Author: Raphaël Lévy

20 critical reviews of influential articles about nanoparticles and cells

I have commented on the 20 highly cited articles below. They all relate to nanoparticles and cells. They were published between 1998 and 2006 and have received more than 1,000 citations each, over 40,000 citations overall.

I have used Twitter to document my reviewing process.

I have copied all of my reviews to PubPeer ; see the link below each papers in the bibliography at the bottom of this post. The orange colour indicates serious problems; the blue colour indicates that important old relevant papers have been overlooked.

You can also find the tweets via the ThreadReaderApp:

 

1             Bruchez, M., Moronne, M., Gin, P., Weiss, S. & Alivisatos, A. P. Semiconductor nanocrystals as fluorescent biological labels. Science 281, 2013-2016, doi:10.1126/science.281.5385.2013 (1998).

=> Comment on PubPeer.

2             Gref, R. et al. ‘Stealth’ corona-core nanoparticles surface modified by polyethylene glycol (PEG): influences of the corona (PEG chain length and surface density) and of the core composition on phagocytic uptake and plasma protein adsorption. Colloids and Surfaces B-Biointerfaces 18, 301-313, doi:10.1016/s0927-7765(99)00156-3 (2000).

=> Comment on PubPeer.

3             Lewin, M. et al. Tat peptide-derivatized magnetic nanoparticles allow in vivo tracking and recovery of progenitor cells. Nature Biotechnology 18, 410-414, doi:10.1038/74464 (2000).

=> Comment on PubPeer.

4             Akerman, M. E., Chan, W. C. W., Laakkonen, P., Bhatia, S. N. & Ruoslahti, E. Nanocrystal targeting in vivo. Proceedings of the National Academy of Sciences of the United States of America 99, 12617-12621, doi:10.1073/pnas.152463399 (2002).

=> Comment on PubPeer.

5             Hirsch, L. R. et al. Nanoshell-mediated near-infrared thermal therapy of tumors under magnetic resonance guidance. Proceedings of the National Academy of Sciences of the United States of America 100, 13549-13554, doi:10.1073/pnas.2232479100 (2003).

=> Comment on PubPeer.

6             Lai, C. Y. et al. A mesoporous silica nanosphere-based carrier system with chemically removable CdS nanoparticle caps for stimuli-responsive controlled release of neurotransmitters and drug molecules. Journal of the American Chemical Society 125, 4451-4459, doi:10.1021/ja028650l (2003).

=> Comment on PubPeer.

7             Wu, X. Y. et al. Immunofluorescent labeling of cancer marker Her2 and other cellular targets with semiconductor quantum dots. Nature Biotechnology 21, 41-46, doi:10.1038/nbt764 (2003).

=> Comment on PubPeer.

8             Gao, X. H., Cui, Y. Y., Levenson, R. M., Chung, L. W. K. & Nie, S. M. In vivo cancer targeting and imaging with semiconductor quantum dots. Nature Biotechnology 22, 969-976, doi:10.1038/nbt994 (2004).

=> Comment on PubPeer.

9             Sondi, I. & Salopek-Sondi, B. Silver nanoparticles as antimicrobial agent: a case study on E-coli as a model for Gram-negative bacteria. Journal of Colloid and Interface Science 275, 177-182, doi:10.1016/j.jcis.2004.02.012 (2004).

=> Comment on PubPeer.

10           Connor, E. E., Mwamuka, J., Gole, A., Murphy, C. J. & Wyatt, M. D. Gold nanoparticles are taken up by human cells but do not cause acute cytotoxicity. Small 1, 325-327, doi:10.1002/smll.200400093 (2005).

=> Comment on PubPeer.

11           El-Sayed, I. H., Huang, X. H. & El-Sayed, M. A. Surface plasmon resonance scattering and absorption of anti-EGFR antibody conjugated gold nanoparticles in cancer diagnostics: Applications in oral cancer. Nano Letters 5, 829-834, doi:10.1021/nl050074e (2005).

=> Comment on PubPeer.

12           Hussain, S. M., Hess, K. L., Gearhart, J. M., Geiss, K. T. & Schlager, J. J. In vitro toxicity of nanoparticles in BRL 3A rat liver cells. Toxicology in Vitro 19, 975-983, doi:10.1016/j.tiv.2005.06.034 (2005).

=> Comment on Pubpeer.

13           Kirchner, C. et al. Cytotoxicity of colloidal CdSe and CdSe/ZnS nanoparticles. Nano Letters 5, 331-338, doi:10.1021/nl047996m (2005).

=> Comment on PubPeer.

14           Loo, C., Lowery, A., Halas, N. J., West, J. & Drezek, R. Immunotargeted nanoshells for integrated cancer imaging and therapy. Nano Letters 5, 709-711, doi:10.1021/nl050127s (2005).

=> Comment on PubPeer.

15           Morones, J. R. et al. The bactericidal effect of silver nanoparticles. Nanotechnology 16, 2346-2353, doi:10.1088/0957-4484/16/10/059 (2005).

=> Comment on PubPeer.

16           Chithrani, B. D., Ghazani, A. A. & Chan, W. C. W. Determining the size and shape dependence of gold nanoparticle uptake into mammalian cells. Nano Letters 6, 662-668, doi:10.1021/nl052396o (2006).

=> Comment on PubPeer.

17           Huang, X. H., El-Sayed, I. H., Qian, W. & El-Sayed, M. A. Cancer cell imaging and photothermal therapy in the near-infrared region by using gold nanorods. Journal of the American Chemical Society 128, 2115-2120, doi:10.1021/ja057254a (2006).

=> Comment on PubPeer.

18           Panacek, A. et al. Silver colloid nanoparticles: Synthesis, characterization, and their antibacterial activity. Journal of Physical Chemistry B 110, 16248-16253, doi:10.1021/jp063826h (2006).

=> Comment on PubPeer.

19           Rosi, N. L. et al. Oligonucleotide-modified gold nanoparticles for intracellular gene regulation. Science 312, 1027-1030, doi:10.1126/science.1125559 (2006).

=> Comment on PubPeer.

20           Xia, T. et al. Comparison of the abilities of ambient and manufactured nanoparticles to induce cellular toxicity according to an oxidative stress paradigm. Nano Letters 6, 1794-1807, doi:10.1021/nl061025k (2006).

=> Comment on PubPeer.

 

 

Why is a leading UK medical journal standing by false data? – BBC Newsnight

BBC Newsnight and Deborah Cohen are following up on their story. The “false data” is a reference to this 2008 paper in the Lancet. Features also the Chair of the Science and Technology Committee Norman Lamb who says

There should be funding consequences for these institutions who fail to investigate alleged misconduct.

[…]

I will be writing back to the Lancet. We need clear answer from them to clear this up.

The stem cell trachea scandal

Yesterday night, BBC Newsnight broadcasted an investigation by journalist Deborah Cohen featuring interviews with my colleague Prof Patricia Murray as well as extremely moving testimony by the mum of Shauna Davidson. Shauna’s mum had been misled on the nature of the intervention on her daughter and even on the cause of her death.

Patricia is a stem cell expert and we’ve had a long term (and ongoing) collaboration on using imaging to track stem cells for evaluation of their safety and efficacy. When, a few years ago, she started to get interested in the Macchiarini scandal and realised that similar experiments on patients had been done in the UK (and continued to be done), she contacted me knowing my interest in ethical issues and scientific misconduct. I am proud to have supported her sterling work in uncovering this scandal – I am also pleased that legal threats have failed to silence us. The extent of conflicts of interest and unresolved matters involving major institutions in the UK is massive. So much so that we have had to go all the way to Parliament (see our two contributions to the Science and Technology committee on Research Integrity inquiry) to get (so far unsatisfactory) responses. We hope that the BBC reporting will help bring much needed clarity, but the obfuscating responses of GOSH and MRC to Deborah’s questions are deeply worrying.

See also the excellent and detailed work of Leonid Schneider on this same scandal.

 

Open peer review of (not so) controversial articles

Publishing articles that are critical of previously published work is notoriously difficult but the secrecy of peer review makes it hard to explain the kind of biases and tricks that one faces in this enterprise. Opening peer review, i.e. sharing reports and responses, would certainly help. Here is an interesting exemple related to an article (nicely discussed by Philip Moriarty in a previous post) which is not even critical of prior literature but touches on the stripy nanoparticles controversy. That was too much for Reviewer #1 (hyperlinks added by me; they point to relevant blog posts here or at PubPeer):

Reviewer #1 (Remarks to the Author):
This paper describes the scanning tunnelling microscopy imaging (STM) of a silver cluster (Ag374). To the best of my knowledge there is no report of such things to date. As such I think this paper should be published but in a specialised journal or a broad journal with reporting functions as Scientific Reports.

The significance of this paper as such is minimal. The STM does not add anything to what X-ray crystallography has shown so far also on the same cluster. In fact it requires strong support from calculation.

The STM itself has been widely published on nanoparticles by the group of Stellacci. The authors do reference a controversy there but do not comment on it an neither add to it.

The approach used is almost identical to the one described by such group in Ong et al ACS Nano (non cited), and the results achieved are similar to the ones described in the same paper and in Moglianetti et al. (not cited). Their minimal difference is that they achieved these results in liquid nitrogen and helium temperature, but low temperature results were described in Biscarini et al. (not cited).

Given the scant discussion in the paper (lacks any point) and the two major objections report, I suggest rejection.

The other, more supportive reports, and the response from the authors, can be downloaded from Nature Communications.

Probes, Patterns, and (nano)Particles

philipmoriarty

Philip Moriarty

This is a guest post by Philip Moriarty, Professor of Physics at the University of Nottingham (and blogger).

“We shape our tools, and thereafter our tools shape us.”

Marshall McLuhan (1911-1980)

My previous posts for Raphael’s blog have focussed on critiquing poor methodology and over-enthusiastic data interpretation when it comes to imaging the surface structure of functionalised nanoparticles. This time round, however, I’m in the much happier position of being able to highlight an example of good practice in resolving (sub-)molecular structure where the authors have carefully and systematically used scanning probe microscopy (SPM), alongside image recognition techniques, to determine the molecular termination of Ag nanoparticles.

For those unfamiliar with SPM, the concept underpinning the operation of the technique is relatively straight-forward. (The experimental implementation rather less so…) Unlike a conventional microscope, there are no lenses, no mirrors, indeed, no optics of any sort [1]. Instead, an atomically or molecularly sharp probe is scanned back and forth across a sample surface (which is preferably atomically flat), interacting with the atoms and molecules below. The probe-sample interaction can arise from the formation of a chemical bond between the atom terminating the probe and its counterpart on the sample surface, or an electrostatic or magnetic force, or dispersion (van der Waals) forces, or, as in scanning tunnelling microscopy (STM), the quantum mechanical tunnelling of electrons. Or, as is generally the case, a combination of a variety of those interactions. (And that’s certainly not an exhaustive list.)

Here’s an example of an STM in action, filmed in our lab at Nottingham for Brady Haran’s Sixty Symbols channel a few years back…

Scanning probe microscopy is my first love in research. The technique’s ability to image and manipulate matter at the single atom/molecule level (and now with individual chemical bond precision) is seen by many as representing the ‘genesis’ of nanoscience and nanotechnology back in the early eighties. But with all of that power to probe the nanoscopic, molecular, and quantum regimes come tremendous pitfalls. It is very easy to acquire artefact-ridden images that look convincing to a scientist with little or no SPM experience but that instead arise from a number of common failings in setting up the instrument, from noise sources, or from a hasty or poorly informed choice of imaging parameters. What’s worse is that even relatively seasoned SPM practitioners (including yours truly) can often be fooled. With SPM, it can look like a duck, waddle like a duck, and quack like a duck. But it can too often be a goose…

That’s why I was delighted when Raphael forwarded me a link to “Real-space imaging with pattern recognition of a ligand-protected Ag374 nanocluster at sub-molecular resolution”, a paper published a few months ago by Qin Zhou and colleagues at Xiamen University (China), the Chinese Academy of Science, Dalian (China), the University of Jyväskylä (Finland), and the Southern University of Science and Technology, Guandong (China). The authors have convincingly imaged the structure of the layer of thiol molecules (specifically, tert-butyl benzene thiol) terminating 5 nm diameter silver nanoparticles.

What distinguishes this work from the stripy nanoparticle oeuvre that has been discussed and dissected at length here at Raphael’s blog (and elsewhere) is the degree of care taken by the authors and, importantly, their focus on image reproducibility. Instead of using offline zooms to “post hoc” select individual particles for analysis (a significant issue with the ‘stripy’ nanoparticle work), Zhou et al. have zoomed in on individual particles in real time and have made certain that the features they see are stable and reproducible from image to image. The images below are taken from the supplementary information for their paper and shows the same nanoparticle imaged four times over, with negligible changes in the sub-particle structure from image to image.

This is SPM 101

This is SPM 101. Actually, it’s Experimental Science 101. If features are not repeatable — or, worse, disappear when a number of consecutive images/spectra are averaged – then we should not make inflated claims (or, indeed, any claims at all) on the basis of a single measurement. Moreover, the data are free of the type of feedback artefacts that plagued the ‘classic’ stripy nanoparticle images and Zhou et al. have worked hard to ensure that the influence of the tip was kept to a minimum.

Given the complexity of the tip-sample interactions, however, I don’t quite share the authors’ confidence in the Tersoff-Hamann approach they use for STM image simulation [2]. I’m also not entirely convinced by their comparison with images of isolated molecular adsorption on single crystal (i.e. planar) gold surfaces because of exactly the convolution effects they point towards elsewhere in their paper. But these are relatively minor points. The imaging and associated analysis are carried out to a very high standard, and their (sub)molecular resolution images are compelling.

As Zhou et al. point out in their paper, STM (or atomic force microscopy) of nanoparticles, as compared to imaging a single crystal metal, semiconductor, or insulator surface, is not at all easy due to the challenging non-planar topography. A number of years back we worked with Marie-Paule Pileni’s group on dynamic force microscopy imaging (and force-distance analysis) of dodecanethiol-passivated Au nanoparticles. We found somewhat similar image instabilities as those observed by Zhou et al…

A-C above are STM data

A-C above are STM data, while D-F are constant height atomic force microscope images [3], of thiol-passivated nanoparticles (synthesised by Nicolas Goubet of Pileni’s group) and acquired at 78 K. (Zhou et al. similarly acquired data at 77K but they also went down to liquid helium temperatures). Note that while we could acquire sub-nanoparticle resolution in D-F (which is a sequence of images where the tip height is systematically lowered), the images lacked the impressive reproducibility achieved by Zhou et al. In fact, we found that even though we were ostensibly in scanning tunnelling microscopy mode for images such as those shown in A-C (and thus, supposedly, not in direct contact with the nanoparticle), the tip was actually penetrating into the terminating molecular layer, as revealed by force-distance spectroscopy in atomic force microscopy mode.

The other exciting aspect of Zhou et al.’s paper is that they use pattern recognition to ‘cross-correlate’ experimental and simulated data. There’s increasingly an exciting overlap between computer science and scanning probe microscopy in the area of image classification/recognition and Zhou and co-workers have helped nudge nanoscience a little more in this direction. Here at Nottingham we’re particularly keen on the machine learning/AI-scanning probe interface, as discussed in a recent Computerphile video…

Given the number of posts over the years at Raphael’s blog regarding a lack of rigour in scanning probe work, I am pleased, and very grateful, to have been invited to write this post to redress the balance just a little. SPM, when applied correctly, is an exceptionally powerful technique. It’s a cornerstone of nanoscience, and the only tool we have that allows both real space imaging and controlled modification right down to the single chemical bond limit. But every tool has its limitations. And the tool shouldn’t be held responsible if it’s misapplied…

[1] Unless we’re talking about scanning near field optical microscopy (SNOM). That’s a whole new universe of experimental pain…

[2] This is the “zeroth” order approach to simulating STM images from a calculated density of states. It’s a good starting point (and for complicated systems like a thiol-terminated Ag374 particle probably also the end point due to computational resource limitations) but it is certainly a major approximation.

[3] Technically, dynamic force microscopy using a qPlus sensor. See this Sixty Symbols video for more information about this technique.

 

The war on (scientific) terror…

Thank you Philip for this post and your support.

Symptoms Of The Universe

I’ve been otherwise occupied of late so the blog has had to take a back seat. I’m therefore coming to this particular story rather late in the day. Nonetheless, it’s on an exceptionally important theme that is at the core of how scientific publishing, scientific critique, and, therefore, science itself should evolve. That type of question doesn’t have a sell-by date so I hope my tardiness can be excused.

The story involves a colleague and friend who has courageously put his head above the parapet (on a number of occasions over the years) to highlight just where peer review goes wrong. And time and again he’s gotten viciously castigated by (some) senior scientists for doing nothing more than critiquing published data in as open and transparent a fashion as possible. In other words, he’s been pilloried (by pillars of the scientific community) for daring to suggest that we do science…

View original post 1,415 more words

Do planes fly and other difficult scientific questions

The Scientist magazine reported on the ACS meeting incident. Here is Chad Mirkin’s response to their questions:

Mirkin disagrees with Levy’s assessment of the endosome entrapment. “Levy’s narcissistic approach is akin to, ‘I bought an airplane, and I can’t make it fly. Therefore, planes don’t fly, despite the fact that I see them all above me,’” he tells The Scientist.

Mirkin stresses the number of studies in which the probes have been used successfully: “There is no controversy . . . There are over 40 papers reporting the successful use of such structures, involving over 100 different researchers, spanning three different continents,” he writes to The Scientist in an email. “I think the data and widespread use of such structures speak to their reliability and utility for measuring RNA content in live cells,” he adds.

After “dishonest Rafael [sic] Levy and his band of trolls“, “scientific terrorist” and “scientific zealot“, I suppose the “narcissistad hominem, could be considered more moderate?

1920px-John_William_Waterhouse_-_Echo_and_Narcissus_-_Google_Art_Project

Echo and Narcissus, John William Waterhouse, 1903, Walker Art Gallery, Liverpool. Narcissus, too busy contemplating his image, cannot see Echo let alone planes flying above him.

As The Scientist notes, I am hardly the only one who cannot make the SmartFlare plane fly. And the plane manufacturer has stopped selling its product and does not answer questions from journalists.