Persius/hicric huggingface dataset:
Baltimore classification

# Overview
Added The Baltimore classification is a classification system which groups viruses into families depending on their type of genome (DNA, RNA, single-stranded (ss), double-stranded (ds) etc.) and their method of replication.
It was created by the American biologist David Baltimore and is the preferred way of classifying viruses today. Other classifications are determined by the type of disease the virus causes (localised, disseminated, persistent, etc.) or its morphology (spherical, dodecahedral, etc.). Neither are particularly satisfactory because very different viruses will sometimes cause the same disease (e.g. hepatitis), and viruses with similar structures will often behave very differently (what's more, the precise structure of viruses is often difficult to determine under the microscope).

# Classifications
Classifying viruses according to their genome means that those in a given category will all behave in much the same way, which offers some indication of how to proceed with further research.
- Type I: dsDNA viruses (Herpesviridae, Poxviridae, Adenoviridae and Papovaviridae)
- Type II: ssDNA viruses (Circoviridae and Parvoviridae)
- Type III: dsRNA viruses (Reoviridae and Birnaviridae)
- Type IV: positive sense ssRNA viruses (Astroviridae, Caliciviridae, Coronaviridae, Flaviviridae, Picornaviridae, Arteriviridae and Togaviridae)
- Type V: negative sense ssRNA viruses (Arenaviridae, Orthomyxoviridae, Paramyxoviridae, Bunyaviridae, Filoviridae and Rhabdoviridae)
- Type VI: positive sense ssRNA viruses that replicate through a DNA intermediate (Reverse transcriptase) (Retroviridae)
- Type VII: dsDNA viruses with ssRNA intermediates (Reverse transcriptase)(Hepadnaviridae)
Bamford-Stevens reaction
The Bamford-Stevens reaction is a chemical reaction whereby treatment of tosylhydrazones with strong base gives alkenes. It is named for the British chemist William Randall Bamford and the Scottish chemist Thomas Stevens Stevens (1900-2000). The usage of aprotic solvents gives predominantly Z-alkenes, while protic solvent gives a mixture of E- and Z-alkenes.
The treatment of tosylhydrazones with alkyl lithium reagents is called the Shapiro reaction.

# Reaction mechanism
The first step of the Bamford-Stevens reaction is the formation of the diazo compound 3.
In protic solvents, the diazo compound 3 decomposes to the carbenium ion 5.
In aprotic solvents, the diazo compound 3 decomposes to the carbene 7.
Bare lymphocyte syndrome

# Overview
Bare lymphocyte syndrome is a condition caused by mutations in certain genes of the major histocompatibility complex or involved with the processing and presentation of MHC molecules. It is a form of severe combined immunodeficiency.

# Historical Perspective

# Classification
- Type 1: MHC class I
- Type 2: MHC class II

# Pathophysiology

# Presentation
The bare lymphocyte syndrome, type II (BLS II) is a rare recessive genetic condition in which a group of genes called major histocompatibility complex class II (MHC class II) are not expressed.
The result is that the immune system is severely compromised and cannot effectively fight infection.  Clinically, this is similar to severe combined immunodeficiency (SCID), in which lymphocyte precursor cells are improperly formed. As a notable contrast, however, bare lymphocyte syndrome does not result in decreased B- and T-cell counts, as the development of these cells is not impaired.
Diarrhea can be among the associated conditions.

# Causes

# Genetics

## BLS II
The genetic basis for BLSII is not due to defects in the MHC II genes themselves.  The genetic basis is the result of mutations in genes that code for proteins (transcription factors) that normally regulate the expression (gene transcription) of the MHC II genes.  That is, one of the several proteins that are required to switch on MHC II genes in various cells types (primarily those in the immune system) is absent.  The genes responsible were cloned by the laboratories of Bernard Mach in Switzerland and Jeremy Boss at Emory University in Atlanta, Georgia.
Mutation in any one of four genes can lead to BLS II.  The genes' names are:
- class II trans-activator (CIITA)
- regulatory factor of the X box 5 (RFX5)
- RFX-associated protein (RFXAP)
- RFX ankyrin repeats (RFXANK; also known as RFXB)

## BLS I
BLS I, also called "HLA class I deficiency", which is much more rare, is associated with TAP2, TAP1, or TAPBP.

# Differentiating  from Other Diseases

# Epidemiology and Demographics

# Risk Factors

# Screening

# Natural History, Complications, and Prognosis

## Natural History

## Complications

## Prognosis

# Diagnosis

## Diagnostic Criteria

## History and Symptoms

## Physical Examination

## Laboratory Findings

## Imaging Findings

## Other Diagnostic Studies

# Treatment

## Medical Therapy
Though BLSII is an attractive candidate for gene therapy, bone marrow transplant is currently the only treatment.

## Surgery

## Prevention
Bronchopulmonary segment
Each of the tertiary bronchi serves a specific bronchopulmonary segment.  These segments each have their own artery.  Thus, each bronchopulmonary segment is supplied by a bronchus, and an artery.
There are 10 bronchopulmonary segments per lung (3 in right superior lobe, 2 in middle right lobe, 5 in both right and left inferior lobe, and 5 in left superior lobe, in which 2 of the five reside in the  lingula), each of which is separated from the others by a layer of connective tissue.
This means that each bronchopulmonary segment is a discrete anatomical and functional unit, and this separation mean that a bronchopulmonary segment can be surgically removed without affecting the function of the other segments.

# Bronchopulmonary segments of right lung
A PALM Seed Makes Another Little Palm
- superior lobe
apical
posterior
anterior
- apical
- posterior
- anterior
- middle lobe
lateral (superior lingular)
medial (inferior lingular)
- lateral (superior lingular)
- medial (inferior lingular)
- inferior lobe
superior
medial-basal
anterior-basal
lateral-basal
posterior-basal
- superior
- medial-basal
- anterior-basal
- lateral-basal
- posterior-basal

# Bronchopulmonary segments of left lung
ASIA ALPS
Apoptotic Antlions Stop In, Suddenly Amalgamating Laboratory Posts
AP And Supine alignment Increases Limited Studies And Makes Baseline Pulmonary Bases Look Bad (a radiology mnemonic)
- superior lobe
apico-posterior (merger of "apical" and "posterior")
anterior
- apico-posterior (merger of "apical" and "posterior")
- anterior
- lingula of superior lobe
inferior lingular
superior lingular
- inferior lingular
- superior lingular
- inferior lobe
superior
antero-medial basal (merger of "anterior basal" and "medial basal")
lateral basal
posterior basal
- superior
- antero-medial basal (merger of "anterior basal" and "medial basal")
- lateral basal
- posterior basal
Battered person syndrome

# Overview
Battered person syndrome is a physical and psychological condition that is classified as ICD-9 code 995.81 "Battered person syndrome" NEC or otherwise included within DSM-IV as a sub-category of post-traumatic stress disorder. This condition has been used as a defense by women who have experienced long-term physical and psychological abuse, and have killed their abusers. This was called battered woman syndrome by Lenore Walker (1979).

# Symptomology
ICD9 code 995.81  shows the syndrome as including "battered person/man/spouse syndrome NEC" and any person presenting with identified physical descriptors rather than psychological descriptors falls under the general heading of "Adult physical abuse", classified under "Injury and Poisoning" . In lay terms, this is a reference to any person who, because of constant and severe domestic violence usually involving physical abuse by a partner, becomes depressed and unable to take any independent action that would allow him or her to escape the abuse. The condition explains why abused people often do not seek assistance from others, fight their abuser, or leave the abusive situation. Sufferers have low self-esteem, and often believe that the abuse is their fault. Such persons usually refuse to press criminal charges against their abuser, and refuse all offers of help, often becoming aggressive or abusive to others who attempt to offer assistance. Often sufferers will even seek out their very abuser for comfort shortly after an incident of abuse.

# Law and medicine intersection
Although the medical condition is not gender specific, the law has been persuaded to remedy perceived gender bias in the operation of the defense of self-defense by admitting evidence of the medical condition as the basis of an excuse (the "battered woman defense") for women who use excessive violence to escape from an abusive relationship and kill their abusers. This has been problematic because there is no consensus in the medical profession that such abuse results in a mental conditions severe enough to excuse alleged offenders. Nevertheless, the law makes reference to DSM-IV mental disorders even though neither the ICD nor the DSM medical classifications as currently drafted, include the syndrome in the sense used by lawyers.

# Notes
Bayer Schering Pharma AG

# Overview
Bayer Schering Pharma AG is a research-centered pharmaceutical company that was formed by the merger of Schering with Bayer on 29 December 2006.  The company was originally founded in 1851 by Ernst Christian Friedrich Schering (1824-1869).  The company employs more than 26,000 people in 140 subsidiaries all over the world.  The company's headquarters are in Berlin-Wedding, Germany and the forerunner company Schering's annual gross revenue was nearly  5 billion (2003).  They retain the largest German manufacturing facility which is located in Bergkamen.
The company focuses on the business areas of gynaecology and andrology, oncology, and also special therapeutics, diagnostical devices, and nuclear medicine.  Schering's best-known product is their line of combined oral contraceptive pills.
Through Bayer Healthcare AG, Bayer Schering Pharma is a full member of the European Federation of Pharmaceutical Industries and Associations (EFPIA).

# Collaborative research
In addition to internal research and development activities, Bayer Schering Pharma is also involved in publicly funded collaborative research projects, with other industrial and academic partners.  One example in the area of non-clinical safety assessment is the InnoMed PredTox. The company is expanding its activities in joint research projects within the framework of the Innovative Medicines Initiative of EFPIA and the European Commission.

# Bayer's takeover bid
On 13 March 2006, Merck KGaA announced a 14.6 billion bid for Schering.  The offer document was due to be issued in early April 2006.
Merck's takeover bid was surpassed by Bayer's $19.5B white-knight bid for Schering on 23 March 2006.  In June 2006 Bayer finally bought the majority of shares, over 96%.  A domination agreement using the code name "Step One" was used for the take-over.  On 17 February 2007 the company publicly announced that 1,000 jobs would be cut through voluntary redundancy from the Berlin operations with effect until March 2008.
Bcl-2-interacting killer
Bcl-2-interacting killer is a protein that in humans is encoded by the BIK gene.

# Function
The protein encoded by this gene is known to interact with cellular and viral survival-promoting proteins, such as BCL2 and the Epstein-Barr virus in order to enhance programmed cell death.  Because its activity is suppressed in the presence of survival-promoting proteins, this protein is suggested as a likely target for antiapoptotic proteins.  This protein shares a critical BH3 domain with other death-promoting proteins, BAX and BAK.

# Interactions
Bcl-2-interacting killer has been shown to interact with BCL2-like 1 and Bcl-2.
Bhattacharya coefficient

# Overview
The Bhattacharya coefficient is an approximate measurement of the amount of overlap between two statistical samples. The coefficient can be used to determine the relative closeness of the two samples being considered.
Calculating the Bhattacharya coefficient involves a rudimentary form of integration of the overlap of the two samples. The interval of the values of the two samples is split into a chosen number of partitions, and the number of members of each sample in each partition is used in the following formula,
where considering the samples a and b, n is the number of partitions, and ai, bi are the number of members of samples a and b in the i'th partition.
This formula hence is larger with each partition that has members from both sample, and larger with each partition that has a large overlap of the two sample's members within it. The choice of number of partitions depends on the number of members in each sample; too few partitions will lose accuracy by over-estimating the overlap region, and too many partitions will lose accuracy by creating individual partitions with no members despite being in a surroundingly populated sample space.
The Bhattacharya coefficient will be 0 if there is no overlap at all due to the multiplication by zero in every partition. This means the distance between fully separated samples will not be exposed by this coefficient alone.
Bifidobacterium animalis
Bifidobacterium animalis is a Gram-positive anaerobic rod-shaped bacterium, which can be found in the intestines of most mammals, including human. It is one of the different species of bifidobacteria in the human large intestine.
Bifidobacterium animalis and Bifidobacterium lactis were previously described as two distinct species. Presently both are considered B. animalis with the subspecies Bifidobacterium animalis subsp animalis and Bifidobacterium animalis subsp lactis.
Both old names B. animalis and B. lactis are still used on product labels, as this species is frequently used as a probiotic. In most cases it is not clear which subspecies is used in the product.

# Trade names
B. animalis, strain number DN 173 010, is used worldwide as a probiotic in the product ActiviaTM, produced by the Danone company (known as Dannon in the US). The company uses different trade names in different countries : Bifidus Digestivum (UK), Bifidus Regularis (US and Mexico), Bifidobacterium Lactis or B.L. Regularis (Canada), Bifidus Essensis (Germany, Netherlands, Romania and Austria), Bifidus Activo (Spain) and Bifidus Actiregularis (Argentina, Chile, Italy and Russia).
These are not scientific names but trade names designed to sound and look like scientifically named organisms. The scientific name is Bifidobacterium animalis subsp lactis DN173010.
Another commonly used strain is marketed as BB-12 (Bb12; Bb-12). This strain is used in products from many different producers worldwide, mainly in dairy products, but also in food supplements (pills). It is marketed by Chr. Hansen Ltd from Denmark. As with the other strain, BB-12 is marketed both as Bifidobacterium animalis and Bifidobacterium lactis, however, the true scientific name of the strain is Bifidobacterium animalis subsp. lactis.

# Health benefits
Both strains mentioned above are well studied and ample literature exists on the efficacy of these bacteria. Some recent references are stated below.
Bb12 :
- Effects of Bifidobacterium lactis Bb12 Supplementation on Intestinal Microbiota of Preterm Infants: a Double-Blind, Placebo-Controlled, Randomized Study. J Clin Microbiol. 2006 November; 44(11): 40254031.
- Adherence of Probiotic Bacteria to Human Intestinal Mucus in Healthy Infants and during Rotavirus Infection. Clin Diagn Lab Immunol. 2001 March; 8(2): 293296.
- Innate mechanisms for Bifidobacterium lactis to activate transient pro-inflammatory host responses in intestinal epithelial cells after the colonization of germ-free rats. Immunology. 2005 August; 115(4): 441450.
DN 173 010 :
- A fermented milk with Bifidobacterium probiotic strain DN-173 010 shortened oro-fecal gut transit time in elderly. Microb Ecology Health Dis,2001; 13: 217-222.
- Bifidobacterium animalis, strain DN-173 010 shortens the colonic transit time in healthy women.
A double-blind randomised controlled study. Aliment Pharmacol Ther, 2002; 16: 587-593.
- Bouvier M, et al. Effects of consumption of a milk fermented by the probiotic Bifidobacterium animalis DN-173 010 on colonic transit time in healthy humans. Bioscience and Microflora, 2001; Vol 20(2): 43-48.
Bilateral vestibulopathy

# Overview
Bilateral Vestibulopathy results as the culmination of damage done to both inner ears. Bilateral Vestibulopathy causes problems in vision, hearing and motor coordination.

# Symptoms
Symptoms typically include imbalance and visual problems. Dark or unsure situations generally increase this imbalance.The imbalance is worse in the dark or in situations where footing is uncertain. Spinning vertigo is unusual. Oscillopsia, visual symptoms of Bilateral Vestibulopathy only occur when the head is moving. For instance, when driving, a person with Bilateral Vestibulopathy may see very blurry objects. Oscillopsia is often common during walking. Transient visual blurring occurs with quick  movements of the head.

# Diagnosis
Your physician will make on your history, physical examination or vestibular tests in a rotary chair. There are several different causes of Bilateral Vestibulopathy, including Gentamicin toxicity, but the rotary chair test will determine the effects on both ears. Tests for syphilis, an antibody test for autoimmune inner ear disease or audiograms may be important in determining if you have bilateral vestibulopathy.

# Treatment
Treatment differs depending on the cause. Each cause has a different treatment, and may involve either medical treatment, surgery, or therapy. If serious damage has already been done, then the focus of treatment is upon avoidance of vestibular suppressants and ototoxins. It is recommended that you tell your physicians to avoid drugs that end in mycin ( Azithromycin, Erythromycin ) because of possible reactions which could lead to setbacks. Vestibular rehabilitation is important. Your physician will try to keep the administering of drugs to a minimum.
Biliary atresia overview

# Overview
Biliary atresia, is a disease of the liver in which the bile ducts, inside and outside, are blocked due to damage and scarring. In the congenital form, the common bile duct between the liver and the small intestine is blocked or absent. The acquired type most often occurs in the setting of autoimmune disease, and is one of the principal forms of chronic rejection of a transplanted liver allograft.
Babies born with biliary atresia can undergo surgery called the Kasai procedure before 8 weeks of age, however, a liver transplant may still be necessary.

# Classification
Biliary atresia can be classified into several subtypes, since it does not arise from a specific cause. As such, it is broadly classified according to syndromic and non-syndromic expression. Davenport et al. grouped biliary atresia based on the similarities between the different presentations.

# Pathophysiology
Biliary atresia is a progressive fibrosing obstructive cholangiopathy of the intrahepatic and extrahepatic biliary system, resulting in obstruction of bile flow and neonatal jaundice.

# Causes
There have been many theories about etiopathogenesis such as Reovirus 3 infection, congenital malformation, congenital CMV infection, autoimmune theory. This means that the etiology and pathogenesis of biliary atresia are largely unknown.

# Differentiating biliary atresia from other Diseases
Biliary atresia must be differentiated from other diseases that present with symptoms typical of cholestasis in neonates, jaundice and acholic pale stools, which are main features of obstructive jaundice, associated with conjugated (direct) hyperbilirubinemia.

# Epidemiology and Demograhpics
Biliary atresia is a very rare disorder. About one in 10,000 to 20,000 babies in the U.S are affected every year. Biliary atresia seems to affect girls slightly more often than boys. Within the same family, it is common for only one child in a pair of twins or only one child within the same family to have it. Asians and African-Americans are affected more frequently than Caucasians. There does not appear to be any link to medications or immunizations given immediately before or during pregnancy.

# Natural History, Complications, and Prognosis
If left untreated, patients with biliary atresia may progress to develop cirrhosis and liver failure. No cure exists for biliary atresia, but the timely diagnosis and surgical intervention improves short- and long-term outcomes in most patients. Special attention to the nutritional needs and diet are essential for children with this disorder. Special supplements, formulas, and dietary restrictions may be necessary for affected infants.
Biological transmutation
A biological transmutation is defined as a nuclear transmutation occurring in living organisms.

# Observation
By definition, chemical reactions rearrange the bindings of atoms, but do not change the number of protons or neutrons in the nucleus of atoms.
Defining the kind of an atom as the number of neutrons and the number of protons in its nucleus, the evolution over time of the number of atoms of a given kind in a system where only chemical reactions occurs
will therefore be the difference between the number of atoms of that kind entering and exiting the system.  Some scientists claim to have observed biochemical systems where this relation does not hold:  the systems were inexplicably gaining or losing atoms of some kinds, indicating non-chemical reactions and possibly transmutation.  Phenomena reported include:
- Anomalous increase in calcium and decrease in magnesium, during the synthesis of egg shells
- Anomalous excretion of magnesium

# Orthodox view and responses from proponents
The phenomenon is rejected by mainstream science on the following grounds:
- Nuclear reactions such as transmutations require, according to current models, relatively large amounts of energy per particle.
The precise energies involved are codified in the curve of binding energy.  The current consensus is that biological systems get their energy from
biochemical reactions;  the low energies involved in chemical reactions makes nuclear transmutations difficult to explain in the frame of current theories
- The biological system would have to have a means of controlling the high energies produced by nuclear reactions, which would otherwise damage the biological system by breaking many chemical bonds.
Proponents respond that evidence shows that transmutations do occur, and that the lack of a theoretical model adequately explaining the mechanisms involved (that is, without a source for, or the emission of, deadly amounts of energy) does not render that evidence invalid.

# Proponents involved in the controversy
The most prominent defender of the existence of biological transmutations
is the French scientist Corentin Louis Kervran, who investigated discrepancies
between the dietary or environmental intake of elements such as calcium, potassium or magnesium
by various organisms and the quantities they hold or excrete.  For instance he
investigated the source
-f calcium chickens use for their eggshells, and concluded that they probably convert it from dietary
potassium.
The "Prof. Dr. L.W.J. Holleman Stichting" foundation also supports research in this field.

# Links to cold fusion
Interest has been revived with the controversy on cold fusion.  In 2003, Russian researchers claimed to have converted nuclear waste into non-radioactive elements using microbiological cultures.