Persius/hicric huggingface dataset:
Endometrial biopsy (patient information)
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# Overview
Endometrial biopsy is a procedure in which a tissue sample is taken from the lining of the uterus (endometrium), and is checked under a microscope for any abnormal cells or signs of cancer.

# How is the Endometrial biopsy done?
This procedure may be done with or without anesthesia. You will lie on your back with your feet in stirrups.
The health care provider will do a pelvic examination, and will insert an instrument (speculum) into the vagina to hold it open and see the cervix.
The cervix is cleaned with an antiseptic liquid and then grasped with an instrument (tenaculum) to hold the uterus steady. A device called a cervical dilator may be needed to stretch the cervical canal if there is tightness (stenosis). Then a small, hollow plastic tube is gently passed into the uterine cavity.
Gentle suction removes a sample of the lining. The tissue sample and instruments are removed. A specialist called a pathologist examines the sample under a microscope.

# Who needs Endometrial biopsy?
The test is done to find the cause of:
Abnormal menstrual periods (heavy, prolonged, or irregular bleeding)
Bleeding after menopause
Bleeding from taking hormone therapy medications
Thickened uterine lining seen on ultrasound
The test is usually done in women over age 35.
This test can also be used to test for endometrial cancer. Sometimes, it is used as part of the diagnosis in women who have been unable to become pregnant (see infertility).

# How to prepare for Endometrial biopsy?
There is no special preparation for the biopsy. You may want to take ibuprofen (Advil, Motrin IB) or acetaminophen (Tylenol) 1 hour before the procedure to reduce cramping.

# What do I experience during the procedure?
The instruments may feel cold. You may feel some pain when the cervix is grasped. You may have some cramping as the instruments enter the uterus and the sample is collected.

# Where to find centers that perform Endometrial biopsy?
Directions to Hospitals Performing Endometrial biopsy

# Possible complications
- Infection
- Making a hole in (perforating) the uterus or tearing the cervix (rarely)
- Prolonged bleeding
- Slight spotting

# Results

## Normal Results
The biopsy is normal if the cells in the sample have no abnormalities.

## Abnormal Results
Abnormal menstrual periods may be caused by:
- Endometrial cancer or precancer (hyperplasia)
- Uterine fibroids
- Uterine polyps
- Hormone imbalance
If the lining is being tested for infertility, the sample may determine if hormones are properly stimulating the lining so that the fertilized egg can implant.
Other conditions under which the test may be performed:
- Abnormal bleeding if a woman is taking the breast cancer medication, tamoxifen
- Anovulatory bleeding
- Endometritis

# Sources
Endosperm expression gene transcriptions

# Human genes

# Gene expressions

# Consensus sequences
Endosperm expression (TGTGTCA).

# Hypotheses
- A1BG has no Endosperm expression in either promoter.
- A1BG is not transcribed by Endosperm expression.
- Endosperm expression does not participate in the transcription of A1BG.

# Endosperm expression samplings
Copying an apparent consensus sequence of TGTGTCA and putting it in "F" finds one located between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence TGTGTCA (starting with SuccessablesEE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- negative strand, negative direction, looking for TGTGTCA, 1, TGTGTCA at 4198.
- positive strand, negative direction, looking for TGTGTCA, 0.
- negative strand, positive direction, looking for TGTGTCA, 0.
- positive strand, positive direction, looking for TGTGTCA, 1, TGTGTCA at 3413.
- inverse complement, negative strand, negative direction, looking for TGACACA, 0.
- inverse complement, positive strand, negative direction, looking for TGACACA, 0.
- inverse complement, negative strand, positive direction, looking for TGACACA, 0.
- inverse complement, positive strand, positive direction, looking for TGACACA, 1, TGACACA at 2076.

## EE (4560-2846) UTRs
- Negative strand, negative direction: TGTGTCA at 4198.

## EE positive direction (4050-1) distal promoters
- Positive strand, positive direction: TGTGTCA at 3413.
- Positive strand, positive direction: TGACACA at 2076.

# Endosperm expression random dataset samplings
- EEr0: 1, TGTGTCA at 3959.
- EEr1: 0.
- EEr2: 0.
- EEr3: 0.
- EEr4: 0.
- EEr5: 1, TGTGTCA at 2839.
- EEr6: 0.
- EEr7: 0.
- EEr8: 0.
- EEr9: 0.
- EEr0ci: 0.
- EEr1ci: 0.
- EEr2ci: 0.
- EEr3ci: 0.
- EEr4ci: 0.
- EEr5ci: 0.
- EEr6ci: 0.
- EEr7ci: 0.
- EEr8ci: 0.
- EEr9ci: 0.

## EEr arbitrary (evens) (4560-2846) UTRs
- EEr0: TGTGTCA at 3959.

## EEr arbitrary negative direction (evens) (2846-2811) core promoters
- EEr5: TGTGTCA at 2839.

## EEr arbitrary positive direction (odds) (4050-1) distal promoters
- EEr5: TGTGTCA at 2839.

## EEr alternate positive direction (evens) (4050-1) distal promoters
- EEr0: TGTGTCA at 3959.

# Endosperm expression analysis and results
Endosperm expression (TGTGTCA).
Comparison:
The occurrences of real EEs are greater than the randoms. This suggests that the real EEs are likely active or activable.

# Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
Esophageal atresia (patient information)
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# Overview
Esophageal atresia is a disorder of the digestive system in which the esophagus does not develop properly. The esophagus is the tube that normally carries food from the mouth to the stomach.

# What are the symptoms of Esophageal atresia?
- Bluish coloration to the skin (cyanosis) with attempted feedings
- Coughing, gagging, and choking with attempted feeding
- Drooling
- Poor feeding

# What causes Esophageal atresia?
Esophageal atresia is a congenital defect, which means it occurs before birth. There are several types. In most cases, the upper esophagus ends and does not connect with the lower esophagus and stomach. The top end of the lower esophagus connects to the windpipe. This connection is called a tracheoesophageal fistula (TEF). Some babies with TEF will also have other problems, such as heart or other digestive tract disorders.
Other types of esophageal atresia involve narrowing of the esophagus, and may also be associated with other birth defects.

# Who is at highest risk?
Esophageal atresia occurs in about 1 out of 4,000 births.

# Diagnosis
Before birth, an ultrasound performed on the pregnant mother may show too much amniotic fluid, which can be a sign of esophageal atresia or other blockage of the digestive tract.
The disorder is usually detected shortly after birth when feeding is attempted and the infant coughs, chokes, and turns blue. As soon as the diagnosis is suspected, an attempt to pass a small feeding tube through the mouth or nose into the stomach should be made. The feeding tube will not be able to pass all the way to the stomach in a baby with esophageal atresia.
An x-ray of the esophagus shows an air-filled pouch and air in the stomach and intestine. If a feeding tube has been inserted, it will appear coiled up in the upper esophagus.

# When to seek urgent medical care?
This disorder is usually diagnosed shortly after birth.
Call your baby's health care provider if the baby vomits repeatedly after feedings, or if the baby develops breathing difficulties.

# Treatment options
Esophageal atresia is considered a surgical emergency. Surgery to repair the esophagus should be done quickly after the baby is stabilized so that the lungs are not damaged and the baby can be fed.
Before the surgery, the baby is not fed by mouth. Care is taken to prevent the baby from breathing secretions into the lungs.

# Where to find medical care for Esophageal atresia?
Directions to Hospitals Treating Esophageal atresia

# What to expect (Outlook/Prognosis)?
An early diagnosis gives a better chance of a good outcome.

# Possible complications
The infant may breath saliva and other secretions into the lungs, causing aspiration pneumonia, choking, and possibly death.
Other complications may include:
- Feeding problems
- Reflux (the repeated bringing up of food from the stomach) after surgery
- Narrowing (stricture) of the esophagus due to scarring from surgery
Prematurity may complicate the condition.

# Sources
Glycoprotein 2-beta-D-xylosyltransferase

# Overview
In enzymology, a glycoprotein 2-beta-D-xylosyltransferase (EC 2.4.2.38) is an enzyme that catalyzes the chemical reaction
The 5 substrates of this enzyme are UDP-D-xylose, ], -beta-D-]], ], and ], whereas its 5 products are UDP, ], -], -beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-]], and ].
This enzyme belongs to the family of glycosyltransferases, specifically the pentosyltransferases.  The systematic name of this enzyme class is UDP-D-xylose:glycoprotein (D-xylose to the 3,6-disubstituted mannose of N4-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)--beta-D-man nosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glu cosaminyl}asparagine) 2-beta-D-xylosyltransferase. Other names in common use include beta1,2-xylosyltransferase, UDP-D-xylose:glycoprotein (D-xylose to the 3,6-disubstituted mannose, of, 4-N-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)--beta-D-, mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-, and glucosaminyl}asparagine) 2-beta-D-xylosyltransferase.  This enzyme participates in glycan structures - biosynthesis 1.
Granulosa cell tumour primary prevention
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# Overview

# Primary Prevention
- There are no standard recommendations for screening for ovarian cancer.
- BRCA testing may be done in women at high risk for ovarian cancer.
- Removal of the  and tubes in women who have a mutation in the BRCA1 and BRCA2 genes may reduce the risk of developing ovarian cancer, although ovarian cancer may still develop in other areas of the pelvis.
HFrEF exacerbation (Assessment and Plan)
Author: William J Gibson MD, PhD
History of HFrEF (last TTE XX;LVEF XX%) secondary to XX  . Current exacerbation most likely precipitated by . Possible other etiologies (although less likely): ischemia/infarction(15%), HTN, renal failure -> inc. preload, drugs/toxins (eg etoh), new structural/valvular pathology, no history COPD, low suspicion for PE.  and  on exam. Weight on admission XX lb ; dry weight reportedly XX lb.
Dx:
- EKG, trend troponins, CXR
- tele; strict I/O; cardiac diet (2L fluid, 2g Na); daily weights
- BID BMP/Mg
- TTE (always if first presentation, repeat if concern for new structural/functional changes)
- If new: perform ischemic workup (stress test, cath), if no evidence of ischemia on TEE: A1c, lipid panel, TSH, iron studies, SPEP, ANA, consider MRI.
Tx:
Contractility:
Preload: IV lasix BID or PO torsemide BID or Bumex drip (0-2 mg/hr). If diuresis inadequate with these agents can give metolazone 30 min before loop diuretic.
Afterload: captopril Q8H (titrate quickly and then convert to lisinopril), or . ACE first line as mortality benefit in all. Isordil/hydralazine has mortality benefit in blacks.
Neurohormonal blockade: Continue home . Spironolactone and eplerenone inhibit aldosterone and decrease mortality in randomized trials (RALES trial; EMPHASIS-HF trial). Hold if AKI.
References:
Jondeau G, Neuder Y, Eicher JC, et al. B-CONVINCED: Beta-blocker CONtinuation Vs. INterruption in patients with Congestive heart failure hospitalizED for a decompensation episode. Eur Heart J. 2009;30(18):2186-92.
RALES trial: Pitt B, Zannad F, Remme WJ, et al. The effect of spironolactone on morbidity and mortality in patients with severe heart failure. Randomized Aldactone Evaluation Study Investigators. N Engl J Med. 1999;341(10):709-17.
EMPHASIS-HF trial: Zannad F, Mcmurray JJ, Krum H, et al. Eplerenone in patients with systolic heart failure and mild symptoms. N Engl J Med. 2011;364(1):11-21.
HLH (Hemophagocytic lymphohistiocytosis)
Hemophagocytic lymphohistiocytosis (HLH) is an unusual syndrome characterized by fever, splenomegaly, jaundice, and the pathologic finding of hemophagocytosis. This is phagocytosis by macrophages of erythrocytes, leukocytes, platelets, and their precursors in bone marrow and other tissues.
HLH may be associated with malignant, genetic, or autoimmune diseases. It is also prominently linked with Epstein-Barr virus (EBV) infection.
Hyperproduction of cytokines, including interferon-g and tumor necrosis factor-a, by EBV-infected T lymphocytes may play a role in the pathogenesis of HLH. EBV-associated HLH may mimic T-cell lymphoma and is treated with cytotoxic chemotherapy. In contrast, hemophagocytic syndromes associated with nonviral pathogens often respond to treatment of the underlying infection.
HLH comprises familial (primary) hemophagocytic lymphohistiocytosis (FHL) and secondary HLH (SHLH), both clinically characterized by the features described above, in particular fever, hepatosplenomegaly, and cytopenia.
FHL, an autosomal recessive disease, is invariably fatal when untreated. It is associated with defective triggering of apoptosis and reduced cytotoxic activity, resulting in a widespread accumulation of T lymphocytes and activated macrophages.
Hyperlipoproteinemia laboratory findings

# Overview
Complete fasting lipid profile should be obtained for making the diagnosis of hyperlipidemia and risk stratification for coronary heart diseases. In the absence of symptoms or signs suggestive of a particular disorder, a limited workup should also be performed to rule out secondary hyperlipidemias.

# Laboratory Findings

## Complete Lipid Profile
The US National Cholesterol Education Program Adult Treatment Panel III (NCEP ATP III) suggests screening asymptomatic individuals with a complete fasting lipid profile every 5 years, with a shorter interval for those with high-normal lipid levels and longer interval for low-risk individuals with low or normal lipid levels. Obtain complete lipid profile after 9 to 12-hour fast. The reference values according to ATP III classification for making the diagnosis and risk stratification are depicted below:

## Other Laboratory Tests
For careful medical evaluation, physicians must take into consideration all medications (both prescription and over-the-counter medications) and perform following tests to rule out secondary hyperlipidemias:
- Random blood sugar
- HbA1c
- Serum thyroid-stimulating hormone
- Liver function tests
- Renal function tests
- Urinalysis
Other tests that may be done to have a definitive diagnosis include:
- Apobetalipoprotein (apoB) quantification (by ultracentrifugation and electrophoresis)
- Studies of cells called fibroblasts (to see how the body absorbs LDL cholesterol)
- Gene analysis or receptor analysis (to identify the specific defect associated with hyperlipidemia)
Many different types of mutations have been identified in the LDL-receptor (LDLR) gene. They have been categorized into four classes of alleles based on the phenotypic behavior of the mutant protein:
- Class I - Null, in which LDL-receptor synthesis is defective.
- Class II - Transport defect, in which intracellular transport from the endoplasmic reticulum to the Golgi apparatus is defective.
- Class III - Binding defect, in which LDL-receptors are synthesized and transported to the cell surface normally, but binding of LDL-cholesterol is defective.
- Class IV - Internalization defect, in which the LDL-receptors reach the cell surface and bind LDL-cholesterol normally, but LDL internalization is defective.

## Approach
Shown below is a diagnostic algorithm to diagnose hyperlipidemia.
IMITREX injection nonclinical toxicology

# Nonclinical Toxicology

### Carcinogenesis, Mutagenesis, Impairment of Fertility
Carcinogenesis: In carcinogenicity studies, rats and mice were given sumatriptan by oral gavage. Mice were dosed for 78 weeks and rats were dosed for 104 weeks. Average exposures achieved in mice receiving the highest dose were approximately 110 times the exposure attained in humans after the maximum recommended single dose of 6 mg. The highest dose to rats was approximately 260 times the maximum single dose of 6 mg on a mg/m2 basis. There was no evidence of an increase in tumors in either species related to sumatriptan administration.
Mutagenesis: Sumatriptan was not mutagenic in the presence or absence of metabolic activation when tested in 2 gene mutation assays (the Ames test and the in vitro mammalian Chinese hamster V79/HGPRT assay). It was not clastogenic in 2 cytogenetics assays (the in vitro human lymphocyte assay and the in vivo rat micronucleus assay).
Impairment of Fertility: A fertility study (Segment I) by the subcutaneous route, during which male and female rats were dosed daily with sumatriptan prior to and throughout the mating period, has shown no evidence of impaired fertility at doses equivalent to approximately 100 times the maximum recommended single human dose of 6 mg on a mg/m2 basis.
However, following oral administration, a treatment-related decrease in fertility, secondary to a decrease in mating, was seen for rats treated with 50 and 500 mg/kg/day. The no-effect dose for this finding was approximately 8 times the maximum recommended single human dose of 6 mg on a mg/m2 basis. It is not clear whether the problem is associated with the treatment of males or females or both.

### Animal Toxicology and/or Pharmacology
Corneal Opacities: Dogs receiving oral sumatriptan developed corneal opacities and defects in the corneal epithelium. Corneal opacities were seen at the lowest dosage tested, 2 mg/kg/day, and were present after 1 month of treatment. Defects in the corneal epithelium were noted in a 60-week study. Earlier examinations for these toxicities were not conducted and no-effect doses were not established; however, the relative exposure at the lowest dose tested was approximately 5 times the human exposure after a 100-mg oral dose or 3 times the human exposure after a 6-mg subcutaneous dose.
Melanin Binding: In rats with a single subcutaneous dose (0.5 mg/kg) of radiolabeled sumatriptan, the elimination half-life of radioactivity from the eye was 15 days, suggesting that sumatriptan and its metabolites bind to the melanin of the eye. The clinical significance of this binding is unknown.
IMITREX tablet dosage and administration

# Dosage and Administration

### Dosing Information
The recommended dose of IMITREX Tablets is 25 mg, 50 mg, or 100 mg. Doses of 50 mg and 100 mg may provide a greater effect than the 25-mg dose, but doses of 100 mg may not provide a greater effect than the 50-mg dose. Higher doses may have a greater risk of adverse reactions .
If the migraine has not resolved by 2 hours after taking IMITREX Tablets, or returns after a transient improvement, a second dose may be administered at least 2 hours after the first dose. The maximum daily dose is 200 mg in a 24-hour period.
Use after IMITREX Injection: If the migraine returns following an initial treatment with IMITREX (sumatriptan succinate) Injection, additional single IMITREX Tablets (up to 100 mg/day) may be given with an interval of at least 2 hours between tablet doses.
The safety of treating an average of more than 4 headaches in a 30-day period has not been established.

### Dosing in Patients With Hepatic Impairment
If treatment is deemed advisable in the presence of mild to moderate hepatic impairment, the maximum single dose should not exceed 50 mg .
Inappropriate sinus tachycardia overview

# Overview
Inappropriate sinus tachycardia  is an uncommon form of supraventricular tachycardia (SVT).

# Epidemiology and Demographics
The condition was first formally recognized as a veritable syndrome in 1979.

# Pathophysiology
The mechanism of the arrhythmia primarily involves the sinus node and peri-nodal tissue and does not require the AV node for maintenance.  These patients have no apparent heart disease or other causes of sinus tachycardia. IST is thought to be due to abnormal autonomic control or dysautonomia.  An autoimmune mechanism has been suggested as several studies have detected autoantibodies that activate beta adrenoreceptors in a portion of patients.
Killer cell immunoglobulin-like receptor
Killer cell immunoglobulin-like receptor is a receptor for natural killer cells.

# Genes
- two domains, long cytoplasmic tail: KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL4, KIR2DL5A, KIR2DL5B,
- two domains, short cytoplasmic tail: KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS4, KIR2DS5
- three domains, long cytoplasmic tail: KIR3DL1, KIR3DL2, KIR3DL3
- three domains, short cytoplasmic tail: KIR3DS1
Lisinopril clinical laboratory findings

# Serum Electrolytes
Hyperkalemia, hyponatremia.

# Creatinine, Blood Urea Nitrogen
Minor increases in blood urea nitrogen and serum creatinine, reversible upon discontinuation of therapy, were observed in about 2% of patients with essential hypertension treated with lisinopril alone. Increases were more common in patients receiving concomitant diuretics and in patients with renal artery stenosis. Reversible minor increases in blood urea nitrogen and serum creatinine were observed in approximately 11.6% of patients with heart failure on concomitant diuretic therapy. Frequently, these abnormalities resolved when the dosage of the diuretic was decreased.

# Hemoglobin and Hematocrit
Small decreases in hemoglobin and hematocrit (mean decreases of approximately 0.4 g% and 1.3 vol %, respectively) occurred frequently in patients treated with lisinopril but were rarely of clinical importance in patients without some other cause of anemia. In clinical trials, less than 0.1% of patients discontinued therapy due to anemia. Hemolytic anemia has been reported; a causal relationship to lisinopril cannot be excluded.

# Liver Function Tests
Rarely, elevations of liver enzymes and/or serum bilirubin have occurred.
In hypertensive patients, 2% discontinued therapy due to laboratory adverse experiences, principally elevations in blood urea nitrogen (0.6%), serum creatinine (0.5%) and serum potassium (0.4%).
In the heart failure trials, 3.4% of patients discontinued therapy due to laboratory adverse experiences; 1.8% due to elevations in blood urea nitrogen and/or creatinine and 0.6% due to elevations in serum potassium.
In the myocardial infarction trial, 2% of patients receiving lisinopril discontinued therapy due to renal dysfunction (increasing creatinine concentration to over 3 mg/dL or a doubling or more of the baseline serum creatinine concentration); less than 1% of patients discontinued therapy due to other laboratory adverse experiences: 0.1% with hyperkalemia and less than 0.1% with hepatic enzyme alterations.
Megakaryocyte-associated tyrosine kinase
Megakaryocyte-associated tyrosine-protein kinase is an enzyme that in humans is encoded by the MATK gene.
The protein encoded by this gene has amino acid sequence similarity to Csk tyrosine kinase and has the structural features of the CSK subfamily: SRC homology SH2 and SH3 domains, a catalytic domain, a unique N terminus, lack of myristylation signals, lack of a negative regulatory phosphorylation site, and lack of an autophosphorylation site. This protein is thought to play a significant role in the signal transduction of hematopoietic cells. It is able to phosphorylate and inactivate Src family kinases, and may play an inhibitory role in the control of T-cell proliferation. This protein might be involved in signaling in some cases of breast cancer. Three alternatively spliced transcript variants that encode different isoforms have been described for this gene.

# Interactions
Megakaryocyte-associated tyrosine kinase has been shown to interact with CD117 and TrkA.