is the human orthologue of the mouse MBII-142 snoRNA  and is predicted to guide 2'O-ribose methylation of 18S ribosomal RNA (rRNA) at residue C1272 .
Small nucleolar RNA SNORD67
SNORD67 (also known as HBII-166)  is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifiying RNA is located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
HBII-166 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.
snoRNA HBII-166 is the human orthologue of the mouse MBII-166  and is predicted to guide 2'O-ribose methylation of spliceosomal RNA U6 at residue C60 .