Acronym in scent detection and civil security: EDC for explosive detection canine

Explosive-sniffing dogs are trained and employed to detect hidden reactive substances with a destructive potential. Such dogs are called bomb dogs,  or—more formal—explosive detection canines (EDCs) [1,2]. They are becoming best friends of security officials and safety personal who are in charge of protecting public places and controlling conflict zones.

EDCs do not smell bombs. But they can be trained to be highly alert to the ingredients of explosive materials. At the MSA Security Training Academy, for example, odors of chemical vapors are imprinted on the olfactory cortex of the dog's brains—Pavlov-style by task repetition and reward [2]:

MSA's dogs begin building their vocabulary of suspicious odors working with rows of more than 100 identical cans laid out in a grid. Ingredients from the basic chemical families of explosives—such as powders, commercial dynamite, TNT, water gel and RDX, a component of the plastic explosives C4 and Semtex—are placed in random cans. In addition, urea nitrate and hydrogen peroxide—primary components of improvised explosive devices—have joined the training regime.

EDCs learn not to scratch a potentially threatening material or device (avoiding a possible blow-up), but to respond by just sitting down when they sense one. Today, EDCs at airports, train stations, stadiums, fairs and banks are not even noticed by travelers and visitors; and if, they are greated with a friendly look or smile. The simple presents of EDCs hopefully keeps people safe and threats away. 

Keywords: threat protection, chemistry, sensory system, dog's nose, Canis lupus.

References and more to explore
[1] MSA Security: Bomb Dogs [www.msasecurity.net/bomb-dogs/].
[2] Joshua Levine: The education of a bomb dog. Smithsonian July-August 2013, 44 (4), pp. 72-78 [http://www.smithsonianmag.com/ideas-innovations/The-Education-of-a-Bomb-Dog-213881241.html#Bomb-Dogs-explosive-detection-canine-training-1.jpg].

Silicene: a honeycombed, atom-thick sheet of silicon named to recall similarly structured graphene

Silicene sheets can be epitaxially grown on a close-packed silver surface, Ag(111), via silicon atomic flux under ultrahigh vacuum conditions [1]. The condensed atoms arrange themselves within a two-dimensional honycomb lattice, geometrically resembling the structure of carbon atoms in graphene sheets. Chemists like to indicate structural and functional similarity of compounds in the ending of their names:  hence, the name silicene, which rhymes with graphene.

Equal or similar topology, however, does not necessarily imply property similarity. So far, many silicene properties have been predicted rather than measured, since the graphen-like form of silicon proves hard to handle [2].  Whereas graphene is very stable, silicene is reacting with other molecules and materials in its neighborhood. Silicene sheets also show a tendency to crinkle. Yet, the interest in silicene, its properties and potential applications is rapidly growing [3-5].

And to continue with the analogy of chemical elements of the carbon group (Group IV or Group 14), germanene—the planar, hexagonal germanium allotrope—could then be the next thin sheet.   

The CurlySMILES notation for silicene is [Si]{alall=silicene}, in which the square bracket code (SQC) for silicon is annotated with al for atomic layer and all for allotrope. The analogous linear notation for graphene and germanene are [C]{alall=graphene} and [Ge]{alall=germanene}, respectively.

Keywords: inorganic chemistry, material science, nanotechnology, epitaxy, spontaneous organization, honeycomb lattice, allotropes.

References and more to explore
[1] B. Lalmi et al.: Epitaxial growth of a silicene sheet. Appl. Phys. Lett. 2010, 97, pp. 223109-223110. doi: 10.1063/1.3524215.
[2] G. Brumfiel: Sticky problems snares wonder material. Nature March 14, 2013, 495, pp. 152-153. doi: 10.1038/495152a.
[3] B. Feng et al.: Evidence of Silicene in Honeycomb Structures of Silicon on Ag(111). Nano Lett. 2012, 12 (3), pp. 3507-3511. doi: 10.1021/nl301047g.
[4] Z. Ni et al.: Tunable Bandgap in Silicene and Germanene. Nano Lett. 2012, 12 (1), pp. 113-118. doi: http://dx.doi.org/10.1021/nl203065e.
[5] Foresight Institute: Silicene: silicon's answer to graphene [www.foresight.org/nanodot/?p=5642].

Translating the names of chemical compounds and compound classes

Chemists are typically not trained as translators. The latter, on the other hand, often do not have a background in chemistry and materials science. The translation of chemical compound and class names can easily turn into a non-trivial task.

In some cases translation is a simple matter of dictionary knowledge and look-up. For example, the names of the so-called “standard amino acids, ” a set of  α-amino acids, display overall name consistency across languages (one-word names with the exceptions of aspartic acid and glutamic acid [1]): for a given molecular structure the linguistic root of an amino acid name is recognizable—language-specific names are just spelled differently based on language character. As “trivial names ” they have not been derived by employment of a nomenclature scheme.

Generally, for complex chemical structures and nanoscale architectures, it can be a challenge to correctly translate a chemical compound name or chemical class name, which commonly is constructed from prefixes, suffixes, locants and (sub)structure (functional group) names. Bernardo Herold emphasizes a basic two-step approach, to which one should adhere, when translating a chemical term from English into a target language (or vice versa) [2]:

1. Establish the required rules of nomenclature in the target language.
2. Translate a name based on the vocabulary and rules of the target language.

Language-specific spelling is the main reason why composed chemical names cannot always be translated successively name-part by name-part. In particular, the spelling of the names of certain chemical groups varies between languages, giving rise to different alphabetical ordering—for example, phenyl in English and German becomes phényle in French, fenyl in Dutch and fenil in Italian, Portuguese and Spanish. Herold demonstrates how the English-language name 3-methyl-5-phenylpyridine is correctly translated—according to IUPAC rules—into the Romanic-language name 3-fenil-5-metilpiridina [2].

In addition to language-adjusted nomenclature application, the understanding of the language-specific grammar is important. It determines features such as word order and word concatenation: potassium bromide in English is Kaliumbromid (one word) in German and  bromuro de potasio  (change of word order and insertion of preposition) in Spanish.  

Chemical nomenclature books are available in several languages [3].

Keywords: multilingual collaboration, linguistics, chemical terminology, IUPAC naming, disambiguation.

References and more to explore
[1] Latintos: Amino acids in English, French, German, Italian, Portuguese and Spanish [golatintos.blogspot.com/2010/02/amino-acids-in-english-french-german.html].
[2] Bernardo Herold: Why Translate Nomenclature? Chemistry International May-June 2013, 35 (3), pp. 12-15 [www.iupac.org/publications/ci/2013/3503/5_herold.html].
[3] International Union of Pure and Applied Chemistry - Nomenclature Books: www.chem.qmul.ac.uk/iupac/bibliog/books.html. 

Synonyms for sand corn, the common name of a flowering plant native to the western United States and parts of New Mexico

Sand corn is a flowering plant found in dry habitats of the western United States; for example in northwest Nevada. It has two accepted scientific names: Zigadenus paniculatus (Nutt.) S. Watson and  Toxicoscordion paniculatum (Nutt.) Rydb. [1-5].  Its scientific classification: order Liliales. In the literature, sand corn is taxonomically grouped either into Lilliaceae (lily family) or Melanthiaceae, the latter not unanimously recognized as a family and sometimes considered as part of the lily family.

Sand corn, also written sand-corn, is often referred to by its other common name: foothill deathcamas (also written: foothill death camas). This name indicates the poisonous character of the plant, which becomes relevant, when sand corns are growing on rangeland: intoxication of livestock may result from their alkaloid components such as zygacine [3].

Another synonym, panicled death camas [4], makes a reference to the often bending or nodding panicle with sometimes over fifty flowers (see Thomas Creek plant)—each having six small tepals with yellow-green splotch at base and showy, yellow anthers [5].

Keywords: botany, taxonomy, nomenclature, scientific name.

References and more to explore
[1] USDA Plants Profile: Zigadenus paniculatus (Nutt.) S. Watson [plants.usda.gov/java/profile?symbol=ZIPA2].
[2] Kew Royal Botanic Garden: Toxicoscordion paniculatum (Nutt.) Rydb., Bull. Torrey Bot. Club 30: 272 (1903) [apps.kew.org/wcsp/namedetail.do?name_id=289937].
[3] K. D. Welch et al.: The acute toxocity of the death camas (Zigadenus species) alkaloid zygacine in mice, including the effect of methyllycaconitine coadministration on zygacine toxity. J. Anim. Sci. 2011, 89 (5), pp. 1650-1657.  
doi: 10.2527/jas.2010-3444.
[4] Calflora Taxon Report 8367:  Zigadenus paniculatus [www.calflora.org/cgi-bin/species_query.cgi?where-taxon=Zigadenus+paniculatus].
[5] Laird R. Blackwell: Tahoe Wildflowers. Morris Book Publishing, LLC, Guilford, Connecticut, 2007; page 37.

A term in microbial ecology: disappearing microbiota hypothesis

Occurrences of certain medical conditions and diseases such as asthma, food allergies, hay fever, eczema, diabetes, obesity and celiac disease are dramatically going up. The physician and director of the Human Microbiome Program, Martin Blaser at New York University's School of Medicine is hypothesizing that the disappearance of microbiota from the human body is to blame. This loss of  microbiome species is largely caused by our obsessive use of antibacterial soaps and lotions as well as frequent treatments with antibiotics [1,2]:

Though they have always known that antibiotics kill “good” bacteria as well as “bad,” doctors generally assumed the body's microbial community was resilient enough to bounce back. But new studies show that the microbiome struggles to recover from repeated assaults, and may lose species permanently. Blaser suspects that diversity loss is cumulative, worsening from one generation to the next. He calls it “the disappearing microbiota hypothesis.” [boldface by author]

How clean should we be, without cleaning out the good microbes—or disturbing the balance between good, bad and neutral ones—that live behind our ears, in our armpits and in our gut and mouth?

Keywords: microbial diversity, microbiome, microbiology, medicine, hygiene, human health.

References and more to explore
[1] Martin J. Blaser, M. D. [http://www.med.nyu.edu/biosketch/blasem01/research].
[2] Richard Conniff: The Body Eclectic. Smithsonian May 30, 2013, 44 (2), pp. 40-47 [www.smithsonianmag.com/science-nature/Microbes-The-Trillions-of-Creatures-Governing-Your-Health-204134001.html].

Trendy and inspirational: the suffixes -ome and -omics

In the beginning there was the word genome for the complete set of genetic material present in a cell or organism. The German botanist Hans Winkler came up with this term in 1920 [1]. It is a portmanteau blending the words gene and chromosome. An Oxford Dictionary of 2002 further tells us that [2]:

a  couple of terms have been formed on its model [the portmanteau genome]: proteome, the complete set of proteins produced from the instructions coded in a cell's genetic material, and metabolome (from metabolism), the complete set of metabolic processes within a cell. These seem to have been created partly by blending and partly by analogy with the older sense of the ending.

The older sense of -ome is the meaning of having a specified nature; for example, rhizome for the subterranean roots and shoots of a plant [2].

Now, ten years later, there are hundreds or even thousands of words derived by following the nomenclatural model creating the established terms genome, proteome and metabolome. The word transcriptome refers to the set of RNA molecules expressed from the genome. Emerging terms include variome for the set of genetic variation across a population of a species, epigenome for the set of chemical compounds involved in not-DNA-encoded gene expression, interactome for the set of molecular interactions in a biological system such as a cell, and fluxome for the set of small molecules changing along metabolic pathways in a dynamic system (due to flux responses resulting from both genetic and metabolic regulation). Terms you certainly will find more often in future publications include phenome for the set of physical descriptions that can ideally be related to genotype, regulome for the set of regulatory compounds in a cell, integrome for unions of 'omics data sets, omnisciome for the entirety of knowledge about a cell, organism or system, toxome for the set of cellular processes responsive to small molecules and involved in their toxicological activities, and lipidome for the set of all fatty molecules in an organism [3].

The name of a scientific field associated with an ome-ending word is typically built by replacing the suffix -ome with -omics. Genomics, proteomics, and metabolomics are well known examples. Transcriptomics, variomics, epigenomics, interactomics, fluxomics, phenomics, regulomics, integromics and lipidomics are emerging names and disciplines of scientific study. Omnisciomics and toxomics may follow. Data and knowledge within these fields have not all been derived from recent studies, some insight has been accumulated over decades. But recent advances, driven by modern analytical devices and high-throughput technology, are accelerating application and impact of these fields. Dedicated to the integration of  'omics domains is a peer-reviewed journal with the name OMICS [4].

And then there is the ending -etics, as in genetics. The distinction between 'omics and 'etics may seem confusing for outsiders. Let's conclude this with the description of the fine line between epigenomics and epigenitcs [5]: “Epigenetics focuses on processes that regulate how and when certain genes are turned on and turned off, while epigenomics pertains to analysis of epigenetic changes across many genes in a cell or entire organism.”

Keywords: biochemistry, linguistics, nomenclature, terminology, meta-data, integrative research.

References and more to explore
[1] Where the Word 'Genome' Came From [www.npr.org/templates/story/story.php?storyId=128410577].
[2] Michael Quinion: Ologies and Ismas. A Dictionary of Word Beginnings and Endings. Oxford University Press, Oxford and New York, 2002..
[3] Monya Baker: The 'omes puzzle. Nature February 28, 2013, 494, pp.416-419. doi: 10.1038/494416a. 
[4] OMICS: A Journal of Integrative Biology [www.liebertpub.com/OMI].
[5] National Cancer Institute: Epigenomics and Epigenetics Research [epi.grants.cancer.gov/epigen.html].

“How pinteresting”

Pinteresting, rhyming with interesting, is an adjective derived from the latter and the name of an exciting, rapidly evolving online pinboard, named Pinterest. This hot social network tool helps you collect and share pictures, illustrations, graphs, schemes and anything else visual. It lets you organize things on boards—making your great stuff or little niche toy available online and ready for repinning. For example, Axeleratio's Pinterest Boards contain a Sculptures & Architecture, Plant Life and a Petroversity board. The number of creative and pinteresting boards is increasing daily. People also use Pinterest to market their business, sell products and build their brands [1]. Pinterestingly, there is a board with the title “Pinteresting” [2]. Keep staying pinterested!

Dog sculpture pinned to my Sculptures & Architecture board

Pinning tips and trends can be found in the Pinterest Blog [3]. The Pinterest Twitter microblog, @Pinterest, has over one million followers. Also, more and more businesses are taking note on what Pinterest can do for them [4]. It eventually will pay to keep your level of pinterestness or pinterestedness high. Pinteressantissimo!

Keywords: Internet, social media marketing, visual platform, networking.

References and more to explore
[1] Jason Miles and Karen Lacey: Pinterest Power. Mc-Graw Hill, New York, 2013.
[2] Pinteresting: pinterest.com/bop/pinteresting.
[3] Pinterest Blog: blog.pinterest.com.
[4] Samantha Noble: Pinterst Tips for Business Profile Pages [www.stateofsearch.com/pinterest-business-profile-pages].