Persius/hicric huggingface dataset:
Sensitivity (tests)

# Overview
Sensitivity refers to the statistical measure of how well a binary classification test correctly identifies a condition. In epidemiology, this is referred to as medical screening tests that detect preclinical disease. In quality control, this is referred to as a recall rate, whereby factories decided if a new product is at an acceptable level to be mass-produced and sold for distribution.

# Critical Considerations
- The results of the screening test are compared to some absolute (Gold standard); for example, for a medical test to determine if a person has a certain disease, the sensitivity to the disease is the probability that if the person has the disease, the test will be positive.
- The sensitivity is the proportion of true positives of all diseased cases in the population.  It is a parameter of the test.
- High sensitivity is required when early diagnosis and treatment is beneficial, and when the disease is infectious.

# Worked Example

# Definition
A sensitivity of 100% means that the test recognizes all sick people as such.
Sensitivity alone does not tell us how well the test predicts other classes (that is, about the negative cases).  In the binary classification, as illustrated above, this is the corresponding  specificity test, or equivalently, the sensitivity for the other classes.
Sensitivity is not the same as the positive predictive value (ratio of true positives to combined true and false positives), which is as much a statement about the proportion of actual positives in the population being tested as it is about the test.
The calculation of sensitivity does not take into account indeterminate test results. If a test cannot be repeated, the options are to exclude indeterminate samples from analyses (but the number of exclusions should be stated when quoting sensitivity), or, alternatively, indeterminate samples can be treated as false negatives (which gives the worst-case value for sensitivity and may therefore underestimate it).

# SPPIN and SNNOUT

# Terminology in Information Retrieval
In information retrieval, positive predictive value is called precision, and  sensitivity is called recall.
F-measure: can be used as a single measure of performance of the test.  The F-measure is the harmonic mean of precision and recall:
In the traditional language of statistical hypothesis testing, the sensitivity of a test is called the statistical power of the test, although the word power in that context has a more general usage that is not applicable in the present context.  A sensitive test will have fewer  Type II errors.

# Related Chapters
- binary classification
- receiver operating characteristic
- specificity (tests)
- statistical significance
- Type I and type II errors
- Selectivity

# Online Calculators
- MedCalc's Sensitivity/Specificity Calculator
Sertraline overdose

# Overdosage topics
Overdose dosage
Manifestation
Overdose Management

## Overdose dosage
The largest known ingestion was 13.5 grams in a patient who took sertraline hydrochloride alone
and subsequently recovered. However, another patient who took 2.5 grams of sertraline
hydrochloride alone experienced a fatal outcome.

## Manifestation
Other important adverse events reported with sertraline hydrochloride overdose (single or multiple drugs) include bradycardia, bundle branch block, coma, convulsions, delirium,
hallucinations, hypertension, hypotension, manic reaction, pancreatitis, QT-interval
prolongation, serotonin syndrome, stupor and syncope.

## Overdose Management
Treatment should consist of those general measures employed in the
management of overdosage with any antidepressant.
Ensure an adequate airway, oxygenation and ventilation. Monitor cardiac rhythm and vital
signs. General supportive and symptomatic measures are also recommended. Induction of emesis
is not recommended. Gastric lavage with a large-bore orogastric tube with appropriate airway
protection, if needed, may be indicated if performed soon after ingestion, or in symptomatic
patients.
Activated charcoal should be administered. Due to large volume of distribution of this drug,
forced diuresis, dialysis, hemoperfusion and exchange transfusion are unlikely to be of benefit.
No specific antidotes for sertraline are known.
In managing overdosage, consider the possibility of multiple drug involvement. The physician
should consider contacting a poison control center on the treatment of any overdose. Telephone
numbers for certified poison control centers are listed in the Physicians Desk Reference
(PDR).
Adapted from the FDA Package Insert.
Serum total protein
Serum total protein, also called plasma total protein or total protein, is a biochemical test for measuring the total amount of protein in blood plasma or serum.
Protein in the plasma is made up of albumin and globulin.  The globulin in turn is made up of 1, 2, , and  globulins. These fractions can be quantitated using protein electrophoresis, but the total protein test is a faster and cheaper test that estimates the total of all fractions together.  The traditional method for measuring total protein uses the biuret reagent, but other chemical methods are now available. The measurement is usually performed on automated analysers along with other laboratory tests.
The reference range for total protein is 60-85g/L.  Concentrations below the reference range usually reflect low albumin concentration, for instance in liver disease or acute infection.  Concentrations above the reference range are found in paraproteinemia, Hodgkin's lymphoma or leukaemia.
Silphium laciniatum
Silphium laciniatum (Compass Flower, Compass Plant or Rosinweed) is a species of flowering plant in the genus Silphium. It is native to east-central North America, from southern Ontario and New York south to Alabama and west across the prairies to North Dakota and Colorado south to Texas.
It is a perennial herbaceous plant similar in appearance to a sunflower, growing to 1-4 m tall, with bristly-hairy stems. The leaves are alternately arranged, and deeply pinnately lobed; the basal leaves up to 40 cm long, becoming smaller higher up the stem. The flowers are produced in flowerheads (capitula) 5-12 cm diameter, with a ring of ray florets surrounding the 2-3 cm diameter center of disc florets. Flowering is in late summer, typically from July to September.
Compass plants are so named because they tend to align their foliage north and south to present the minimum surface area to the hot noon sunshine. The taproot of the compass plant may grow to more than 9-14 ft. deep, making it hardy and resistant to drought.
The plant was used in Native American herbal medicine as a vermifuge, and to treat coughs and asthma.
Simulated pregnancy
A simulated pregnancy is a deliberate attempt to create the false impression of pregnancy.
It should not be confused with false pregnancy, where the woman believes that she is truly pregnant. On that note, women have the option of using artificially supplied hormones to cause their bodies to effectively experience a false pregnancy, which would appear to be the truest form of simulated pregnancy yet discovered.
Women who wish to experience pregnancy to look pregnant, generally for social or psychological purposes, have the option of body suits and the like to wear under their clothes.
Sleep onset latency

# Overview
In sleep science, sleep onset latency (SOL) is the length of time that it takes to accomplish the transition from full wakefulness to sleep, normally to the lightest sleep stage non-REM.
Daytime tests, such as the MSLT, measure sleep onset latency as an indication of excessive daytime sleepiness (EDS).  A sleep onset latency of 15-25 minutes in a person's biological daytime is considered normal. A shorter latency is likely a sign that a person suffers from sleep deprivation.  A sleep onset latency of less than five minutes indicates either very unhealthy daytime sleepiness or one of several sleep disorders, for example narcolepsy.
A long SOL at bedtime can be an indication of a sleep disorder, including but not limited to insomnia.
Snakebites overview

# Overview
A snakebite is a bite inflicted by a snake. Snakes often bite their prey when feeding, but occasionally, they bite humans. People can avoid and treat snakebites by knowing their etiology, along with prevention tips, and first-aid and hospital treatment.

# Epidemiology and Demographics
Every state but Maine, Alaska and Hawaii is home to at least one of 20 domestic poisonous snake species. About 8,000 people a year receive venomous bites in the United States; nine to 15 victims die. Some experts say that because victims can't always positively identify a snake, they should seek prompt care for any bite, though they may think the snake is nonpoisonous. Some deaths are sudden, however in fact it is uncommon to die within four hours of a snake bite.  In the 1900s, the untreated death rates were as high as 40% to 50%.  Improved supportive treatment and the availability of effective antivenoms has reduced this considerably.

# Natural History, Complications and Prognosis
Recovery is usually complete, though the patient usually develops a sensitivity to equine immunoglobulin. If the patient develops serum sickness, the severity is reduced by steroid administration (eg. prednisolone 1mg/kg every 8 hours) until resolution occurs. A course of steroids is recommended in all patients who receive polyvalent antivenoms.
Social neuroscience
Social neuroscience is an interdisciplinary field that utilizes the complementary insights and approaches of neuroscience and social science to analyze social and affective aspects of human behavior. An emerging field, it is closely related to affective neuroscience and cognitive neuroscience, focusing on how the brain mediates social interactions.

# Overview
Social neuroscience investigates the biological mechanisms that underlie social processes and behavior, widely considered one of the major problem areas for the neurosciences in the 21st century, and applies concepts and methods of biology to develop theories of social processes and behavior in the social and behavioral sciences.
Throughout most of the 20th century, social and biological explanations were widely viewed as incompatible. But advances in recent years have led to the development of a new approach synthesized from the social and biological sciences. The new field of social neuroscience emphasizes the complementary relationship between the different levels of organization spanning the social and biological domains  i.e., molecule, cell, organ, system, person, interpersonal, social group, societal  and the use of multi-level analyses to foster understanding of the mechanisms underlying the human mind and behavior.
A variety of techniques are used in social neuroscience to investigate the confluence of neural and social processes, including Functional MRI, Transcranial magnetic stimulation, Event-related potentials, Electrocardiograms, Electromyograms, Galvanic skin response, and studies of Focal Brain Lesion patients.
Space-filling model
Space-filling models (also known as calotte models or CPK models by Corey, Pauling and Koltun), like ball-and-stick models, belong to the 3D or spatial molecular models, which serve to display the structure of chemical products and substances or biomolecules.
The calotte model is a further development of the ball-and-stick model, with which the configuration of molecules can be vividly presented. With it, the atoms of individual elements are represented by multicolored spherical sections. Atom size, bond angle and bond length correspond to the actual relationships.
The result is a clear and (depending on construction materials and execution)  flexible model of the molecule. Presentation is also possible using software.
Specials Laboratory
Specials Laboratory started back in 1999 with 3 people and now has around 135 employees based across three MHRA-licensed sites.
In recent years, Specials Laboratory have launched a number of services to assist hospitals across the UK. They provide hospitals with a space and time saving Over Labelling service, which involves the bespoke design and labelling of products.
Specials Laboratory offer a service to manufacture Investigational Medicinal Products (IMPs), in order to meet the supply needs of hospital-based clinical trials. Specials Laboratory has three sites and each are licensed to offer a IMP manufacturing service for non-sterile medicines for use in small clinical studies. This GMP manufacturing service supports clinical trial pharmacists and technicians, University medical schools and research doctors carrying out such trials and requiring an outsourced manufacturing partner.
Specificity (tests)

# Overview
The specificity is a statistical measure of how well a binary classification test correctly identifies the negative cases. It is the probability that a test correctly classifies individuals without preclinical disease as negative. It is a proportional measurement and is often expressed in terms of percentage.

# Calculation
For example, given a medical test that determines if a person has a certain disease, the specificity of the test to the disease is the probability that the test indicates `negative' if the person does not have the disease.
That is, the specificity is the proportion of true negatives of all negative cases in the population. It is a parameter of the test.
High specificity is important when the treatment or diagnosis is harmful to the patient mentally and/or physically.

# Worked example

# Definition
A specificity of 100% means that the test recognizes all healthy people as healthy. The maximum is trivially achieved by a test that claims everybody healthy regardless of the true condition. Therefore, the specificity alone does not tell us how well the test recognizes positive cases.  We also need to know the sensitivity of the test to the class, or equivalently, the specificities to the other classes.
A test with a high specificity has a low  Type I error rate.
Specificity is sometimes confused with the precision or the positive predictive value, both of which refer to the fraction of returned positives that are true positives. The distinction is critical when the classes are different sizes. A test with very high specificity can have very low precision if there are far more true negatives than true positives, and vice versa.<

# SPPIN and SNNOUT

# Related Chapters
- binary classification
- receiver operating characteristic
- sensitivity (tests)
- statistical significance
- Type I and type II errors
- Selectivity

# Online Calculators
- MedCalc's Sensitivity/Specificity Calculator
Speech disfluencies
Speech disfluencies are any of various breaks, irregularities, or utterances that are often not consistent with any specific grammatical construction and occur within the flow of otherwise fluent speech. These include, for example, words and sentences that are cut off mid-utterance, phrases that are restarted or repeated, repeated syllables, grunts or unrecognizable utterances occurring as 'fillers', and 'repaired' utterances.
- "The best part of my job is...well...the best part of my job is the responsibility."
- "The soup is, ... the soup is too hot and it would burn if you ... it would burn you if you tried to eat it."
- "Fool me once, shame on - uh, shame on you. Fool me - ... you can't get fooled again."

# Fillers
Fillers are parts of speech which are not generally recognized as purposeful or containing formal meaning, usually expressed as pauses such as uh or er, but also extending to repairs ("He was wearing a black shirt and uh, blue pants"), and articulation problems such as stuttering.  Use is normally frowned upon in mass media such as news reports or films, but they occur regularly in everyday conversation, sometimes representing upwards of 20% of "words" in conversation.

# Language-dependence
Research in computational linguistics has revealed a correlation between native language and patterns of disfluencies in spontaneously uttered speech. In addition to this research, there are other subjective accounts reported by individuals. According to one commentator, Americans use pauses such as "um" or "uh," the British say "er" or "erm", the French use something like "euh," the German say "ah" (pronounced eh or er), Japanese use "ahh", "ano", or "eto", and Hebrew and Spanish speakers use something like "ehhh", "como", and "este" in Mexican Spanish. In Mandarin "neige" & "jiege" are used while "Serbian" and "Croatian" speakers vocalize an "ovay".

# Research
Recent linguistic research has suggested that non-pathological disfluencies may contain a variety of meaning; the frequency of "uh" and "um" in English is often reflective of a speaker's alertness or emotional state. Some have hypothesized that the time of an "uh" or "um" is used for the planning of future words; other researchers have suggested that they are actually to be understood as full-fledged function words rather than accidents, indicating a delay of variable time yet to come. There is some debate as to whether to consider them a form of white noise or as a meaning-filled part of language.
Speech disfluencies have also become important in recent years with the advent of speech-to-text programs and other attempts at enabling computers to make sense of human speech.
In America, since the 1980s, the word "like" has been used as a discourse marker similar to filled pauses like "um" or "uh" and is widespread among youth. For example, "I, like, don't know" instead of "I, uh, don't know" (see Valley speak for more information).
Spermidine synthase
Spermidine synthase is an enzyme (EC 2.5.1.16) that catalyzes the transfer of the propylamine group from S-adenosylmethioninamine to putrescine in the biosynthesis of spermidine. The systematic name is S-adenosyl 3-(methylthio)propylamine:putrescine 3-aminopropyltransferase and it belongs to the group of aminopropyl transferases. It does not need any cofactors. Most spermidine synthases exist in solution as dimers.

# Specificity
With exception of the spermidine synthases from Thermotoga maritimum and from Escherichia coli, which accept different kinds of polyamines, all enzymes are highly specific for putrescine. No known spermidine synthase can use S-adenosyl methionine. This is prevented by a conserved aspartatyl residue in the active site, which is thought to repel the carboxyl moiety of S-adenosyl methionine. The putrescine-N-methyl transferase whose substrates are putrescine and S-adenosyl methionine and which is evolutionary related to the spermidine synthases lacks this aspartyl residue. It is even possible to convert the spermidine synthase by some mutations to a functional putrescine-N-methyltransferase.

# Mechanism
It is assumed that the synthesis of spermidine follows the Sn2 mechanism. There is some uncertainty if the reaction occurs via a ping-pong or via a ternary-complex mechanism. Some kinetic data, but not all, suggest a ping-pong mechanism, while the investigation of the stereochemical path of the reaction argues for a ternary-complex mechanism. Prior to the nucleophilic attack of the putrescine onto the S-adenosylmethioninamine the putrescine has to be deprotonated rendering the nitrogen nucleophilic since the putrescine is protonated at physiological pH and is therefore inactive.

# Inhibitors
The spermidine synthase can be inhibited by a wide variety of analogues of putrescine, S-adenosyl methioninamine and transition state analogues as Adodato (for further information see here)
Starvation overview

# Overview
Starvation is a severe reduction in vitamin, nutrient, and energy intake, and is the most extreme form of malnutrition.

# Pathophysiology
When food intake ceases, the body enters the starvation response. Initially, the body's glycogen stores are used up in about 24 hours. The level of insulin in circulation is low and the level of glucagon is very high. The main means of energy production is lipolysis. Gluconeogenesis converts glycerol into glucose and the Cori cycle converts lactate into usable glucose.  Two systems of energy enter the gluconeogenesis: proteolysis provides alanine and lactate produced from pyruvate, while acetyl CoA produces dissolved nutrients (Ketone bodies), which can be detected in urine and are used by the brain as a source of energy.
In terms of insulin resistance, starvation conditions make more glucose available to the brain.

# Diagnosis

## Physical Examination
Cachexia is present as individuals experiencing starvation lose substantial fat and muscle mass as the body breaks down these tissues for energy.

## Electrocardiogram
Electrocardiogram of patients with starvation may show QT lengthening.

# Treatment

## Medical Therapy
Starving patients can be treated, but this must be done cautiously to avoid refeeding syndrome. Rest and warmth must be provided and maintained. Small sips of water mixed with glucose should be given in regular intervals. Fruit juices can also be given. Later, food can be given gradually in small quantities. The quantity of food can be increased over time. Proteins may be administered intravenously to raise the level of serum proteins.

## Primary Prevention
For the individual, prevention consists of ensuring they eat plenty of food, varied enough to provide a nutritionally complete diet.  Short of sitting in front of a potentially starving person and offering him or her food, addressing societal mechanisms by which people are denied access to food is a more complicated matter. Supporting farmers in areas of food insecurity through such measures as free or subsidized fertilizers and seeds increases food harvest and reduces food prices.
Stochastic calculus
Stochastic calculus is a branch of mathematics that operates on  stochastic processes. It allows a consistent theory of integration to be defined for integrals of stochastic processes with respect to stochastic processes. It is used to model systems that behave randomly.
The best-known stochastic process to which stochastic calculus is applied is the Wiener process (named in honor of Norbert Wiener), which is used for modeling Brownian motion as described by Albert Einstein and other physical diffusion processes in space of particles subject to random forces.  Since the 1970's, the Wiener process has been widely applied in financial mathematics to model the evolution in time of stock and bond prices.
The main flavours of stochastic calculus are the Ito calculus and its variational relative the Malliavin calculus.  For technical reasons the Ito integral is the most useful for general classes of processes but the related Stratonovich integral is frequently useful in problem formulation (particularly in engineering disciplines.) The Stratonovich integral can readily be expressed in terms of the Ito integral.  Another benefit of the Stratonovich integral is that it enables some problems to be expressed in a co-ordinate system invariant form and is therefore invaluable when developing stochastic calculus on manifolds other than Rn.
The Dominated convergence theorem does not hold for the Stratonovich  integral, consequently it is very difficult to prove results without re-expressing the integrals in Ito form.

# Ito integral
The Ito integral is central to the study of stochastic calculus. The integral \int H\,dX is defined for a semimartingale X and locally bounded predictable process H.

# Stratonovich integral
The Stratonovich integral can be defined in terms of the Ito integral as
The alternative notation
is also used to denote the Stratonovich integral.