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The “Must Downloads” of PLOS ONE: A 10 Year Anniversary Collection

In the new PLOS ONE 10 Year Anniversary Collection: The Must Downloads, Associate Editor Jenna Quinto explores the ratio between two primary article-level metrics and highlights PLOS ONE articles that were downloaded at exceptional rates.

When PLOS ONE was launched ten years ago, the concept of using article-level metrics to estimate the impact of a scientific publication was still in its infancy. Instead, researchers were used to relying on journal-level metrics, such as impact factor, as proxies of the significance of an individual article. Today, the use of article-level metrics (ALMs) has gained traction in the scientific community, thanks in part to their inclusion with every PLOS article beginning in 2009, and to a growing recognition of the limitations of journal-level metrics [1,2].

However, breaking down the individual components of an article’s metrics is not always straightforward. There are primary metrics, such as the number of times an article has been cited or shared on Twitter, as well as secondary metrics that can be calculated by combining primary metrics or by comparing the metrics of one article with the metrics of another. While there is great power in having such information, deriving meaning and context from the numbers can be a challenge.

In this 10 Year Anniversary Collection, we highlight one of these secondary metrics: the ratio between the number of times an article has been downloaded and the number of times it has been viewed. For PLOS articles, this value is expressed as a percentage of article views that lead to a PDF or XML download (Fig. 1). The metric is based on the idea that a researcher who has taken the time to download the article for future consideration has engaged with it more deeply than someone who has viewed the online version, so a higher percentage of downloads-to-views implies a higher degree of engagement by the scientific community. This metric may also be an early predictor of future citations, as the number of PDF downloads is the access metric most strongly correlated with the number of citations [3].

Figure 1. Views and downloads metrics for Issac et al. [5] as of September 22, 2017, available at http://journals.plos.org/plosone/article/metrics?id=10.1371/journal.pone.0000296, and for all PLOS articles under the Metrics tab.

 

Across all PLOS publications until May 2013, the overall downloads-to-views percentage was 24.7% [4]. Therefore, for this collection, we highlighted PLOS ONE articles from each year that have a ratio at least 50% greater than this average. These articles have impressive metrics ranging from 37.1% to 49.8% of views leading to a download and are representative of a broad range of scientific disciplines found in PLOS ONE.

 

2007 – Metrics for endangered mammals

Speaking of metrics, the work of Issac et al. [5] presented a new method for quantifying a species’ contribution to phylogenetic diversity using a measure termed the “Evolutionary Distinctiveness” (ED). This statistical value could then be used to set conservation priorities, as species with a higher ED have fewer close relatives and are at an increased risk for extinction. Combining the ED score with data on globally endangered (GE) species, the authors then created an “EDGE” score to come up with a top 100 list of mammals requiring attention, many of which had not been previously considered as conservation priorities.

 

2008 – Key players in mammalian germ cell development

This study by Hayashi et al. [6] explored the role of microRNAs in the developing mammalian embryo, specifically in the development of primordial germ cells and the process of early spermatogenesis. Using mice as a model, they discovered characteristic spatial and temporal expression patterns of microRNA clusters and demonstrated that biogenesis of microRNA was required for the development of male germ cells. The findings of this study highlighted the functional requirements of microRNA in these early developmental pathways.

 

2009 – Identifying brain networks using spontaneous neuronal activity

He et al. [7] demonstrated that functionally-relevant brain networks, such as the visual, auditory, and somatosensory systems, have specific patterns of activity that are distinct from the activity of the whole brain. Using functional magnetic resonance imaging (fMRI), these brain networks could be identified using only spontaneous activity patterns without any a priori anatomical information, illustrating the modularity and organization of the human brain.

 

2010 – Misrepresentation by extracellular microRNA levels

Circulating microRNAs are of great interest as diagnostic biomarkers, particularly for the detection of cancer. However, the work of Pigati et al. [8] demonstrated that the abundance of a microRNA in a bodily fluid doesn’t necessarily correlate with the cellular profile. By comparing the composition of microRNAs within mammary cells to microRNAs released by cells into the blood, milk, and ductal fluid, they found that certain microRNA species were selectively retained and released. In addition, the patterns of release differed between normal and malignant cells, implying that the mechanism of microRNA release may vary based on the cellular state.

 

2011 – Strategies for early Alzheimer’s disease

A pair of articles tackled the challenge of diagnosing and treating Alzheimer’s disease in its early stages. Han et al. [9] used mass spectrometry-based shotgun lipidomics to analyze plasma contents and found that some sphingolipid and ceramide species were present in different amounts in people with Alzheimer’s. In addition, the levels of specific lipids correlated with the cognitive status of the individual. Majumder et al. [10] used a mouse model of Alzheimer’s disease to determine whether inducing autophagy with the compound rapamycin could reduce plaques and tangles. While early, prophylactic treatment led to a reduction in plaques, tangles, and cognitive decline, treatment after the establishment of plaques had no effect, implying that strategically inducing autophagy many only be effective in early stages.

 

2012 – Tool for identifying nucleosomal sequences

Nucleosomes are units in eukaryotic chromatin that include a DNA segment surrounding histone proteins. Using the Saccharomyces cerevisiae genome as a starting point, Chen et al. [11] found that certain physicochemical features of DNA, like base stacking, bending stiffness, and Z-DNA, could be used to identify the presence of a nucleosome in an uncharacterized DNA sequence. Based on these findings, they developed a web-based tool called the iNuc-PhysChem (available at http://lin.uestc.edu.cn/server/iNuc-PhysChem), which had a correct identification rate of 96% in a benchmark dataset.

 

2013 – Global profile of stroke risk for people with atrial fibrillation

Kakkar et al. [12] describe findings from an international cohort study of over 10,000 individuals across five continents who were recently diagnosed with non-valvular atrial fibrillation. This affliction is the most common heart rhythm disorder and is associated with an increased risk of stroke. While Vitamin K antagonists have been traditionally used for stroke prevention in this population, the findings of this study demonstrated that actual treatment use was not consistent with established guidelines, leaving many patients who were at an increased risk for stroke without the recommended treatment.

 

2014 – CRISPR for citrus

While much of the excitement around the CRISPR/Cas9 gene editing approach has focused on its potential applications in human health, targeted genetic engineering in plants also has significant implications. This study by Jia et al. [13] described the first application of CRISPR technology in citrus fruits, specifically with the popular and pervasive sweet orange (Citrus sinensis, cultivar Valencia). They developed an improved method of agroinfiltration, a process which enhances transient protein expression, to deliver the Cas9 endonuclease and single-guide RNA, achieving a greater than 3% mutation rate with no observed off-target effects.

 

2015 – Simple method for detecting antibiotic-resistant bacteria

Bacteria that produce carbapenemase are of public health concern due to their resistance to carbapenem antibiotics, which are typically used as a last resort when an infection has proven resistant to standard antibiotic treatments. While previous methods existed for detecting these bacteria, van der Zwaluw et al. [14] developed an alternative approach, named the Carbapenem Inactivation Method (CIM), that could be used to quickly screen bacteria in health care settings at approximately 1/20th of the standard cost.

 

2016 – RNA splicing therapy for Duchenne muscular dystrophy

Goemans et al. [15] report on an open-label extension of a Phase I/IIa, dose-escalation study for the experimental drug drisapersen, an exon-skipping oligonucleotide that restores production of a partially functional dystrophin protein. Twelve participants with Duchenne muscular dystrophy were followed for three and a half years. While some adverse events were observed in all subjects, there was also some improvement in the 6-Minute Walk Test in comparison to the anticipated decline. While investigation of drisapersen has been discontinued in favor of second generation oligonucleotides, this study provided the longest-duration dataset of an exon-skipping therapy to date.

 

While these articles represent a wide spectrum of research, a commonality between them is their utility to the scientific community, whether as a baseline finding to build upon, or as a tool for future use. By exploring the ratio between two primary ALMs, we are able to derive a meaningful secondary metric that can be used to recognize articles with a high degree of scientific engagement. For more examples of how article-level metrics can be used to evaluate an article’s impact, we encourage exploration of the Altmetrics Collection and the PLOS ONE 10 Year Anniversary Collection on 10 Highly Cited Articles.

 

References:

 

  1. Lariviere V, Kiermer V, MacCallum CJ, McNutt M, Patterson M, Pulverer B, Swaminathan S, Taylor S, Curry S. A simple proposal for the publication of journal citation distributions. Biorxiv. 2016 Jan 1:062109.

 

  1. San Francisco Declaration on Research Assessment: Putting science into the assessment of research. http://www.ascb.org/dora/

 

  1. Yan KK, Gerstein M. The spread of scientific information: insights from the web usage statistics in PLoS article-level metrics. PLOS ONE. 2011 May 16;6(5):e19917.

 

  1. Lin J, Fenner M. Altmetrics in evolution: Defining and redefining the ontology of article-level metrics. Information standards quarterly. 2013;25(2):20-6.

 

  1. Isaac NJ, Turvey ST, Collen B, Waterman C, Baillie JE. Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLOS ONE. 2007 Mar 14;2(3):e296.

 

  1. Hayashi K, de Sousa Lopes SM, Kaneda M, Tang F, Hajkova P, Lao K, O’Carroll D, Das PP, Tarakhovsky A, Miska EA, Surani MA. MicroRNA biogenesis is required for mouse primordial germ cell development and spermatogenesis. PLOS ONE. 2008 Mar 5;3(3):e1738.

 

  1. He Y, Wang J, Wang L, Chen ZJ, Yan C, Yang H, Tang H, Zhu C, Gong Q, Zang Y, Evans AC. Uncovering intrinsic modular organization of spontaneous brain activity in humans. PLOS ONE. 2009 Apr 21;4(4):e5226.

 

  1. Pigati L, Yaddanapudi SC, Iyengar R, Kim DJ, Hearn SA, Danforth D, Hastings ML, Duelli DM. Selective release of microRNA species from normal and malignant mammary epithelial cells. PLOS ONE. 2010 Oct 20;5(10):e13515.

 

  1. Han X, Rozen S, Boyle SH, Hellegers C, Cheng H, Burke JR, Welsh-Bohmer KA, Doraiswamy PM, Kaddurah-Daouk R. Metabolomics in early Alzheimer’s disease: identification of altered plasma sphingolipidome using shotgun lipidomics. PLOS ONE. 2011 Jul 11;6(7):e21643.

 

  1. Majumder S, Richardson A, Strong R, Oddo S. Inducing autophagy by rapamycin before, but not after, the formation of plaques and tangles ameliorates cognitive deficits. PLOS ONE. 2011 Sep 28;6(9):e25416.

 

  1. Chen W, Lin H, Feng PM, Ding C, Zuo YC, Chou KC. iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties. PLOS ONE. 2012 Oct 29;7(10):e47843.

 

  1. Kakkar AK, Mueller I, Bassand JP, Fitzmaurice DA, Goldhaber SZ, Goto S, Haas S, Hacke W, Lip GY, Mantovani LG, Turpie AG. Risk profiles and antithrombotic treatment of patients newly diagnosed with atrial fibrillation at risk of stroke: perspectives from the international, observational, prospective GARFIELD registry. PLOS ONE. 2013 May 21;8(5):e63479.

 

  1. Jia H, Wang N. Targeted genome editing of sweet orange using Cas9/sgRNA. PLOS ONE. 2014 Apr 7;9(4):e93806.

 

  1. van der Zwaluw K, de Haan A, Pluister GN, Bootsma HJ, de Neeling AJ, Schouls LM. The carbapenem inactivation method (CIM), a simple and low-cost alternative for the Carba NP test to assess phenotypic carbapenemase activity in gram-negative rods. PLOS ONE. 2015 Mar 23;10(3):e0123690.

 

  1. Goemans NM, Tulinius M, Van den Hauwe M, Kroksmark AK, Buyse G, Wilson RJ, van Deutekom JC, de Kimpe SJ, Lourbakos A, Campion G. Long-term efficacy, safety, and pharmacokinetics of drisapersen in Duchenne muscular dystrophy: results from an open-label extension study. PLOS ONE. 2016 Sep 2;11(9):e0161955.

 

 

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