ABBREVIATIONS AND CONVENTIONS

Verb Tense

ASM strongly recommends that for clarity you use the past tense to narrate particular events in the past, including the procedures, observations, and data of the study that you are reporting. Use the present tense for your own general conclusions, the conclusions of previous researchers, and generally accepted facts. Thus, most of the abstract, Materials and Methods, and Results will be in the past tense, and most of the introduction and some of the Discussion will be in the present tense.

Be aware that it may be necessary to vary the tense in a single sentence. For example, it is correct to say "White (30) demonstrated that XYZ cells grow at pH 6.8," "Figure 2 shows that ABC cells failed to grow at room temperature," and "Air was removed from the chamber and the mice died, which proves that mice require air." In reporting statistics and calculations, it is correct to say "The values for the ABC cells are statistically significant, indicating that the drug inhibited ... ."

For an in-depth discussion of tense in scientific writing, see p. 191-193 in How To Write and Publish a Scientific Paper, 6th ed.

Abbreviations

General. Abbreviations should be used as an aid to the reader rather than as a convenience to the author, and therefore their use should be limited. Abbreviations other than those recommended by the IUPAC-IUB (Biochemical Nomenclature and Related Documents, 1992) should be used only when a case can be made for necessity, such as in tables and figures.

It is often possible to use pronouns or to paraphrase a long word after its first use (e.g., "the drug" or "the substrate"). Standard chemical symbols and trivial names or their symbols (folate, Ala, and Leu, etc.) may also be used.

It is strongly recommended that all abbreviations except those listed below be introduced in the first paragraph in Materials and Methods. Alternatively, define each abbreviation and introduce it in parentheses the first time it is used; e.g., "cultures were grown in Eagle minimal essential medium (MEM)." Generally, eliminate abbreviations that are not used at least three times in the text (including tables and figure legends).

Not requiring introduction. In addition to abbreviations for Système International d'Unités (SI) units of measurement, other common units (e.g., bp, kb, and Da), and chemical symbols for the elements, the following should be used without definition in the title, abstract, text, figure legends, and tables: DNA (deoxyribonucleic acid); cDNA (complementary DNA); RNA (ribonucleic acid); cRNA (complementary RNA); RNase (ribonuclease); DNase (deoxyribonuclease); rRNA (ribosomal RNA); mRNA (messenger RNA); tRNA (transfer RNA); AMP, ADP, ATP, dAMP, ddATP, and GTP, etc. (for the respective 5' phosphates of adenosine and other nucleosides) (add 2'-, 3'-, or 5'- when needed for contrast); ATPase and dGTPase, etc. (adenosine triphosphatase and deoxyguanosine triphosphatase, etc.); NAD (nicotinamide adenine dinucleotide); NAD+ (nicotinamide adenine dinucleotide, oxidized); NADH (nicotinamide adenine dinucleotide, reduced); NADP (nicotinamide adenine dinucleotide phosphate); NADPH (nicotinamide adenine dinucleotide phosphate, reduced); NADP+ (nicotinamide adenine dinucleotide phosphate, oxidized); poly(A) and poly(dT), etc. (polyadenylic acid and polydeoxythymidylic acid, etc.); oligo(dT), etc. (oligodeoxythymidylic acid, etc.); UV (ultraviolet); PFU (plaque-forming units); CFU (colony-forming units); MIC (minimal inhibitory concentration); Tris [tris(hydroxymethyl)aminomethane]; DEAE (diethylaminoethyl); EDTA (ethylenediaminetetraacetic acid); EGTA [ethylene glycol-bis(β-aminoethyl ether)-N,N,N',N'-tetraacetic acid]; HEPES (N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid); PCR (polymerase chain reaction); and AIDS (acquired immunodeficiency syndrome). Abbreviations for cell lines (e.g., HeLa) also need not be defined.

The following abbreviations should be used without definition in tables:

• amt (amount)
• approx (approximately)
• avg (average)
• concn (concentration)
• diam (diameter)
• expt (experiment)
• exptl (experimental)
• ht (height)
• mo (month)
• mol wt (molecular weight)
• no. (number)
• prepn (preparation)
• SD (standard deviation)
• SE (standard error)
• SEM (standard error of the mean)
• sp act (specific activity)
• sp gr (specific gravity)
• temp (temperature)
• tr (trace)
• vol (volume)
• vs (versus)
• wk (week)
• wt (weight)
• yr (year)
  

Reporting Numerical Data

Standard metric units are used for reporting length, weight, and volume. For these units and for molarity, use the prefixes m, µ, n, and p for 10–3, 10–6, 10–9, and 10–12, respectively. Likewise, use the prefix k for 103. Avoid compound prefixes such as mµ or µµ. Parts per million (ppm) may be used when that is the common measure for the science in that field. Units of temperature are presented as follows: 37°C or 324 K.

When fractions are used to express such units as enzymatic activities, it is preferable to use whole units, such as g or min, in the denominator instead of fractional or multiple units, such as µg or 10 min. For example, "pmol/min" is preferable to "nmol/10 min," and "µmol/g" is preferable to "nmol/µg." It is also preferable that an unambiguous form, such as exponential notation, be used; for example,

"µmol g–1 min–1" is preferable to "µmol/g/min." Always report numerical data in the applicable SI units.

Representation of data as accurate to more than two significant figures must be justified by presentation of appropriate statistical analyses.

For a review of some common errors associated with statistical analyses and reports, plus guidelines on how to avoid them, see the article by Olsen (Infect. Immun. 71:6689-6692, 2003).

For a review of basic statistical considerations for virology experiments, see the article by Richardson and Overbaugh (J. Virol. 79:669-676, 2005).

Statistics

If biological variation within a treatment (coefficient of variation, the standard deviation divided by the mean) is small (less than 10%) and the difference among treatment means is large (greater than 3 standard deviations), it is not necessary to report statistics. If the data do not meet these criteria, however, the authors must include an appropriate statistical analysis (e.g., Student's t test, analysis of variance, or Tukey's test, etc.). Statistics should represent the variation among biological units (e.g., replicate incubations) and not just the variation due to method of analysis.

Phylogenetic trees based on nucleotide or amino acid sequence alignments must be supported by appropriate statistical analyses of tree stability (e.g., bootstrap analysis), and nonsupported branches (e.g., bootstrap coefficients below 50%) should be collapsed. A copy of the alignment should be available for examination by the editor or the reviewers upon request.

For a review of some common errors associated with statistical analyses and reports, plus guidelines on how to avoid them, see the article by Olsen (Infect. Immun. 71:6689-6692, 2003).

For a review of basic statistical considerations for virology experiments, see the article by Richardson and Overbaugh (J. Virol. 79:669-676, 2005).

Equations

In mathematical equations, indicate the order of operations clearly by enclosing operations in parentheses, brackets, and braces, in that order: (a + b) x c or a + (b x c), 100 x {[(a/b) x c] + d} or 100 x {a/[(b x c) + d]}. Italicize (or underline) variables and constants (but not numerals), and use roman type for designations:

E0, Eh, Mr, Km, Ks, a + 2b = 1.2 mM, Ca2+ Vmax = exp(1.5x + y), BOD = 2.7x2.

Isotopically Labeled Compounds

For simple molecules, isotopic labeling is indicated in the chemical formula (e.g., 14CO2, 3H20, and H235SO4). Brackets are not used when the isotopic symbol is attached to the name of a compound that in its natural state does not contain the element (e.g., 32S-ATP) or to a word that is not a specific chemical name (e.g., 131I-labeled protein, 14C-amino acids, and 3H-ligands).

For specific chemicals, the symbol for the isotope introduced is placed in brackets directly preceding the part of the name that describes the labeled entity. Note that configuration symbols and modifiers precede the isotopic symbol. The following examples illustrate correct usage.

AEM follows the same conventions for isotopic labeling as the Journal of Biological Chemistry, and more-detailed information can be found in the instructions to authors of that journal (first issue of each year).

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