Life Science’s Average Publishable Unit (APU) Has Increased over the Past Two Decades

<div><p>Quantitative analysis of the scientific literature is important for evaluating the evolution and state of science. To study how the density of biological literature has changed over the past two decades we visually inspected 1464 research articles related only to the biological sciences from ten scholarly journals (with average Impact Factors, IF, ranging from 3.8 to 32.1). By scoring the number of data items (tables and figures), density of composite figures (labeled panels per figure or PPF), as well as the number of authors, pages and references per research publication we calculated an Average Publishable Unit or APU for 1993, 2003, and 2013. The data show an overall increase in the average ± SD number of data items from 1993 to 2013 of approximately 7±3 to 14±11 and PPF ratio of 2±1 to 4±2 per article, suggesting that the APU has doubled in size over the past two decades. As expected, the increase in data items per article is mainly in the form of supplemental material, constituting 0 to 80% of the data items per publication in 2013, depending on the journal. The changes in the average number of pages (approx. 8±3 to 10±3), references (approx. 44±18 to 56±24) and authors (approx. 5±3 to 8±9) per article are also presented and discussed. The average number of data items, figure density and authors per publication are correlated with the journal’s average IF. The increasing APU size over time is important when considering the value of research articles for life scientists and publishers, as well as, the implications of these increasing trends in the mechanisms and economics of scientific communication.</p></div

Change in the average first-quartile publishable unit (AQ1PU) over the past two decades.

<p>Box plots showing the change in the lower quartile group (25^th percentile and less) of the APU as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156983#pone.0156983.g001" target="_blank">Fig 1</a>.</p

Correlation between the APU variables and journal’s average IF.

<p>Linear regression and Spearman’s rank-order correlation (Spearman’s critical rho (N = 10, alpha = 0.05) = 0.648) analysis of average IF and average number of (<b>a</b>) total data items (including supplemental material, +SM) (R² = 0.14, p = 0.04; Spearman’s rho = 0.65, p = 0.05): (<b>b</b>) data items in main article alone (-SM) (R² = 0.17, p = 0.03; rho = -0.56, p = 0.10); (<b>c</b>) PPF (R² = 0.40, p = 0.0002; rho = 0.96, p<0.0001); (<b>d</b>) pages (R² = 0.01, p = 0.71; rho = -0.08, p = 0.84); (<b>e</b>) references (R² = 0.10, p = 0.08; rho = 0.50, p = 0.14); and (<b>f</b>) authors (R² = 0.44, p<0.0001; rho = 0.81, p = 0.007) per publication. Error bars represent standard deviations.</p

Increase in the Average Publishable Unit (APU) over the past two decades of scientific publication.

<p>A total of 1464 research articles were visually-inspected to quantify: the average number of (<b>a</b>) total data items (including supplemental material, +SM); (<b>b</b>) data items in main article alone (-SM); (<b>c</b>) PPF ratio or panels inside composite figures (-SM); (<b>d)</b> pages (-SM), (<b>e</b>) references (+SM), and (<b>f</b>) authors per publications in 1993 (white), 2003 (blue), and 2013 (red) by 10 scholarly journals with diverse average IF (in parenthesis). Box plots display the average median (horizontal line in the box interior), interquartile range or distance between the 25^th and 75^th percentiles (box limits), and the minimum and maximum values (vertical lines issuing from the box) for each variable measured. The mean is indicated by the “+” symbol inside the box interior. Averages considering all articles (487 articles for 1993, 484 for 2003, and 493 for 2013) from all journals are shown on the right-end (note divisor line). Kruskal-Wallis non-parametric statistical test: *P≤0.05; **P≤0.01; ***P≤0.001; ****P≤0.0001. For the year 2013, top and bottom asterisks correspond to statistical analysis between 2013–1993 and 2013–2003, respectively.</p

A Role for <i>LHC1</i> in Higher Order Structure and Complement Binding of the <i>Cryptococcus neoformans</i> Capsule

<div><p>Polysaccharide capsules are important virulence factors for many microbial pathogens including the opportunistic fungus <i>Cryptococcus neoformans</i>. In the present study, we demonstrate an unusual role for a secreted <u>l</u>actono<u>h</u>ydrolase of <i><u>C</u>. neoformans</i>, <i>LHC1</i> in capsular higher order structure. Analysis of extracted capsular polysaccharide from wild-type and <i>lhc1</i>Δ strains by dynamic and static light scattering suggested a role for the <i>LHC1</i> locus in altering the capsular polysaccharide, both reducing dimensions and altering its branching, density and solvation. These changes in the capsular structure resulted in <i>LHC1</i>-dependent alterations of antibody binding patterns, reductions in human and mouse complement binding and phagocytosis by the macrophage-like cell line J774, as well as increased virulence in mice. These findings identify a unique molecular mechanism for tertiary structural changes in a microbial capsule, facilitating immune evasion and virulence of a fungal pathogen.</p></div

wt and <i>lhc1</i>Δ mutant strains of <i>C. neoformans</i> differ in antibody binding and antibody mediated phagocytosis by a J774.16 macrophage-like cell line.

<p>(A) Indicated strains were prepared and stained with indicated monoclonal antibodies as described in Material and Methods. (B) Puncta from cells labeled as in A were quantified from 50 cells. (C) Indicated strains were opsonized with the indicated antibody and then incubated with J774.16 cell monolayers and phagocytic index determined as in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004037#s4" target="_blank">Materials and Methods</a> (N = 4). (D) Fungal Killing Assay: Cells treated as in C, except that incubation was continued for 81 hours and fungal burden assayed by CFU after macrophage lysis (N = 4). *** p<0.001.</p

Microscopic visualization of <i>C. liquefaciens and C. neoformans capsules and growth profile</i>.

<p>Panel A) India ink stain of <i>C. neoformans</i> cells. Panel B) Counterstaining of <i>C. liquefaciens</i> with India ink. Panel C) Growth curves of <i>C. neoformans</i> and <i>C. liquefaciens</i> at 30°C in minimal media.</p

Mutations of <i>PKR1</i>, <i>CAC1</i>, <i>USV101</i> in specific clinical isolates.

<p>Mutations of <i>PKR1</i>, <i>CAC1</i>, <i>USV101</i> in specific clinical isolates.</p

Titan cells generation <i>in vitro</i> is impacted by various environmental conditions.

<p>(<b>A</b>) The sequence of media used at steps 2 and 3 of the protocol was crucial for titan cells generation: yeasts cultured in Yeast Peptone Dextrose (YPD) and transferred to minimal medium (MM) produced significantly more titan cells (cells >10μm, dotted grey line) than yeasts cultured in MM or YPD and transferred in MM or YPD, respectively; (<b>B</b>) Exposure to d light at step 3 had a positive impact on titan cells generation compared to incubation in the dark; (<b>C</b>) Raising the incubation temperature to 37°C at step 3 decreased titan cells formation compared to 30°C; (<b>D</b>) Modification of the initial pH of the MM used at step 3 impacted titan cells formation with pH 5.5 being optimal while a more acidic (pH = 4), a neutral (pH = 7) or an alkaline (pH = 8.5) pH inhibited titan cells formation; (<b>E</b>) The impact of hypoxia was tested by physical (closed cap) and by chemical (COCl₂ in MM at 1 nM) method and compared to normoxia (21% oxygen). Physically- and chemically-induced hypoxia enhances the production of titan cells compared to normoxia with a higher proportion of titan cells in chemically- compared to physically-induced hypoxia. All experiments were performed in triplicate and pooled (mean cell counted ± SD = 2305±1438). Median and IQR are shown in black for each condition (* p<0.0001 vs reference condition). The percentages above each condition represents the % of titan cells observed.</p

Monosaccharide composition of capsular and exo-PS of <i>C. liquefaciens</i> and <i>C. neoformans</i>.

<p>Xyl (Xylose), GlcA (Glucuronic acid), Man (Mannose), Gal (Galactose), Glu (Glucose) and GlcNAc (N-acetylglucosamine).</p