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A. Merritt

Abraham Grace Merritt (January 20, 1884 – August 21, 1943) – known by his byline, A. Merritt – was an American Sunday magazine editor and a writer of fantastic fiction.

The Science Fiction and Fantasy Hall of Fame inducted him in 1999, its fourth class of two deceased and two living writers.

Life
Born in Beverly, New Jersey, he moved to Philadelphia, Pennsylvania in 1894. Originally trained in law, he turned to journalism, first as a correspondent and later as editor. According to Peter Haining, Merritt survived a harrowing experience while a young reporter at The Philadelphia Inquirer about which he refused to ever speak, but would, as Haining claims, mark a turning point in Merritt's life. He was assistant editor of The American Weekly from 1912 to 1937 under Morrill Goddard, then its editor from 1937 until his death. As editor, he hired the unheralded new artists Virgil Finlay and Hannes Bok and promoted the work done on polio by Sister Elizabeth Kenny.

His fiction, eight complete novels and a number of short stories, was only a sideline to his journalism career. One of the best-paid journalists of his era, Merritt made $25,000 per year by 1919, and at the end of his life was earning $100,000 yearly—exceptional sums for the period. His financial success allowed him to pursue world travel—he invested in real estate in Jamaica and Ecuador—and exotic hobbies, like cultivating orchids and plants linked to witchcraft and magic (monkshood, wolfbane, blue datura, peyote, and cannabis).

He was described as a hypochondriac who talked endlessly about his medical symptoms, and showed eccentric behavior like a need to try out any food, tobacco and medicine he found on his coworkers desks. Occasionally he would dress in a kilt and play serenades for his coworkers with some of his huge collection of instruments he kept in a locked closet at work. He was well liked for his fairness and inability to fire any employees.

Merritt married twice, once in the 1910s to Eleanore Ratcliffe, with whom he raised an adopted daughter, and again in the 1930s to Eleanor H. Johnson. He lived in the Hollis Park Gardens neighborhood of Queens, New York City, where he accumulated collections of weapons, carvings, and primitive masks from his travels, as well as a library of occult literature that reportedly exceeded 5000 volumes. He died suddenly of a heart attack, at his winter home in Indian Rocks Beach, Florida, in 1943.

Writing
Merritt's writings were heavily influenced by H. Rider Haggard, Robert W. Chambers, Helena Blavatsky and Gertrude Barrows Bennett (writing as Francis Stevens), with Merritt having "emulated Bennett's earlier style and themes." Merritt's stories typically revolve around conventional pulp magazine themes: lost civilizations, hideous monsters, etc. His heroes are gallant Irishmen or Scandinavians, his villains treacherous Germans or Russians and his heroines often virginal, mysterious and scantily clad.

What sets Merritt apart from the typical pulp author, however, is his lush, florid prose style and his exhaustive, at times exhausting, penchant for adjective-laden detail. Merritt's fondness for micro-description nicely complements the pointillistic style of Bok's illustrations. Merritt's first fantasy story was published in 1917, "Through the Dragon Glass" in the November 14 issue of Frank Munsey's All-Story Weekly. Other short stories and serial novels followed in the Munsey magazines All-Story, Argosy All-Story, and Argosy: The People of the Pit (1918), "The Moon Pool" (1918), The Conquest of the Moon Pool (1919), "Three Lines of Old French" (1919), The Metal Monster (1920), The Face in the Abyss (1923), The Ship of Ishtar (1924), Seven Footprints to Satan (1927), The Snake Mother (1930), Burn Witch Burn! (1932), Dwellers in the Mirage (1932), and Creep, Shadow! (1934). Meanwhile, rather few of his stories appeared elsewhere: The Pool of the Stone God (in his own American Weekly, 1923), The Woman of the Wood (Weird Tales, 1926), The Metal Emperor (Science and Invention, 1927), and The Drone Man (Fantasy Magazine, 1934).

Merritt also contributed to the round robin story The Challenge from Beyond with Lovecraft, Robert E. Howard, C. L. Moore, and Frank Belknap Long.

The Fox Woman and the Blue Pagoda (1946) combined an unfinished story with a conclusion written by Merritt's friend Hannes Bok. The Fox Woman and Other Stories (1949) collected the same fragment, minus Bok's conclusion, with Merritt's short stories. The book The Black Wheel was published in 1948, after Merritt's death; it was written by Bok using previously unpublished material as well. Both these books were also illustrated by Bok and published by the small press The New Collectors Group in hardcover.

After Merritt's death, Sam Moskowitz discovered a number of poems among his papers. Though some may have been written by other authors, they were credited to Merritt when published.

Reputation
Merritt was a major influence on H. P. Lovecraft and Richard Shaver, and highly esteemed by his friend and frequent collaborator Hannes Bok, a science fiction illustrator. Karl Edward Wagner included Burn Witch Burn on his list of "The Thirteen Best Supernatural Horror Novels" in the May 1983 issue of The Twilight Zone Magazine. Michael Moorcock and James Cawthorn list The Ship of Ishtar and Dwellers in the Mirage as two of the novels in their book Fantasy: the 100 Best Books, describing the former book as Merritt "at the peak of his powers", and Merritt's work as a whole being full of "memorable images". Robert Bloch also included Burn Witch Burn on his list of favourite horror novels. Gary Gygax, co-creator of the game Dungeons & Dragons, listed Merritt in "Appendix N" of the Dungeon Masters Guide and often noted that he was one of his favorite fantasy authors. In the Lensman series by E. E. Smith, there is a reference to the novel Dwellers in the Mirage in which the protagonist Kimball Kinnison references the book and a quotation from it "Luka—turn your wheel so I need not slay this woman!"

Novels
(The Moon Pool (1918) + Conquest of the Moon Pool (1919)) (The Face in the Abyss (1923) + The Snake Mother (1930))
 * The Moon Pool (fix-up, 1919) Available online
 * The Metal Monster (1920) Available online
 * The Ship of Ishtar (1924) Available online
 * Seven Footprints to Satan (1927) Available online
 * The Face in the Abyss (fix-up, 1931) Available online
 * Dwellers in the Mirage (1932) Available online
 * Burn, Witch, Burn! (1932) Available online
 * Creep, Shadow! (1934) Available online

Short stories

 * "Through The Dragon Glass" (1917) Available online
 * "The People of the Pit" (1918) Available online
 * "Three Lines of Old French" (1919) Available online
 * "Prologue" (The Metal Monster, 1920)
 * The Pool of the Stone God (as W. Fenimore, 1923) Available online
 * "The Women of the Wood" (1926) Available online
 * "The Drone" (also known as "The Drone Man", 1934) Available online
 * "The Rhythm of the Spheres" (originally a chapter called "The Last Poet and the Robots" or "The Last Poet & the Wrongness of Space" in the 1934 round robin novel titled Cosmos, revised in 1936 as a stand-alone work) Available online
 * "The Whelming of Cherkis" (excerpt from The Metal Monster, 1946)
 * "When Old Gods Wake" (fragment, 1948) Available online
 * "The White Road" (fragment, 1949) Available online
 * "The Fox Woman" (incomplete, 1949) Available online
 * "Pilgrimage, or, Obi Giese" (1985)
 * "Bootleg and Witches" (fragment, 1985)
 * "The Devil in the Heart" (outline, 1985)
 * "The Dwellers in the Mirage" (original ending of the novel with same name, 1985)

Short story collections

 * The Fox Woman and Other Stories (1949)
 * The Fox Woman, 1946
 * The People of the Pit, 1917
 * Through the Dragon Glass, 1917
 * The Drone, 1934
 * The Last Poet and the Robots, 1934
 * Three Lines of Old French, 1919
 * The White Road, 1949
 * When Old Gods Wake, 1948
 * The Woman of the Wood, 1934

Poems

 * "The Birth of Art" (1904)
 * "Song for Wood Horns" (also known as "The Wind Trail", 1910)
 * "The Silver Birches" (1940)
 * "Old Trinity Churchyard" (5 A. M. Spring) (1941)
 * "Sylvane – The Silver Birches" (1973)
 * "In the Cathedral" (1974)
 * "2000 (The Triple Cities)" (1985)
 * "Song for Wood Horn..." (1985)
 * "Silvane—The Silver Birches" (1985)
 * "Madonna" (1985)
 * "The Ladies of the Walnut Tree (A Legend of Tuscany)" (fragments, 1985)
 * "Court of the Moon" (fragment, 1985)
 * "L'envoi to Life" (1985)
 * "Screens" (1985)
 * "Sir Barnabas" (1985)
 * "In the Subway" (1985)
 * "Runes" (1985)
 * "Eheu Fugaces..." (1985)
 * "A Song for Christmas" (1985)
 * "Comic Ragtime Tune" (1985)
 * "Behold the Night He Cometh" (1985)
 * "You Looked at Me" (1985)
 * "Dream Song" (1985)
 * "Castle of Dreams" (1985)
 * "I Wonder Why?" (1985)
 * "My Heart and I" (1985)
 * Think of Me (1985)
 * "The Ballad of the Cub" (1985)
 * "Piddling Pete" (1985)
 * "The Winged Flames" (1985)

Collaborations

 * "The Challenge from Beyond" (round robin short story, with C.L. Moore, H.P. Lovecraft, Robert E. Howard, and Frank Belknap Long, 1935) Available online
 * Cosmos (round robin novel, chapter 11, 1932–34) Available online
 * The Fox Woman and the Blue Pagoda (novel, Hannes Bok fused Merritt's unfinished story with his own conclusion, 1946)
 * The Black Wheel (novel, first seven chapters written by Merritt, completed by Hannes Bok, 1947)

Essays

 * A. Merritt on Modern Witchcraft (1932)
 * Concerning "Burn, Witch, Burn" (1932)
 * Letter (Weird Tales, November 1935) (1935)
 * Man and the Universe (1940)
 * A. Merritt (1940)
 * How We Found Circe (1942)
 * A Tribute (1942)
 * Letter to Mr. Louis De Casanova, July 23, 1931 (1985)
 * Letters and Correspondence (1985)
 * An Autobiography of A. Merritt (1985) with Walter Wentz
 * A. Merritt—His Life and Times (1985) with Jack Chapman Miske
 * What is Fantasy? (1985)
 * Background of "Dwellers in the Mirage" (1985)
 * Background of "Burn, Witch, Burn" (1985)
 * Background of "Creep, Shadow!" (1985)
 * A. Merritt's Own Selected Credo (1985)

Adaptations
Merritt's work has been adapted only rarely for films. These include:

 * Seven Footprints to Satan (1929), adapted from the novel of the same name and directed by Benjamin Christensen.
 * The Devil-Doll (1936), adapted from the novel Burn Witch Burn! and directed by Tod Browning.
 * Muñecos infernales (1961), adapted from the novel Burn Witch Burn! (uncredited) and directed by Benito Alazraki.

title: A. Merritt


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Head-driven phrase structure grammar

Head-driven phrase structure grammar (HPSG) is a highly lexicalized, constraint-based grammar developed by Carl Pollard and Ivan Sag. It is a type of phrase structure grammar, as opposed to a dependency grammar, and it is the immediate successor to generalized phrase structure grammar. HPSG draws from other fields such as computer science (data type theory and knowledge representation) and uses Ferdinand de Saussure's notion of the sign. It uses a uniform formalism and is organized in a modular way which makes it attractive for natural language processing.

An HPSG includes principles and grammar rules and lexicon entries which are normally not considered to belong to a grammar. The formalism is based on lexicalism. This means that the lexicon is more than just a list of entries; it is in itself richly structured. Individual entries are marked with types. Types form a hierarchy. Early versions of the grammar were very lexicalized with few grammatical rules (schema). More recent research has tended to add more and richer rules, becoming more like construction grammar.

The basic type HPSG deals with is the sign. Words and phrases are two different subtypes of sign. A word has two features: [PHON] (the sound, the phonetic form) and [SYNSEM] (the syntactic and semantic information), both of which are split into subfeatures. Signs and rules are formalized as typed feature structures.

Sample grammar
HPSG generates strings by combining signs, which are defined by their location within a type hierarchy and by their internal feature structure, represented by attribute value matrices (AVMs). Features take types or lists of types as their values, and these values may in turn have their own feature structure. Grammatical rules are largely expressed through the constraints signs place on one another. A sign's feature structure describes its phonological, syntactic, and semantic properties. In common notation, AVMs are written with features in upper case and types in italicized lower case. Numbered indices in an AVM represent token identical values.

In the simplified AVM for the word (in this case the verb, not the noun as in "nice walks for the weekend") "walks" below, the verb's categorical information (CAT) is divided into features that describe it (HEAD) and features that describe its arguments (VALENCE).

"Walks" is a sign of type word with a head of type verb. As an intransitive verb, "walks" has no complement but requires a subject that is a third person singular noun. The semantic value of the subject (CONTENT) is co-indexed with the verb's only argument (the individual doing the walking). The following AVM for "she" represents a sign with a SYNSEM value that could fulfill those requirements.

Signs of type phrase unify with one or more children and propagate information upward. The following AVM encodes the immediate dominance rule for a head-subj-phrase, which requires two children: the head child (a verb) and a non-head child that fulfills the verb's SUBJ constraints.

The end result is a sign with a verb head, empty subcategorization features, and a phonological value that orders the two children.

Although the actual grammar of HPSG is composed entirely of feature structures, linguists often use trees to represent the unification of signs where the equivalent AVM would be unwieldy.

Implementations
Various parsers based on the HPSG formalism have been written and optimizations are currently being investigated. An example of a system analyzing German sentences is provided by the Freie Universität Berlin. In addition the CoreGram project of the Grammar Group of the Freie Universität Berlin provides open source grammars that were implemented in the TRALE system. Currently there are grammars for German, Danish, Mandarin Chinese, Maltese, and Persian that share a common core and are publicly available.

Large HPSG grammars of various languages are being developed in the Deep Linguistic Processing with HPSG Initiative (DELPH-IN). Wide-coverage grammars of English, German, and Japanese are available under an open-source license. These grammars can be used with a variety of inter-compatible open-source HPSG parsers: LKB, PET, Ace, and agree. All of these produce semantic representations in the format of “Minimal Recursion Semantics,” MRS. The declarative nature of the HPSG formalism means that these computational grammars can typically be used for both parsing and generation (producing surface strings from semantic inputs). Treebanks, also distributed by DELPH-IN, are used to develop and test the grammars, as well as to train ranking models to decide on plausible interpretations when parsing (or realizations when generating).

Enju is a freely available wide-coverage probabilistic HPSG parser for English developed by the Tsujii Laboratory at The University of Tokyo in Japan.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

title: Head-driven phrase structure grammar


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Wood hoopoe

The wood hoopoes or scimitarbills are a small African family, Phoeniculidae, of near passerine birds. They live south of the Sahara Desert and are not migratory. While the family is now restricted to Sub-Saharan Africa, fossil evidence shows that it once had a larger distribution. Fossils attributed to this family have been found in Miocene rocks in Germany.

The wood hoopoes are related to the kingfishers, the rollers, and the hoopoe, forming a clade with this last according to Hackett et al. (2008). A close relationship between the hoopoe and the wood hoopoes is also supported by the shared and unique nature of their stapes. The wood hoopoes most resemble the true hoopoes with their long down-curved bills and short rounded wings. According to genetic studies, the two genera, Phoeniculus and Rhinopomastus, appear to have diverged about ten million years ago, so some systematists treat them as separate subfamilies or even separate families.

Description
The wood hoopoes are a morphologically distinct group, unlikely to be mistaken for any other. These species are medium-sized (23 - 46 cm long, much of which is the tail). They have metallic plumage, often blue, green or purple, and lack a crest. The sexes are similar in all but two species, the forest wood hoopoe and the common scimitarbill. Their bills are either red or black, although young red-billed species also have black bills and bill colour is correlated with age. The legs are scarlet or black, short, with thick tarsi. They climb tree trunks in the manner of a woodpecker, and when feeding on the ground they hop rather than walking like the true hoopoe. Their tails are long and strongly graduated (the central feathers are the longest), and marked conspicuously with white, as are their wings.

Range and behaviour
These are birds of open woodland, savannah, or thornbrush, and are mainly arboreal. They require large trees both for feeding on as well as to provide hollows for nesting and nocturnal roosting. Two species are found exclusively in rainforest, the forest wood hoopoe and the white-headed wood hoopoe. All the other species are found in more open woodland and bush.

They feed on arthropods, especially insects, which they find by probing with their bills in rotten wood and in crevices in bark. They nest in unlined tree holes, laying two to four eggs, which are blue, grey, or olive, and unmarked in most species.

Hoopoes hunt for prey primarily on the ground as they use their tongue-like beaks to pick up insects on the soil or grass. The Hoopoe's tongue occupy 2/3 length of the beak.

Species
There are eight species.

Family: Phoeniculidae

title: Wood hoopoe


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DNA microarray

A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles (10−12 moles) of a specific DNA sequence, known as probes (or reporters or oligos). These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA (also called anti-sense RNA) sample (called target) under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target. The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm and the first computerized image based analysis was published in 1981. It was invented by Patrick O. Brown. An example of its application is in SNPs arrays for polymorphisms in cardiovascular diseases, cancer, pathogens and GWAS analysis. It is also used for the identification of structural variations and the measurement of gene expression.

Principle

The core principle behind microarrays is hybridization between two DNA strands, the property of complementary nucleic acid sequences to specifically pair with each other by forming hydrogen bonds between complementary nucleotide base pairs. A high number of complementary base pairs in a nucleotide sequence means tighter non-covalent bonding between the two strands. After washing off non-specific bonding sequences, only strongly paired strands will remain hybridized. Fluorescently labeled target sequences that bind to a probe sequence generate a signal that depends on the hybridization conditions (such as temperature), and washing after hybridization. Total strength of the signal, from a spot (feature), depends upon the amount of target sample binding to the probes present on that spot. Microarrays use relative quantitation in which the intensity of a feature is compared to the intensity of the same feature under a different condition, and the identity of the feature is known by its position.

Uses and types
Many types of arrays exist and the broadest distinction is whether they are spatially arranged on a surface or on coded beads:
 * The traditional solid-phase array is a collection of orderly microscopic "spots", called features, each with thousands of identical and specific probes attached to a solid surface, such as glass, plastic or silicon biochip (commonly known as a genome chip, DNA chip or gene array). Thousands of these features can be placed in known locations on a single DNA microarray.
 * The alternative bead array is a collection of microscopic polystyrene beads, each with a specific probe and a ratio of two or more dyes, which do not interfere with the fluorescent dyes used on the target sequence.

DNA microarrays can be used to detect DNA (as in comparative genomic hybridization), or detect RNA (most commonly as cDNA after reverse transcription) that may or may not be translated into proteins. The process of measuring gene expression via cDNA is called expression analysis or expression profiling.

Applications include:

Specialised arrays tailored to particular crops are becoming increasingly popular in molecular breeding applications. In the future they could be used to screen seedlings at early stages to lower the number of unneeded seedlings tried out in breeding operations.

Fabrication
Microarrays can be manufactured in different ways, depending on the number of probes under examination, costs, customization requirements, and the type of scientific question being asked. Arrays from commercial vendors may have as few as 10 probes or as many as 5 million or more micrometre-scale probes.

Spotted vs. in situ synthesised arrays

Microarrays can be fabricated using a variety of technologies, including printing with fine-pointed pins onto glass slides, photolithography using pre-made masks, photolithography using dynamic micromirror devices, ink-jet printing, or electrochemistry on microelectrode arrays.

In spotted microarrays, the probes are oligonucleotides, cDNA or small fragments of PCR products that correspond to mRNAs. The probes are synthesized prior to deposition on the array surface and are then "spotted" onto glass. A common approach utilizes an array of fine pins or needles controlled by a robotic arm that is dipped into wells containing DNA probes and then depositing each probe at designated locations on the array surface. The resulting "grid" of probes represents the nucleic acid profiles of the prepared probes and is ready to receive complementary cDNA or cRNA "targets" derived from experimental or clinical samples. This technique is used by research scientists around the world to produce "in-house" printed microarrays in their own labs. These arrays may be easily customized for each experiment, because researchers can choose the probes and printing locations on the arrays, synthesize the probes in their own lab (or collaborating facility), and spot the arrays. They can then generate their own labeled samples for hybridization, hybridize the samples to the array, and finally scan the arrays with their own equipment. This provides a relatively low-cost microarray that may be customized for each study, and avoids the costs of purchasing often more expensive commercial arrays that may represent vast numbers of genes that are not of interest to the investigator. Publications exist which indicate in-house spotted microarrays may not provide the same level of sensitivity compared to commercial oligonucleotide arrays, possibly owing to the small batch sizes and reduced printing efficiencies when compared to industrial manufactures of oligo arrays.

In oligonucleotide microarrays, the probes are short sequences designed to match parts of the sequence of known or predicted open reading frames. Although oligonucleotide probes are often used in "spotted" microarrays, the term "oligonucleotide array" most often refers to a specific technique of manufacturing. Oligonucleotide arrays are produced by printing short oligonucleotide sequences designed to represent a single gene or family of gene splice-variants by synthesizing this sequence directly onto the array surface instead of depositing intact sequences. Sequences may be longer (60-mer probes such as the Agilent design) or shorter (25-mer probes produced by Affymetrix) depending on the desired purpose; longer probes are more specific to individual target genes, shorter probes may be spotted in higher density across the array and are cheaper to manufacture. One technique used to produce oligonucleotide arrays include photolithographic synthesis (Affymetrix) on a silica substrate where light and light-sensitive masking agents are used to "build" a sequence one nucleotide at a time across the entire array. Each applicable probe is selectively "unmasked" prior to bathing the array in a solution of a single nucleotide, then a masking reaction takes place and the next set of probes are unmasked in preparation for a different nucleotide exposure. After many repetitions, the sequences of every probe become fully constructed. More recently, Maskless Array Synthesis from NimbleGen Systems has combined flexibility with large numbers of probes.

Two-channel vs. one-channel detection

Two-color microarrays or two-channel microarrays are typically hybridized with cDNA prepared from two samples to be compared (e.g. diseased tissue versus healthy tissue) and that are labeled with two different fluorophores. Fluorescent dyes commonly used for cDNA labeling include Cy3, which has a fluorescence emission wavelength of 570 nm (corresponding to the green part of the light spectrum), and Cy5 with a fluorescence emission wavelength of 670 nm (corresponding to the red part of the light spectrum). The two Cy-labeled cDNA samples are mixed and hybridized to a single microarray that is then scanned in a microarray scanner to visualize fluorescence of the two fluorophores after excitation with a laser beam of a defined wavelength. Relative intensities of each fluorophore may then be used in ratio-based analysis to identify up-regulated and down-regulated genes.

Oligonucleotide microarrays often carry control probes designed to hybridize with RNA spike-ins. The degree of hybridization between the spike-ins and the control probes is used to normalize the hybridization measurements for the target probes. Although absolute levels of gene expression may be determined in the two-color array in rare instances, the relative differences in expression among different spots within a sample and between samples is the preferred method of data analysis for the two-color system. Examples of providers for such microarrays includes Agilent with their Dual-Mode platform, Eppendorf with their DualChip platform for colorimetric Silverquant labeling, and TeleChem International with Arrayit.

In single-channel microarrays or one-color microarrays, the arrays provide intensity data for each probe or probe set indicating a relative level of hybridization with the labeled target. However, they do not truly indicate abundance levels of a gene but rather relative abundance when compared to other samples or conditions when processed in the same experiment. Each RNA molecule encounters protocol and batch-specific bias during amplification, labeling, and hybridization phases of the experiment making comparisons between genes for the same microarray uninformative. The comparison of two conditions for the same gene requires two separate single-dye hybridizations. Several popular single-channel systems are the Affymetrix "Gene Chip", Illumina "Bead Chip", Agilent single-channel arrays, the Applied Microarrays "CodeLink" arrays, and the Eppendorf "DualChip & Silverquant". One strength of the single-dye system lies in the fact that an aberrant sample cannot affect the raw data derived from other samples, because each array chip is exposed to only one sample (as opposed to a two-color system in which a single low-quality sample may drastically impinge on overall data precision even if the other sample was of high quality). Another benefit is that data are more easily compared to arrays from different experiments as long as batch effects have been accounted for.

One channel microarray may be the only choice in some situations. Suppose $$i$$ samples need to be compared: then the number of experiments required using the two channel arrays quickly becomes unfeasible, unless a sample is used as a reference.

A typical protocol

This is an example of a DNA microarray experiment which includes details for a particular case to better explain DNA microarray experiments, while listing modifications for RNA or other alternative experiments.

 * 1) The two samples to be compared (pairwise comparison) are grown/acquired. In this example treated sample (case) and untreated sample (control).
 * 2) The nucleic acid of interest is purified: this can be RNA for expression profiling, DNA for comparative hybridization, or DNA/RNA bound to a particular protein which is immunoprecipitated (ChIP-on-chip) for epigenetic or regulation studies. In this example total RNA is isolated (both nuclear and cytoplasmic) by Guanidinium thiocyanate-phenol-chloroform extraction (e.g. Trizol) which isolates most RNA (whereas column methods have a cut off of 200 nucleotides) and if done correctly has a better purity.
 * 3) The purified RNA is analysed for quality (by capillary electrophoresis) and quantity (for example, by using a NanoDrop or NanoPhotometer spectrometer). If the material is of acceptable quality and sufficient quantity is present (e.g., >1μg, although the required amount varies by microarray platform), the experiment can proceed.
 * 4) The labeled product is generated via reverse transcription and followed by an optional PCR amplification. The RNA is reverse transcribed with either polyT primers (which amplify only mRNA) or random primers (which amplify all RNA, most of which is rRNA). miRNA microarrays ligate an oligonucleotide to the purified small RNA (isolated with a fractionator), which is then reverse transcribed and amplified.
 * 5) * The label is added either during the reverse transcription step, or following amplification if it is performed. The sense labeling is dependent on the microarray; e.g. if the label is added with the RT mix, the cDNA is antisense and the microarray probe is sense, except in the case of negative controls.
 * 6) * The label is typically fluorescent; only one machine uses radiolabels.
 * 7) * The labeling can be direct (not used) or indirect (requires a coupling stage). For two-channel arrays, the coupling stage occurs before hybridization, using aminoallyl uridine triphosphate (aminoallyl-UTP, or aaUTP) and NHS amino-reactive dyes (such as cyanine dyes); for single-channel arrays, the coupling stage occurs after hybridization, using biotin and labeled streptavidin. The modified nucleotides (usually in a ratio of 1 aaUTP: 4 TTP (thymidine triphosphate)) are added enzymatically in a low ratio to normal nucleotides, typically resulting in 1 every 60 bases. The aaDNA is then purified with a column (using a phosphate buffer solution, as Tris contains amine groups). The aminoallyl group is an amine group on a long linker attached to the nucleobase, which reacts with a reactive dye.
 * 8) ** A form of replicate known as a dye flip can be performed to control for dye artifacts in two-channel experiments; for a dye flip, a second slide is used, with the labels swapped (the sample that was labeled with Cy3 in the first slide is labeled with Cy5, and vice versa). In this example, aminoallyl-UTP is present in the reverse-transcribed mixture.
 * 9) The labeled samples are then mixed with a proprietary hybridization solution which can consist of SDS, SSC, dextran sulfate, a blocking agent (such as Cot-1 DNA, salmon sperm DNA, calf thymus DNA, PolyA, or PolyT), Denhardt's solution, or formamine.
 * 10) The mixture is denatured and added to the pinholes of the microarray. The holes are sealed and the microarray hybridized, either in a hyb oven, where the microarray is mixed by rotation, or in a mixer, where the microarray is mixed by alternating pressure at the pinholes.
 * 11) After an overnight hybridization, all nonspecific binding is washed off (SDS and SSC).
 * 12) The microarray is dried and scanned by a machine that uses a laser to excite the dye and measures the emission levels with a detector.
 * 13) The image is gridded with a template and the intensities of each feature (composed of several pixels) is quantified.
 * 14) The raw data is normalized; the simplest normalization method is to subtract background intensity and scale so that the total intensities of the features of the two channels are equal, or to use the intensity of a reference gene to calculate the t-value for all of the intensities. More sophisticated methods include z-ratio, loess and lowess regression and RMA (robust multichip analysis) for Affymetrix chips (single-channel, silicon chip, in situ synthesized short oligonucleotides).

Microarrays and bioinformatics

The advent of inexpensive microarray experiments created several specific bioinformatics challenges: the multiple levels of replication in experimental design (Experimental design); the number of platforms and independent groups and data format (Standardization); the statistical treatment of the data (Data analysis); mapping each probe to the mRNA transcript that it measures (Annotation); the sheer volume of data and the ability to share it (Data warehousing).

Experimental design
Due to the biological complexity of gene expression, the considerations of experimental design that are discussed in the expression profiling article are of critical importance if statistically and biologically valid conclusions are to be drawn from the data.

There are three main elements to consider when designing a microarray experiment. First, replication of the biological samples is essential for drawing conclusions from the experiment. Second, technical replicates (e.g. two RNA samples obtained from each experimental unit) may help to quantitate precision. The biological replicates include independent RNA extractions. Technical replicates may be two aliquots of the same extraction. Third, spots of each cDNA clone or oligonucleotide are present as replicates (at least duplicates) on the microarray slide, to provide a measure of technical precision in each hybridization. It is critical that information about the sample preparation and handling is discussed, in order to help identify the independent units in the experiment and to avoid inflated estimates of statistical significance.

Standardization
Microarray data is difficult to exchange due to the lack of standardization in platform fabrication, assay protocols, and analysis methods. This presents an interoperability problem in bioinformatics. Various grass-roots open-source projects are trying to ease the exchange and analysis of data produced with non-proprietary chips:

For example, the "Minimum Information About a Microarray Experiment" (MIAME) checklist helps define the level of detail that should exist and is being adopted by many journals as a requirement for the submission of papers incorporating microarray results. But MIAME does not describe the format for the information, so while many formats can support the MIAME requirements, no format permits verification of complete semantic compliance. The "MicroArray Quality Control (MAQC) Project" is being conducted by the US Food and Drug Administration (FDA) to develop standards and quality control metrics which will eventually allow the use of MicroArray data in drug discovery, clinical practice and regulatory decision-making. The MGED Society has developed standards for the representation of gene expression experiment results and relevant annotations.

Data analysis

Microarray data sets are commonly very large, and analytical precision is influenced by a number of variables. Statistical challenges include taking into account effects of background noise and appropriate normalization of the data. Normalization methods may be suited to specific platforms and, in the case of commercial platforms, the analysis may be proprietary. Algorithms that affect statistical analysis include:

 * Image analysis: gridding, spot recognition of the scanned image (segmentation algorithm), removal or marking of poor-quality and low-intensity features (called flagging).
 * Data processing: background subtraction (based on global or local background), determination of spot intensities and intensity ratios, visualisation of data (e.g. see MA plot), and log-transformation of ratios, global or local normalization of intensity ratios, and segmentation into different copy number regions using step detection algorithms.
 * Class discovery analysis: This analytic approach, sometimes called unsupervised classification or knowledge discovery, tries to identify whether microarrays (objects, patients, mice, etc.) or genes cluster together in groups. Identifying naturally existing groups of objects (microarrays or genes) which cluster together can enable the discovery of new groups that otherwise were not previously known to exist. During knowledge discovery analysis, various unsupervised classification techniques can be employed with DNA microarray data to identify novel clusters (classes) of arrays. This type of approach is not hypothesis-driven, but rather is based on iterative pattern recognition or statistical learning methods to find an "optimal" number of clusters in the data. Examples of unsupervised analyses methods include self-organizing maps, neural gas, k-means cluster analyses, hierarchical cluster analysis, Genomic Signal Processing based clustering and model-based cluster analysis. For some of these methods the user also has to define a distance measure between pairs of objects. Although the Pearson correlation coefficient is usually employed, several other measures have been proposed and evaluated in the literature. The input data used in class discovery analyses are commonly based on lists of genes having high informativeness (low noise) based on low values of the coefficient of variation or high values of Shannon entropy, etc. The determination of the most likely or optimal number of clusters obtained from an unsupervised analysis is called cluster validity. Some commonly used metrics for cluster validity are the silhouette index, Davies-Bouldin index, Dunn's index, or Hubert's $$\Gamma$$ statistic.
 * Class prediction analysis: This approach, called supervised classification, establishes the basis for developing a predictive model into which future unknown test objects can be input in order to predict the most likely class membership of the test objects. Supervised analysis for class prediction involves use of techniques such as linear regression, k-nearest neighbor, learning vector quantization, decision tree analysis, random forests, naive Bayes, logistic regression, kernel regression, artificial neural networks, support vector machines, mixture of experts, and supervised neural gas. In addition, various metaheuristic methods are employed, such as genetic algorithms, covariance matrix self-adaptation, particle swarm optimization, and ant colony optimization. Input data for class prediction are usually based on filtered lists of genes which are predictive of class, determined using classical hypothesis tests (next section), Gini diversity index, or information gain (entropy).
 * Hypothesis-driven statistical analysis: Identification of statistically significant changes in gene expression are commonly identified using the t-test, ANOVA, Bayesian method Mann–Whitney test methods tailored to microarray data sets, which take into account multiple comparisons or cluster analysis. These methods assess statistical power based on the variation present in the data and the number of experimental replicates, and can help minimize Type I and type II errors in the analyses.

 * Dimensional reduction: Analysts often reduce the number of dimensions (genes) prior to data analysis. This may involve linear approaches such as principal components analysis (PCA), or non-linear manifold learning (distance metric learning) using kernel PCA, diffusion maps, Laplacian eigenmaps, local linear embedding, locally preserving projections, and Sammon's mapping.
 * Network-based methods: Statistical methods that take the underlying structure of gene networks into account, representing either associative or causative interactions or dependencies among gene products. Weighted gene co-expression network analysis is widely used for identifying co-expression modules and intramodular hub genes. Modules may corresponds to cell types or pathways. Highly connected intramodular hubs best represent their respective modules.

Microarray data may require further processing aimed at reducing the dimensionality of the data to aid comprehension and more focused analysis. Other methods permit analysis of data consisting of a low number of biological or technical replicates; for example, the Local Pooled Error (LPE) test pools standard deviations of genes with similar expression levels in an effort to compensate for insufficient replication.

Annotation
The relation between a probe and the mRNA that it is expected to detect is not trivial. Some mRNAs may cross-hybridize probes in the array that are supposed to detect another mRNA. In addition, mRNAs may experience amplification bias that is sequence or molecule-specific. Thirdly, probes that are designed to detect the mRNA of a particular gene may be relying on genomic EST information that is incorrectly associated with that gene.

Data warehousing
Microarray data was found to be more useful when compared to other similar datasets. The sheer volume of data, specialized formats (such as MIAME), and curation efforts associated with the datasets require specialized databases to store the data. A number of open-source data warehousing solutions, such as InterMine and BioMart, have been created for the specific purpose of integrating diverse biological datasets, and also support analysis.

Alternative technologies
Advances in massively parallel sequencing has led to the development of RNA-Seq technology, that enables a whole transcriptome shotgun approach to characterize and quantify gene expression. Unlike microarrays, which need a reference genome and transcriptome to be available before the microarray itself can be designed, RNA-Seq can also be used for new model organisms whose genome has not been sequenced yet.

Glossary

 * An array or slide is a collection of features spatially arranged in a two dimensional grid, arranged in columns and rows.
 * Block or subarray: a group of spots, typically made in one print round; several subarrays/ blocks form an array.
 * Case/control: an experimental design paradigm especially suited to the two-colour array system, in which a condition chosen as control (such as healthy tissue or state) is compared to an altered condition (such as a diseased tissue or state).
 * Channel: the fluorescence output recorded in the scanner for an individual fluorophore and can even be ultraviolet.
 * Dye flip or dye swap or fluor reversal: reciprocal labelling of DNA targets with the two dyes to account for dye bias in experiments.
 * Scanner: an instrument used to detect and quantify the intensity of fluorescence of spots on a microarray slide, by selectively exciting fluorophores with a laser and measuring the fluorescence with a filter (optics) photomultiplier system.
 * Spot or feature: a small area on an array slide that contains picomoles of specific DNA samples.
 * For other relevant terms see:
 * Glossary of gene expression terms
 * Protocol (natural sciences)

title: DNA microarray


text:
Ground roller

The ground rollers, Brachypteraciidae, are a small family of non-migratory birds restricted to Madagascar. They are members of the order Coraciiformes and are most closely related to the rollers in the family Coraciidae.

Description
Ground rollers share the generally crow-like size and build of the true rollers, ranging from 25 to(-) in length, and also hunt reptiles and large insects. They are more terrestrial than Coracidae species, and this is reflected in their longer legs and shorter, more rounded wings.

They lack the highly colourful appearance of the true rollers, and are duller in appearance, with striped or flecked plumage. They are much more elusive and shy than their relatives, and are normally difficult to find in the Malagasy forests. Often the hooting breeding call is all that betrays their presence.

These birds nest as solitary pairs in holes in the ground which they excavate themselves, unlike the true rollers, which rarely nest in ground holes and even then do not dig their own nests.

Taxonomy
The phylogenetic relationship between the six families that make up the order Coraciiformes is shown in the cladogram below. The number of species in each family is taken from the list maintained by Frank Gill, Pamela C. Rasmussen and David Donsker on behalf of the International Ornithological Committee (IOC).

mtDNA analyses confirmed the systematics of this group but indicated that merging Geobiastes into Brachypteracias, as was usually done since the 1960s, should be reversed at least until a more comprehensive review (e.g. supported by fossils) is possible (Kirchman et al., 2001). Also, 2000-year-old subfossil remains of ground rollers are known from the Holocene of Ampoza (Goodman, 2000); Eocene remains from Europe at first tentatively assigned to this family were later recognized as quite distinct (Mayr & Mourer-Chauviré 2000). Presently, there is no indication that ground rollers ever occurred anywhere outside Madagascar (Mayr & Mourer-Chauviré, 2001).

Species
There are five extant species in four genera in the family Brachypteraciidae:

An extinct species, the Ampoza ground roller (Brachypteracias langrandi), of presumed Holocene age, was described in 2000 based on a single humerus.

title: Ground roller


text:
User:Optigan

29 years old, architect, resident of Oslo.

Interests include architecture, history, geography, politics, music, film, traveling.

title: User:Optigan


text:
Klaus Mann

Klaus Heinrich Thomas Mann (18 November 1906 – 21 May 1949) was a German writer and dissident. He was the son of Thomas Mann, a nephew of Heinrich Mann and brother of Erika Mann (with whom he maintained a lifelong close relationship) and Golo Mann.

Klaus moved to the USA to escape Nazism, and after training in counterintelligence as one of the Ritchie Boys, he served in Europe during the World War II, becoming one of the first outsiders to witness the horrors of the concentration camps. His books Escape to Life (co-written with his sister Erika Mann), and The Turning Point have attained a historical importance as frequently cited primary documents of the experience of exile undergone by members of the German intelligentsia and arts community who fled the Third Reich. This genre is referred to as Exillitterateur.

He is best known for his 1936 novel, Mephisto, about an actor who sells his soul to the devil, by attaching his career to the rise of the Nazis, which was made into a film of the same name, in 1981—a book that was banned in Western Germany after the war. A semi-fictional work whose protagonist is modeled on Mann's former lover Gustaf Gründgrens, Mephisto contains enough historical truth to have been banned for nearly a half-century—remaining under legal taboo for decades even after Gründgrens death—on grounds of personality rights. (That is, the character Höffgen in Mephisto was found to resemble Gründgrens so closely that the portrayal was considered a violation of his rights of publicity.)

Life and career
Born in Munich, Klaus Mann was the son of German writer Thomas Mann and Katia Pringsheim. His father was baptized as a Lutheran, while his mother was from a family of secular Jews. Due to his being the grandson of Júlia da Silva Bruhns, he was also of Portuguese-Indigenous Brazilian partial descent.

Mann's early life was described by him as romantic, in beautiful upper-class surroundings (Je suis de mon temps. Kind dieser Zeit) but his homosexuality complicated his early adulthood, and he developed a difficult relationship with his father. Mann began writing short stories in 1924 and the following year became drama critic for a Berlin newspaper. His first literary works were published in 1925.

In 1924 he had become engaged to his childhood friend Pamela Wedekind, the eldest daughter of the playwright Frank Wedekind, who was also a close friend of his sister Erika. The engagement was broken off in January 1928.

In 1927, after a short time in various schools, he traveled with his sister Erika Mann, a year older than himself, around the world, visiting the U.S. In 1929, they reported on the trip in essays published as a collaborative travelogue entitled Rundherum. During his early travels often by car throughout Europe and North Africa as well as America and Asia, Erika took the wheel and determined the itinerary to compensate for Mann's inability to make personal and useful decisions. That assistance continued even into his later adulthood but could not save him from his own self-destructive behaviors and excessive drug use.

During the time Erika travelled with Klaus to North Africa in 1929, they met Annemarie Schwarzenbach, a Swiss writer and photographer, who remained close to them for the next few years. Klaus made several trips abroad with Annemarie, the final one to a Soviet writers' congress in Moscow in 1934. During this time and after direct contact with Russian authors and intellectuals, he initiated his critical thinking towards communist ideals and totalitarian ideologies.

Drug use
Since young adulthood, Klaus used drugs, mostly opiates, to which he later became heavily addicted. His diaries document an attempted morphine injection in 1933 when Hitler took power. Initially, the aspiring writer used opium, Eukodal and later heroin, possibly to increase his creative energy, as artists and intellectuals in literary circles often did at the time. He underwent drug detoxification in Budapest during his travels, and at the Kilchberg Sanatorium in Switzerland. After 1936, during his stay in New York his drug use and sexual adventures became unconstrained.

1930s
In 1932 Klaus wrote the first part of his autobiography, which was well received until Hitler came to power. In 1933 Klaus participated with Erika in a political cabaret, called Die Pfeffermühle (The Pepper-Mill), which came to the attention of the Nazi regime. The play, which included a daring critique of Hitler, was first performed in Munich and subsequently in Zürich. To escape prosecution he left Germany in March 1933 for Paris, later visiting Amsterdam and Switzerland, where his family had a house.

The same year, Klaus Mann and Annemarie Schwarzenbach, together with Fritz Landshoff and Dutch publisher Emanuel Querido, founded Die Sammlung, a literary magazine, first published in September 1933 in Amsterdam. It was primarily affiliated with a number of influential German writers who fled from the Hitler regime during the first years of the establishment and consolidation of Nazi rule, but other internationally acclaimed authors such as Aldous Huxley and Heinrich Mann contributed essays and editorial work. The magazine was funded by Annemarie Schwarzenbach and Klaus's father Thomas Mann. Klaus served as editor-in-chief from 1933 to 1935, when Die Sammlung' ceased publication, in part due to disagreements between Klaus and his father, as well as other contributors, over frequent politically motivated content.

Klaus Mann not only played an important role in the consolidation of the German Exilliteratur but also communicated with authors who remained in Germany after 1933. In a letter exchange with Gottfried Benn, whose ambivalence towards Nazi rule was well known, Klaus expressed concern about Benn's continued membership in the national German academy of writers, pointing out the moral dilemma it posed, even urging him to leave the country to join the German intellectuals in exile. His work Escape to Life, co-authored by his sister Erika, who at the time was a successful writer for the BBC, was the culmination of his efforts to unite German intellectuals against the de-humanizing politics of the German National Socialists.

In 1933 Klaus Mann also made acquaintance with Julien Green, who was a successful French author, and engaged in the French Resistance. Green, who lived in America, attempted to rationalize his homosexual tendencies in the context of religion. Text published by Green indicated a shared sexual behavior with a preference for underaged men. From the homosexual relationships Klaus experienced during his life, however, he tended to seek a bond with men equal to his age or older. In November 1934 Klaus was stripped of German citizenship by the Nazi regime. He became a Czechoslovak citizen.

Mephisto
In 1936, Klaus Mann wrote his most famous novel, Mephisto, which was first published in Amsterdam. The novel portrays actor Hendrik Höfgen's rise to nationwide fame in 1936, from humble beginnings in the Hamburger Künstlertheater (Hamburg Artists' Theater) in 1926. After fleeing to Paris on receiving news of the Nazis' rise to power, worried about his communist past, he is helped by a former co-actress from Hamburg, Angelika Siebert, who travels to Berlin to convince the girlfriend of a Luftwaffe general to have him pardoned. On returning to Berlin he quickly manages to win over Lotte and her general, and with his support has a wonderful career.

On obtaining the role of Mephisto in Faust Part One he realizes that he actually made a pact with evil (i.e. Nazism) and lost his humane values (even denouncing his mistress as "Black Venus"). There are situations where Höfgen tries to help his friends or tell the prime minister about concentration camp hardships, but he is always concerned not to lose his Nazi patrons.

The character of Hendrik Höfgen was based on his former brother-in-law, the actor Gustaf Gründgens. Gründgens' adopted son brought a legal case to have the novel banned after its first publication in West Germany in the early 1960s. After seven years of legal hearings, the West German Supreme Court upheld the ban, although it continued to be available in East Germany and abroad. The ban was lifted, and the novel published in West.

In 1981, the novel was made into a film co-written and directed by István Szabó, starring Klaus Maria Brandauer, which faithfully followed the plot of the novel. As Höfgen's associates and friends flee or are driven underground by the Nazi regime, the popularity of his character ends up superseding his own existence, until he finds that his best performance is keeping up appearances for his Nazi patrons.

Move to the USA
In 1936, he moved to the United States, living in Princeton, New Jersey, and New York. In the summer of 1937, he met his partner for the rest of the year, Thomas Quinn Curtiss, who was later a longtime film and theater reviewer for Variety and the International Herald Tribune. Mann's novel Der Vulkan was published in 1939 at the onset of World War 2, and was another attempt by him to portray not only Germans but other European exiles during that time. Despite considered one of his best novels, it never generated any significant sales and was only translated into French.

In 1940 Klaus Mann founded another literary magazine for German writers living in exile in the United States, Decision. It lasted for only a year, but consolidated American intellectual opposition to the war with Sherwood Anderson, W. Somerset Maugham, Vincent Sheean and Robert E. Sherwood onto its board of directors. At the time, he was living in February House, and his housemates W. H. Auden and Carson McCullers provided editorial and layout assistance. He eventually moved to his father's house in Pacific Palisades when he was unable to support himself financially.

Mann became a U.S. citizen in 1943. The process of naturalization was delayed because of an investigation the FBI conducted into Klaus Mann's political and sexual activities, as he was openly gay, but not an adherent of marxist ideologies. Throughout his life in the U.S., he identified himself as a liberal antifascist and cosmopolitan.

World War II
In World War II, after training at Camp Ritchie, and becoming one of the Ritchie Boys, a US Army counterintelligence unit, he served as a staff sergeant of the 5th U.S. Army and the British Corps in Italy. Klaus was engaged in psychological warfare designing leaflets intended for German soldiers stationed in Italy and North Africa. In Italy, he was also involved with difficult interrogations of German POWs, including seasoned SS officers.

In his second 1942 autobiography (Der Wendepunkt, the Turning Point), he critically observed the segregation of white army personnel from their black counterparts at Camp Ritchie. In summer 1945, he was sent by units of the U.S. 5th Army and the British 8th Army to Germany. Klaus Mann, a German-American, used the publication Stars and Stripes to report from Postwar-Germany.

As he visited liberated concentration camps in official function, he was one of the first eye-witnesses to report on the horrors of mass extermination during Nazi rule in Germany. Audiovisual documents of his emotional reporting at these sites in the later 1940s became historical records and are still regarded today as a verification of these crimes against humanity.

Death and legacy
Mann died in Cannes from an overdose of sleeping pills on 21 May 1949, following further drug treatment. His death is generally reported as a suicide, linked to financial pressures, opiate addiction, and disillusionment over his treatment by the USA as a homosexual, and supposed communist, but Mann's biographer Frederic Spotts argues that the engaged author's communications and attitude preceding his sudden overdose suggest accident rather than suicide. He was buried in Cannes at the Cimetière du Grand Jas.

A number of biographies of Klaus Mann appeared much later after his suicide in Cannes in 1949. Other than one German language author, Nicole Schaenzler, all biographies were written and edited by English or American contributors. Because he wrote frequent autobiographical content, a separation of his literary achievements, mostly unsuccessful during his time, from his life, are difficult. Mann remained active in literary circles, and his personal and spiritual connections with André Gide, and later examination of Gide in his work Avant la Lettre (1943) shed significant light on his time and himself.

Later historians celebrated Klaus Mann as a modern liberal or transnational who attempted to break down national boundaries, but Klaus's biographical notes reveal that he felt essentially German, and had positive memories of his upbringing in Bavaria. In a pursuit to describe post-war Germany after the destructions of World War 2, he attempted to find his origins while collecting painful impressions from a Germany occupied by foreign military forces and impacted by the loss of its original borders.

Novels and autobiographies

 * Der fromme Tanz, 1925
 * Anja und Esther, 1925
 * Kindernovelle, 1926 [published in the U.S. as The 5th Child, 1927]
 * Revue zu Vieren, 1927
 * Alexander, Roman der Utopie, 1929
 * Auf der Suche nach einem Weg, 1931
 * Kind dieser Zeit, 1932
 * Treffpunkt im Unendlichen, 1932
 * Journey into Freedom, 1934
 * Symphonie Pathétique, 1935
 * Mephisto, 1936
 * Vergittertes Fenster, 1937
 * Escape to Life, 1939 (with Erika Mann)
 * Der Vulkan, 1939
 * The Turning Point, 1942
 * Avant la lettre, 1943
 * André Gide and the Crisis of Modern Thought, 1943
 * The Chaplain, 1945

Essays and travel reports

 * Vor dem Leben, Erzählungen. Enoch Verlag, Hamburg 1925 (heute enthalten in Maskenscherz. Die frühen Erzählungen).
 * Kindernovelle, Erzählung. Enoch, Hamburg 1926 (ebd.).
 * Rundherum. Ein heiteres Reisebuch. (Mit Erika Mann). S. Fischer, Berlin 1929. Neuausgabe Rowohlt, Reinbek 1996, ISBN 3-499-13931-6.
 * Abenteuer. Novellen. Reclam, Leipzig 1929.
 * Auf der Suche nach einem Weg. Aufsätze. Transmare Verlag, Berlin 1931.
 * Das Buch von der Riviera (Mit Erika Mann). aus der Reihe: Was nicht im „Baedeker“ steht, Band XII. Piper, München 1931. Neuausgabe Rowohlt, Reinbek 2003, ISBN 3-499-23667-2; Neuausgabe Kindler, Hamburg 2019, ISBN 978-3-463-40715-9.
 * Die Sammlung. Literarische Monatsschrift. (Unter dem Patronat von André Gide, Aldous Huxley, Heinrich Mann herausgegeben von Klaus Mann.) Querido, Amsterdam. September 1933 – August 1935. Neuausgabe Rogner und Bernhard Verlag, München 1986 bei Zweitausendeins. Zwei Bände. ISBN 3-8077-0222-9.
 * Vergittertes Fenster. Novelle (über die letzten Tage von Ludwig II. von Bayern). Querido Verlag, Amsterdam 1937; danach S. Fischer, Frankfurt am Main 1960 (heute enthalten in Speed. Die Erzählungen aus dem Exil.)
 * Escape to Life Deutsche Kultur im Exil. (Zusammen mit Erika Mann). Houghton Mifflin, Boston 1939. Neuausgabe Rowohlt, Reinbek 1991, ISBN 3-499-13992-8.
 * The Other Germany. (Zusammen mit Erika Mann), Modern Age, New York 1940 (Volltext im Internet Archive).
 * Decision. A Review of Free Culture. Ed. by Klaus Mann. New York, Januar 1941 – Februar 1942.
 * André Gide and the Crisis of Modern Thought. Creative Age, New York 1943 (dt.: Andre Gide und die Krise des modernen Denkens). Neuausgabe Rowohlt, Reinbek 1995, ISBN 3-499-15378-5.
 * Heart of Europe. An Anthology of Creative Writing in Europe 1920–1940. Ed. by Hermann Kesten and Klaus Mann. L. B. Fischer, New York 1943.
 * André Gide: Die Geschichte eines Europäers. Steinberg, Zürich 1948.
 * Die Heimsuchung des europäischen Geistes. Essay 1948. Neuausgabe bei Transit Buchverlag 1993, ISBN 3-88747-082-6 (auch enthalten in Auf verlorenem Posten. S. 523–542).

Film adaptations

 * Mephisto, directed by István Szabó (1981, based on the novel Mephisto)
 * Treffpunkt im Unendlichen, directed by Heinrich Breloer and Horst Königstein (1984, TV film, based on the novel Treffpunkt im Unendlichen)
 * Flight North, directed by Ingemo Engström (1986, based on the novel Journey into Freedom)
 * The Volcano, directed by Ottokar Runze (1999, based on the novel Der Vulkan)

title: Klaus Mann