Schlagwort-Archive: allergy

When a scientific journal is modifying your images

The Journal of Allergy and Clinical Immunology (JACI) is ranking 2nd out of 28 allergy journals having an IF of 10,8.

Working on an image duplication pipeline we found images in numerous JACI papers that have been heavily modified (for Pubpeer examples see 1, 2, 3, 4, 5, …). AFAIK from several authors the modifications happened without their knowledge. As the duplications are always at the outer edges and originate from the same image, we assume from the beginning that JACI inserted “new background” for the “journal style” letter boxes.

Difficult to understand? Here is an example from the first reference.

 

JACI is known to ignore misconduct allegations while they are now responding to post publication peer review. Maybe an image is more worth than 1000 words?

… there were unexpected duplications …. The duplications occurred when the publisher’s compositor vendor styled the figure panel label for print. The error did not impact the analysis, results, or conclusions of the article. The original figure appears below. The authors were not responsible for the error. Measures have been taken to prevent reoccurrence of this error for which the publisher accepts full responsibility and apologizes.

So photoshopping is no more allowed at the JACI office in Colorado– but who is accepting this “full responsibility”?

29 Aug 2021

@spy_sci pointed  out this morning to a paper in “Cell Journal”  with a similar phenomenon while also @Cheshire has found that multiple times over the past year.  @SmutClyde contributed another example from Bioscience Reports

 

A new hypothesis why atopic dermatitis and asthma may be linked by vitamin D

We had a major discussion before our 2010 paper where I argued that rare variants should have been included. Ten years after there is a nice paper using massive exome sequencing that finally includes them. The respiratory tract isn’t so much influenced by rare variants but there is a strong effect in  the immune system.

Qanli Wang https://www.biorxiv.org/content/10.1101/2020.12.13.422582v1, posted December 13, 2020.

And there is another interesting fact.

Surveying the contribution of rare variants to the genetic architecture of human disease through exome sequencing of 177,882 UK Biobank participants …if we look at the …. European population who are carriers of a filaggrin (FLG) PTV, we find those carriers have significantly higher risk for well-known associations, such as dermatitis  … and asthma … Concomitant increases in vitamin D levels suggest risk of melanoma and basal cell carcinoma in FLG PTV carriers could be attributable to increased sensitivity to ultraviolet B radiation.

So far, I have only assumed some asthma/allergy priming effect of oral vitamin D in the newborn gut.

This paper now argues for an increased vitamin D sensitivity in the skin of  FLG dermatitis patients which is interesting given the largely contradictory data of serum vitamin D and atopic dermatitis. Maybe dermatologists should focus their research more on local vitamin D turnover?

Blaming genes for resistance to environmental stressors

This something that I always avoided in human research – blaming genes for resistance to environmental stressors.

Nevertheless a Californian group (https://doi.org/10.1371/journal.pgen.1008528) now tested 101 mouse strains for lung resistance with exposure to diesel exhaust particles (DEP). After sensitizing the animals with dust mite and aluminium they could also test metacholine hyperreactivity (AHR).

Strains that exhibited the highest lung resistance after control exposure were not necessarily the same as those with high lung resistance after DEP exposure. It is unclear which strain was used for the consecutive GWAS. Did they put all mice into one cage for that?

The metacholine AHR GWAS results are not very impressive. And there seem to be also errors, as for example the lead SNP on chr 19 (rs51547574, near IL33) is shown with different allele frequencies in text and Fig 2.  As the expression quantitative trait locus (eQTL) for Il33 is not in the lung, I think there is nothing to memorize here – IL33 is just a gatekeeper for surface integrity.

In a next step I wouldhave expected a GWAS for resistance change after DEP but FIG 3 only gives the result of Δ AHRDEP—AHRPBS data at an abitrary methacholine dose of 10mg/ml. The identifed locus could be interesting but as the LD there is rather high without any corresponding eQTL (I always wondered why there has never been a significance threshold for LD blocks, only for isolated SNPs?), the logic of the paper is broken here. Induction of lung resistance by DEP was significantly blunted in Dapp1-/- female mice? What about male Gm5105-/- Mttp-/- , and Lamtor3-/- animals?

Hopefully nobody else will now try to find diesel, ozone, NOx resistance genes in humans as this is not a a scientific but a political issue…

What is wrong with the 2011 NEJM paper?

N Engl J Med 2011;364:701-9 is another paper with 1000+ citations  that had a lasting impression on some but not all people.

First, I can’t remember of any study with such an enormous selection bias  where >94% of individuals have been lost.

Second, we should not forget that farm is not protective per se – farmers may just avoid a known allergy risk factor.  PARSIFAL participants in this study included Steiner schools — anthroposophic medicine mostly avoids vitamin D (ref). This is of course a major issue for any cross-sectional study that doesn’t take into account the temporality of events.

Third, in PARSIFAL dust from children’s mattresses were collected by vacuuming — it is not very likely that many helminthic eggs were transported  from stable to bedroom. In GABRIELA, only airborne dust samples  were collected which again may miss helminth eggs although being certainly present in stable dust.

Fourth, more  microbial exposure and more fungal taxa on farms are a trivial finding.

The inverse associations of the diversity scores with asthma were not confounded by status with respect to living on a farm because adjustment did not change the respective point estimates for asthma (Table 2), although the associations became nonsignificant.

Small sample size, borderline p-values even after a long fishing expedition?

What do these strange “probability” plots  really show – the probability of asthma or the probability to live on a farm?

N Engl J Med 2011;364:701-9 Figure 3 Does it refute any general effect of diversity?

The plots are misleading if adjustment for farm living does not change the parameter estimates for bacterial/fungal diversity.

Sixth – even many years later, the main findings of this study have not been independently replicated. There is not any single study that shows listeriosis (Listeria) or diphtheria (Corynebacterium)  to be protective.

medRxiv

ArXiv is operational since 1991, bioRxiv since 2013 and since 2019 there is now also medrxiv. More details  at https://www.bmj.com/content/365/bmj.l2301

The main arguments in favour of sharing work in its preliminary form are, firstly, that science works faster if work is made available sooner after it is completed and, secondly, that articles are improved by feedback from a wider group of readers, alongside formal peer review by a few experts. Simple estimates suggest that halving the delay to sharing a research result can double the speed at which research progresses. Ambitious research funders are now embracing preprints and other measures that aim to accelerate the pace of research.

Although there was a mixed reception in the beginning, see Science back in 2017

MedArXiv will have a hard time attracting preprints if mainstream medical journal editors decide they won’t publish final versions of the papers. Currently, The BMJ and The Lancet are among the few medical journals that have explicitly said that posting a preprint doesn’t preclude publication; Nature and Science, which both occasionally publish medical studies, have the same policy. But at the JAMA Network, which publishes a dozen journals, the issue is hotly debated.

@medRxiv opened on June 6. So far they have only 304 followers on Twitter (and no allergy paper in the archive).

As the current “Allergy” editor and the publisher (John Wiley and Sons A/S)  agreed to preprints last week, I have submited now my first preprint paper. Therefore, there are now 305 followers and 1 allergy paper :-)

IL33, allergy and helminths: Shot in the leg?

Ever since our NEJM paper in 2010 that showed an IL33/ST2 association there are new studies on IL33.

Grotenboer 2013 did a functional annotation of the gene and it’s receptor in humans while there is no more doubt about the involvement of IL33 in human allergy.  Right now IL33 suppression is already used as an experimental screening test for allergic reactivity with ongoing phase II studies of anti-IL33 or anti ST2. Good IL33 reviews can be found for example in frontiers in immunology by Tataori et al. or in nature immunology by Smith.

These reviews do not tell you so much about the regulation while regulation has recently elucidated by Gour et al. who describe a tropomyosin–dectin-1 interaction of the human host. Why is tropomyosin such a frequent target of human IgE?

Muscle protein tropomyosin is an important IgE target in a number of nematode infections; Onchocerca volvulus ; Ascaris lumbricoides; Anisakis simplex; and tropomyosin from the blood fluke Schistosoma mansoni is also a human IgE antigen. Tropomyosin is highly conserved across many invertebrates and is responsible for much of the IgE cross-reactivity between Ascaris and dust-mites.

I haven’t found any good  answer to this question. As tropomyosin affects contractility – this seems like “shooting into the leg” of worms whenever they attempt to invade.

Maybe Gour et al. did not know the earlier dissertation from Berlin that already showed a reduced inflammation in the OVA mouse model by administration of recombinant tropomyosin.

The broad cross reactivity to tropomyosin gives rise to the question if helminth tropomyosin could induce allergic reactions to itself and/or tropomyosin of different organisms. Considering the fact that filarial nematodes express tropomyosin on their surface […] and that the continuing turnover of microfilariae confronts the host with relevant amounts of tropomyosin makes this question even more appropriate.

Worms seems to be attacked by anti-worm-surface-tropomyosin IgE whenever the worm tries to invade  the epithelium during an acute infection. During invasion extracellular IL33 is cleaved into a shorter form with enhanced activity attracting more immune cells.
During chronic infestation nothing happens as long as the worm does not invade and doesn’t trigger any IL33 alarmin. As there is continuous tropomyosin antigen antigen contact, the host is slowly desensitzed, clearing IgE in favor of IgG4.

Is this also a model that explains allergy? We don’t know the details but maybe this antigen recognition / response system is being disturbed where allergens like Der p1 mimicking a worm infection by tropomyosin can trigger the allergic reaction in particular as Der p1 a cysteine protease also mimicks an invasion signal.

23.12.2019 Addendum

Parasite tropomyosin ist detected in in 55%-62% of patients (cockroach tropomyosin rPer a 7, Ascaris tropomyosin rAsc l 3).

People who behave fraudently

Richard Smith 3:58 “People who behave fraudently tend to behave fraudently in all aspects of their live”

8:05 “Universities have no interest to discover fraud” 10:42 “Journals don’t have the legal standing” 10:58 “we need some kind of national bodies”

A step forward in allergy research

The most recent paper of my Australian collaborators is a relevant step forward: Polymorphisms affecting vitamin D-binding protein modify the relationship between serum vitamin D (25[OH]D3) and food allergy. Basically they show an

… association between serum 25-hydroxyvitamin D3 (25[OH]D3) levels and food allergy at age 1 year (338 challenge-proven food-allergic and 269 control participants) and age 2 years (55 participants with persistent and 50 participants with resolved food allergy)… Analyses were stratified by genotype at rs7041 as a proxy marker of DBP levels… Low serum 25(OH)D3 level (<50 nM/L) at age 1 years was associated with food allergy, particularly among infants with the GG genotype (odds ratio [OR], 6.0; 95% CI, 0.9-38.9) … Maternal antenatal vitamin D supplementation was associated with less food allergy, particularly in infants with the GT/TT genotype (OR, 0.10; 95% CI, 0.03-0.41)… This increases the biological plausibility of a role for vitamin D in the development of food allergy.

Maybe it would be helpful to have also “real” DBP levels for estimating bioavailability (and even data of supplement use) but already the reported results are another strong argument for the vitamin D – allergy axis. This is also largely in line with what I predicted back in 2012

Both vitamin D insufficiency and vitamin D supplementation have been linked to allergy and asthma. This apparent paradox is explained by epigenetic programming in pregnancy by low vitamin D levels and the excessive high supplementation in the newborn period.

Maybe I should have emphasized that genetic variants in the vitamin D pathway are also important for biological effects.

Is this a retraction of the hygiene hypothesis?

There are news about the hygiene hypothesis.

Home cleanliness resulted only in quantitative reduction of floor dust, which mainly indicates removal of superficial dirt with a rather cosmetic effect. Conventional cleaning does not eradicate microorganisms sustainably, because emptied microbial niches are instantly recolonized by ventilation and living carrier.

Sure. Is this a retraction of the hygiene hypothesis? weiterlesen

Take care of your last sentence

I have been told long ago to take care of the last sentence in a paper, avoiding any unjustified conclusion or any unwarranted speculation. Let’s start with a fully justified last sentence in the new volume of  “International Nutrition: Achieving Millennium Goals and Beyond

Bildschirmfoto 2014-04-02 um 08.44.39
Bildschirmfoto 2014-04-02 um 08.44.49

It says that Take care of your last sentence weiterlesen

Bullet points for future allergy research

Maybe this is a difficult task – defining an agenda for future research. Here are some thoughts as we don’t know the reasons for the allergy epidemic even after 100 years of research. And we don’t have any cure yet, there is some relief of symptoms and there are some limited curative efforts but we don’t have any real understanding of what is going on. The following research areas may therefore be identified in NON-therapeutic research: Bullet points for future allergy research weiterlesen

We feel good

If you are writing some kind of online diary your mood is already surveilled by wefeelfine.

However, if you are an allergic patient, you may be interested in a new project of the German Pollenstiftung that runs an online pollen diary. We have pollen counts for a long time but we do not know so much about thresholds and individual variation.
We feel good weiterlesen

Shift happens

The current issue of the blue journal has more stuff on the vitamin D hypothesis (that has been shifted recently into the opposite direction). I agree with the editorial that

Intervention studies of vitamin D in the primary prevention and treatment of asthma raise a number of difficult scientific, ethical, and regulatory issues.

That may be true while the editorial includes the widely quoted myth that immunological effects occur only at high doses Shift happens weiterlesen

Asthma is a iatrogenic disease

The new Lancet has a paper from our own group as well as another one from ISAAC. We have already suggested earlier that asthma is a iatrogenic disease- the ISAAC paper now confirms at least the long suspected association with paracetamol use – gratulations to my London friend who had been working so long on this hypothesis. The accompanying editorial puts in into context:

Furthermore, although many important potential confounders were included in multivariate analyses, confounding by underlying respiratory disease, differences in hygiene, and use of other antipyretics might also explain the findings.

To put it more on a general level – more iatrogenic factors cannot be excluded, yea, yea.