Persius/hicric huggingface dataset:
TLX
Nuclear receptor TLX (homologue of the Drosophila tailless gene) also known as NR2E1 (Nuclear receptor subfamily 2 group E member 1) is a protein that in humans is encoded by the NR2E1 gene. TLX is a member of the nuclear receptor family of intracellular transcription factors.

# Function
TLX regulates the expression of another nuclear receptor, RAR.
TLX also is essential for normal brain-eye coordination and appears to play a role in control of aggressive behavior.
Adult neural stem cells are nuclear receptor TLX-positive and TLX expression in these cells is crucial in maintaining their undifferentiated state. Furthermore, TLX regulates adult neural stem cell proliferation. Removal of TLX from the adult mouse brain resulted in a reduction of stem cell proliferation and spatial learning.
Tlx-positive cells of the subventricular zone of adult mouse brain are self-renewing stem cells. Mutation of the Tlx gene in adult mouse brain leads to complete loss of neurogenesis in the subventricular zone. Tlx is also required for transition from radial glial cells to astrocyte-like neural stem cells.
UXT
Protein UXT (Ubiquitously eXpressed Transcript protein) also known as androgen receptor trapped clone 27 (ART-27) protein is a protein that in humans is encoded by the UXT gene.

# Function
UXT interacts with the N-terminus of the androgen receptor and plays a role in facilitating receptor-induced transcriptional activation. It is also likely to be involved in tumorigenesis as it is abundantly expressed in tumor tissues. This gene is part of a gene cluster on chromosome Xp11.23. Alternative splicing results in 2 transcript variants encoding different isoforms.
Transcript variant 2 is 575 bp in length, and it codes for a polypeptide sequence that is 157 amino acids long (~ 18 kDa).  It has been shown to interact with two AR N-terminal activation domains that are both required for full transcriptional activation. In addition, it is largely localized to the nucleus and is highly expressed in human prostate epithelial cells as well as breast tissues. ART-27 likely serves to link AR to a larger transcription factor complex as evidenced by its association with a number of proteins including RNA pol II subunit 5, a pair of prefoldin -subunits, and TATA-binding protein-interacting proteins. It also shows homology to prefoldins which are small molecular weight proteins that assemble into molecular chaperone complexes to affect protein folding.
ART-27 is shown to be subject to both cell type and developmental regulation in humans.  Its expression is associated with an abundance of differentiated prostate epithelial cells, and regulated expression in prostate cancer cells results in decreased cell proliferation.  Significantly, because decreased levels of ART-27 are consistently found in prostate cancer cells, it likely plays a role in promoting epithelial differentiation via suppression of proliferative pathways. More recent studies have more definitively identified ART-27 as a corepressor of AR. The fact that the increase in gene transcription exhibited upon ART-27 depletion requires the presence of AR implies that it specifically functions as a corepressor of this receptor.  Despite the lack of information regarding its mechanisms of suppression, ART-27 likely plays multiple roles that inhibit AR-mediated transcription.  In the absence of androgens, ART-27 may bind the AR N terminus and thereby prevent AR-dependent activation of genes involved in cell proliferation.  Other mechanisms may include recruitment of ART-27 to AREs or inhibition of histone methylation which otherwise allows for increased transcription of target genes.

# Interactions
UXT has been shown to interact with Androgen receptor.
YY1
YY1 (Yin Yang 1) is a transcriptional repressor protein in humans that is encoded by the YY1 gene.

# Function
YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. Hence, the YY in the name stands for "yin-yang." YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1. YY1 promotes enhancer-promoter chromatin loops by forming dimers and promoting DNA interactions. Its disregulation disrupts enhancer-promoter loops and gene expression.

# Clinical significance
YY1 heterozygous deletions, missense, and nonsense mutations cause Gabriele-DeVries syndrome (GADEVS) , an autosomal dominant neurodevelopmental disorder  characterized by intellectual disability, dysmorphic facial features, feeding problems, intrauterine growth restriction, variable cognitive impairment, behavioral problems and other congenital malformations. It is available a website to share and collect clinical information between clinical doctors and families of mutated indididuals. 

# Interactions
YY1 has been shown to interact with:
- ATF6,
- EP300,
- FKBP3,
- HDAC3,
- Histone deacetylase 2,
- Myc,
- NOTCH1,
- RYBP, and
- SAP30.
- Seryl-tRNA Synthetase.
ZP2
Zona pellucida sperm-binding protein 2 is a protein that in humans is encoded by the ZP2 gene.

# Function
The zona pellucida is an extracellular matrix that surrounds the oocyte and early embryo. It is composed primarily of three (mouse) or four (human) glycoproteins (ZP1-4) with various functions during fertilization and preimplantation development. The protein encoded by this gene is a structural component of the zona pellucida and functions in secondary binding and penetration of acrosome-reacted spermatozoa. The nascent protein contains a N-terminal signal peptide sequence, a conserved ZP domain, a consensus furin cleavage site, and a C-terminal transmembrane domain. It is hypothesized that furin cleavage results in release of the mature protein from the plasma membrane for subsequent incorporation into the zona pellucida matrix. However, the requirement for furin cleavage in this process remains controversial based on mouse studies.
The sperm-binding domain on the ZP2 protein is necessary in both humans and mice for oocyte-sperm recognition and penetration of the zona pellucida. It is also responsible for the primary block to polyspermy in mammals.  The oocyte has cortical granules peripherally located under the cortex that contain a proteolytic protein called ovastacin. After the sperm binds to ZP2, the cortical granules are exocytosed releasing ovastacin into the perivitelline space.  Ovastacin cleaves ZP2 at the N terminus, preventing more sperm from binding and penetrating the oocyte, thus hardening the zona pellucida. Ovastacin is only found in oocytes, and is part of the astacin family of metalloendoproteases. Female mice engineered without ovastacin showed that ZP2 was not cleaved after fertilization.

# 3D structure
The crystal structure of the sperm-binding domain of ZP2 at 0.95 A resolution (PDB: 5II6) showed that is shares the same ZP-N fold first identified in structures of ZP3 (PDB: 3D4C, 3D4G, 3EF7, 3NK3, 3NK4). This provided experimental evidence for the suggestion that the N-terminal region of ZP2 consists of three ZP-N repeats  and revealed that - despite insignificant sequence identity - ZP2 is structurally similar to VERL, the vitelline envelope receptor for egg lysin of the mollusk abalone (PDB: 5II4, 5II5, 5MR2, 5IIC, 5IIA, 5IIB, 5MR3). This established a link between invertebrate and vertebrate fertilization by suggesting that, despite being separated by 600 million years of evolution, mollusk and human use a common protein fold to interact with sperm.
ZP3
Zona pellucida sperm-binding protein 3, also known as zona pellucida glycoprotein 3 (Zp-3) or the sperm receptor, is a ZP module-containing protein that in humans is encoded by the ZP3 gene. ZP3 is the receptor in the zona pellucida which binds sperm at the beginning of fertilization.

# Function
The zona pellucida (ZP) is a specialized extracellular matrix that surrounds the oocyte and early embryo. It is composed of three or four glycoproteins (ZP1-4) with various functions during oogenesis, fertilization and preimplantation development. The protein encoded by this gene is a major structural component of the ZP and functions in primary binding and stimulation of the sperm acrosome reaction. The nascent protein contains a N-terminal signal peptide sequence, a conserved "ZP domain" module, a consensus furin cleavage site (CFCS), a polymerization-blocking external hydrophobic patch (EHP), and a C-terminal transmembrane domain. Cleavage at the CFCS separates the mature protein from the EHP, allowing it to incorporate into nascent ZP filaments. A variation in the last exon of this gene has previously served as the basis for an additional ZP3 locus; however, sequence and literature review reveals that there is only one full-length ZP3 locus in the human genome. Another locus encoding a bipartite transcript designated POMZP3 contains a duplication of the last four exons of ZP3, including the above described variation, and maps closely to this gene.

# 3D Structure
X-ray crystallographic studies of the N-terminal half of mammalian ZP3 (PDB: 3D4C, 3D4G, 3EF7) as well as its full-length avian homolog (PDB: 3NK3, 3NK4) revealed that the protein's ZP module consists of two immunoglobulin-like domains, ZP-N and ZP-C. The latter, which contains EHP as well as a ZP3-specific subdomain, interacts with the ZP-N domain of a second molecule to generate an antiparallel homodimeric arrangement required for protein secretion.
ZP4
Zona pellucida sperm-binding protein 4, ZP-4 or avilesine, named after its discoverer Manuel Aviles Sanchezis a protein that in humans is encoded by the ZP4 gene.

# Function
The zona pellucida is an extracellular matrix that surrounds the oocyte and early embryo. It is composed primarily of three or four glycoproteins with various functions during fertilization and preimplantation development. The nascent protein contains a N-terminal signal peptide sequence, a conserved zona pellucida-like domain, a consensus furin cleavage site, and a C-terminal transmembrane domain. It is hypothesized that furin cleavage results in release of the mature protein from the plasma membrane for subsequent incorporation into the zona pellucida matrix. However, the requirement for furin cleavage in this process remains controversial based on mouse studies.
Previously, this gene has been referred to as ZP1 or ZPB and thought to have similar functions as mouse Zp1. However, a human gene with higher similarity and chromosomal synteny to mouse Zp1 has been assigned the symbol ZP1 and this gene has been assigned the symbol ZP4.
Rb
RB or Rb may stand for:
- the chemical element Rubidium
- The  Nissan RB engine
- the IATA code for Syrian Arab Airlines
- the Retinoblastoma protein, found mutated in many cancers, including retinoblastoma cancer
- an abbreviation for retinoblastoma, a cancer of the eye
- RB, the name used for a series of buses manufactured by Hyundai Motor Company
- an abbreviation for right back, a defensive position in football (soccer)
- an abbreviation for running back, an offensive position in football (American)
- Radio Bremen, a German broadcasting station in Bremen
- re-entry body (US Navy term for re-entry vehicle, rv)
- Rehoboth Beach, Delaware
- Road bike
- The Ruby programming language's typical filename extension, .rb
- .rb is also the extension associated with Rocket Ebook files.
- Rolls-Barnoldswick, one of the design and production sites for Rolls-Royce jet engines
- Rafael Benitez Liverpool manager
- Rancho Bernardo, a community in northern San Diego
de:RB
ko:RB
it:RB
no:RB
ksh:RB (Watt e datt?)
sl:RB
fi:Rb
sv:RB
SB

# Curators
Anyone should feel free to add themselves as a curator for this consensus protocol.  You do not need to be a curator in order to contribute.  The OpenWetWare community is currently discussing the idea of protocol curators.  Please contribute.

# Abstract
SB (Sodium Borate or Sodium Boric Acid) buffer is a agarose gel electropheresis buffer for DNA gels. It has low conductivity and allows for less heat buildup and thus higher voltage and faster runs.

## Reagents
- Sodium Borate decahydrate (Borax)
- Boric Acid
- dH2O

# Procedure
A simple version of this buffer can be easily made as a 20X (100 mM) concentrate.
- 38.17 g Sodium Borate decahydrate
- 33 g Boric Acid
- Bring to 1L with dH2O
- Dilute to 1X and use to make gel and running buffer.

# Troubleshooting
There are some caveats here. Loading DNA that is in a high-salt solution (some DNA ladders, loading dyes, or restriction enzyme buffers) can increase the local conductivity around the sample and change its running characteristics - meaning that samples in different buffers won't always run at the same speed. The quickest solution here is actually to dilute the sample to the largest volume that you can load in the well.
In addition, one should minimize the amount of indicator dye in the loading dye, as this is a salt and contributes significantly to this problem. Using a fainter dye helps to increase the resolution of these gels.

# Notes
It should be noted that there are several other "next-gen" electropheresis buffers, notably LA - Lithium acetate, which is touted as being superior in many respects to SB.
WD
What are you looking for?
- Warty dyskeratoma,  a benign skin condition characterized by epidermal proliferation
- WDR77, a human gene that encodes WD repeat-containing protein 77
- Wilderness diarrhea, another name for traveler's diarrhea (enteric bacterial, viral, or parasitic infection common among travelers and individuals exposed to contaminated food or drinking water)
- Wilson's disease,  an inherited disorder characterized by increased copper concentrations in the liver, brain, and other organs
CDER Product-Specific Guidances Withdrawn Listing 
 Updated April 10th, 2023 
 
Date PSG Posted or  Federal Register Notice / 
Active Ingredient  Type of Guidance  Route and Dosage Form  RLD 
Revised  Withdrawal Date 
BUTENAFINE 
Draft  Topical Cream  021408  03/01/2012  02/01/2015 
HYDROCHLORIDE 
HYDROXYPROGESTERONE 
Draft  Subcutaneous Solution  021945  09/16/2019  04/06/2023 
CAPROATE 
LEVONORGESTREL  Draft  Intrauterine Device  203159  04/01/2014  10/01/2014 
LORCASERIN  Oral Tablet, Extended 
Draft  022529  03/01/2015  03/04/2021 
HYDROCHLORIDE  Release 
LORCASERIN  Oral Tablet, Extended 
Draft  208524  05/01/2017  03/04/2021 
HYDROCHLORIDE  Release 
Oral Tablet, Extended 
LOVASTATIN; NIACIN  Draft  021249  07/01/2009  04/18/2016 
Release 
Oral Tablet, Extended 
NIACIN; SIMVASTATIN  Draft  022078  10/01/2011  04/18/2016 
Release
Guidance for Industry  
 
Animal Models  Essential Elements to 
Address Efficacy Under the Animal Rule 
This file has been replaced by: 
Guidance for Industry Product Development Under the  Animal Rule 
http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/UCM399217.pdf
Animal Models  Essential Elements to 
Address Efficacy Under the Animal Rule  
CONCEPT PAPER  
 
This file has been replaced by: 
Guidance for Industry Product Development Under the  Animal Rule 
http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/UCM399217.pdf
CPG Sec. 510.500 Green Coffee Beans - 
Adulteration with Insects; Mold 
REGULATORY ACTION GUIDANCE: 
The following represents criteria for direct reference seizure *requests to the Office of Human 
and Animal Food Operations (OHAFO) in consultation with the Office of Enforcement and 
Import Operations (OEIO) and CFSAN, and for direct citation by the appropriate Field Office 
within the Human and Animal Food Program*: 
1.  Insects and Mold - an average of 10 percent or more by count of green coffee beans are 
insect infested, including insect damaged, or moldy; 
or 
2.  Graded green coffee beans are poorer than Grade 8 of the New York Green Coffee 
Association. 
NOTE: Criteria for direct reference seizure are determined using the method specified in FDA 
Technical Bulletin Number 5, "Macroanalytical Procedures Manual," Chapter V.1.A - Method 
for Coffee Beans. 
REMARKS: 
If live external infestation is present use the CPG titled "Food Storage and Warehousing - 
Adulteration - Filth" (See Sec. 580.100 for CPG 7103.01) in accordance with "Interpretation of 
Insect Filth" (See Sec. 555.600 for CPG 7120.18). 
SPECIMEN CHARGE: 
Article (Green Coffee Beans) adulterated (when introduced into and while in interstate 
commerce) (while held for sale after shipment in interstate commerce), within the meaning of 21 
U.S.C. 342(a)(3), in that it consists wholly or in part of a filthy substance by reason of presence 
therein of (insects), (insect fragments), and (insect damaged green coffee beans); and that is 
consists in part of a decomposed substance by reason of presence therein of (moldy, decomposed 
green coffee beans). 
NOTE: Psocids, as well as other non-storage insects not normally associated with green coffee 
beans, are to be reported separately from live whole insects or equivalent. The presence of such 
incidental non-storage insects in a lot of green coffee beans does not meet the criteria for direct 
reference seizure under this guide or the guide for food storage and warehousing. Any regulatory 
action based on the presence of such incidental non-storage insects must be referred to  CFSAN/Office of *Compliance*/Division of Enforcement (HFS-605) for coordination and 
review. 
*Material between asterisks is new or revised.* 
Issued: 10/01/80 
Revised: 3/95, 8/96, 5/05 
Updated: 11/29/05
CPG Sec. 515.750 Cocoa Beans - Adulteration 
by Mold, Insect Infestation, and Mammalian 
Excreta 
REGULATORY ACTION GUIDANCE: 
The following represents criteria for direct reference seizure *requests to the Office of Human 
and Animal Food Operations (OHAFO) in consultation with the Office of Enforcement and 
Import Operations (OEIO) and CFSAN, and for direct citation from the appropriate Field Office 
within the Human and Animal Food Program*: 
Examination shows: 
1.  The cocoa beans contain an average of more than 4 percent moldy beans by count; 
2.  The cocoa beans contain an average of more than 4 percent insect infested or insect 
damaged beans, by count; or 
3.  The cocoa beans contain an average of more than 6 percent reject beans (moldy plus 
insect infested or insect damaged beans) by count. 
REMARKS: 
If live external infestation is present use the CPG "Food Storage and Warehousing - Adulteration 
- Filth" (See Sec. 580.100 for CPG 7103.01). 
SPECIMEN CHARGE: 
Article (cocoa beans) adulterated (when introduced into and while in interstate commerce) (while 
held for sale after shipment in interstate commerce), within meaning of 21 U.S.C. 342(a)(3), in 
that it consists wholly or in part of a filthy substance by reason of presence there in of (insects) 
(insect fragments) (insect damaged cocoa beans); and that it consists in part of a decomposed 
substance by reason of the presence therein of (moldy, decomposed cocoa beans). 
CRITERIA FOR RECOMMENDING LEGAL ACTION: 
The following represents criteria for recommending legal action to CFSAN/Office of 
*Compliance*/Division of Enforcement (HFS-605): 
The cocoa beans contain an average of 10 mgs or more mammalian excreta per pound.  NOTE: Analyses for mold, insect damage, and mammalian excreta are conducted using the 
method specified in FDA Technical Bulletin 5, Macroanalytical Procedures Manual, Chapter 
V.4.A - Method for Cocoa Beans. 
*Material between asterisks is new or revised.* 
Issued: 8/1/83 
Revised: 3/95, 8/96, 5/05 
Updated: 11/29/05
CPG Sec. 525.150 Bay (Laurel) Leaves - 
Adulteration by Insect Filth; Mold; Mammalian 
Excreta 
REGULATORY ACTION GUIDANCE: 
The following represents criteria for direct reference seizure *requests to the Office of Human 
and Animal Food Operations (OHAFO) in consultation with the Office of Enforcement and 
Import Operations (OEIO) and CFSAN, and for direct citation by the appropriate Field Office 
within the Human and Animal Food Program*: 
1.  Insect Filth:  
The Bay Leaves contain an average of 5% or more insect infested pieces by weight; 
or 
2.  Mold:  
The Bay Leaves contain an average of 5% or more moldy pieces by weight; 
or 
3.  Excreta:  
The Bay Leaves contain an average of 1 milligram or more mammalian excreta per pound, after 
processing. 
REMARKS: 
Since the majority of spices are imported, determine that the lot in question has not been 
previously examined and released by FDA as an import. If the lot has been examined and 
released previously, submit all available facts to CFSAN/Office of *Compliance*/Division of 
Enforcement (HFS-605) for seizure consideration in the usual manner. 
SPECIMEN CHARGE: 
Article (bay (laurel) leaves) adulterated (when introduced into and while in interstate 
commerce)(while held for sale after shipment in interstate commerce), within meaning of 21 
U.S.C. 342(a)(3), in that it consists wholly or in part of a filthy substance by reason of presence 
therein of (insects), (insect webbing), (insect excreta), (insect damaged bay (laurel) leaves), and 
mammalian excreta); and that it consists in part of a decomposed substance by reason of the 
presence therein of (moldy, decomposed bay (laurel) leaves).  *Material between asterisks is new or revised.* 
Issued: 10/1/80 
Revised: 3/95, 5/05 
Updated: 11/29/05
CPG Sec. 525.200 Capsicum Pods, Ground 
Capsicums Excluding Paprika, Ground Paprika 
- Adulteration with Insect and Rodent Filth, 
Mold, Mammalian Excreta 
REGULATORY ACTION GUIDANCE: 
The following represents the criteria for direct reference seizure *requests to the Office of 
Human and Animal Food Operations (OHAFO) in consultation with the Office of Enforcement 
and Import Operations (OEIO) and CFSAN, and for direct citation by the appropriate Field 
Office within the Human and Animal Food Program*: 
1.  Capsicum pods (includes all capsicums; chili peppers, paprika, etc.), when analyzed 
using MPM V.8.A (Page V-32):  
a.  If the capsicum contains an average of more than 3% insect infested and/or moldy 
pods by weight; 
or 
b.  If the capsicum contains an average of more than 1 milligram of mammalian 
excreta per pound (mammalian excreta should be identified as to source when 
possible). 
2.  Ground capsicums (cayenne, red pepper, etc.), excluding paprika:  
a.  If the average mold count is more than 20% when analyzed using AOAC 915.94, 
15th Ed.; 
or 
b.  If the capsicum powder contains an average of more than 50 insect fragments per 
25 grams or an average of more than 6 rodent hairs per 25 grams using AOAC 
978.22, 15th Ed. 
3.  Ground paprika:  
a.  If the average mold count is more than 20% when analyzed using AOAC 915.94, 
15th Ed.; 
or  b.  If the ground paprika contains an average of more than 75 insect fragments per 25 
grams, or an average of more than 11 rodent hairs per 25 grams, when analyzed 
using 977.25B, 15th Ed. 
REMARKS: 
Since the majority of spices are imported, determine that the lot in question has not been 
previously examined and released by FDA as an import. If the lot has been examined and 
released previously, submit all available facts to CFSAN/Office of *Compliance*/Division of 
Enforcement (HFS-605) for seizure consideration in the usual manner. 
SPECIMEN CHARGE: 
Article (capsicum pods/ground capsicums/ground paprika) adulterated (when introduced into and 
while in interstate commerce)(while held for sale after shipment in interstate commerce), within 
meaning of 21 U.S.C. 342(a)(3), in that it consists wholly or in part of a filthy substance by 
reason of presence therein of (insects), (insect webbing), (insect excreta), (insect fragments), 
(insect damaged capsicum pods/ground capsicums/ground paprika), and (mammalian excreta) 
(rodent hairs); and that it consists in part of a decomposed substance by reason of presence 
therein of (moldy, decomposed capsicum pods/ground capsicums/ground paprika). 
*Material between asterisks is new or revised.* 
Issued: 10/1/80 
Revised: 3/95, 5/05 
Updated: 11/29/05