When my supervisor pitched the PhD to me, it was all about analyzing "big data". I had BSc/MSc experience in wet-lab biology (mainly culturing cells), however I wanted to branch out into Bioinformatics since I am, and always have been, fairly good at programming in C, and data analysis in general.

I chose this particular PhD because the idea was we take a particular tissue from a mouse, run all kinds of different assays on the same pool of cells, and then create an analysis that would essentially get more information out of the data than any 1 assay alone could tell us, by integrating the data together in clever ways. That was the plan anyway.

What actually happened was that the protocol to get this tissue out of the mouse had yet to be developed, and without the tissue there would be no sequencing, and without sequencing there would be no data. So for the first year I had to roll up my sleeves (figuratively), and learn how to kill a mouse quickly and painlessly, to cut out and purify that 1 tissue I needed for sequencing. Again, in reality, this wasn't so simple. Although you don't/didn't need a licence in Germany/Europe to just kill a healthy mouse and take out some tissue (only to kill it in stressful ways, or if it's a mouse with a special phenotype), I feel you should still ideally be taught. Unfortunately, although other PhDs/Postdocs in my lab work with mice, I couldn't get anyone to teach me at the time, so the whole experience was pretty traumatic. I started off by filling up cages with CO2 (completely) and then putting the mice in, rather than what I now know you should do, which is to slowly increase the CO2. This will forever haunt me. I later learned to do cervical dislocation, which is better for everyone.

However, after I was able to sacrifice and extract the tissue I needed, I started getting asked to do more and more frankly grotesque experiments. Draining all the blood from a semi-conscious mouse. Implantation of electrodes. Cold room experiments. I can think of several more, but it's not really suitable for here. Of course this was all legal and above board - and important science that needed to be done - however I just cannot personally continue doing this sort of work. It all makes me feel slightly sick, and more importantly, I hate myself for doing it. What started off as probably 20-40 mice for the data I needed, is probably now at 500-600. Maybe more. I stopped counting.

But the reality I face now is that there are still 2 more years to my PhD to go, and I really don't/can't continue this for another 24 months. I have explained the situation to my PI, but he tells me quite bluntly - "this is what you are required to do as part of your PhD". On one occasion he said if I didn't do it, that's OK, but "you won't have enough data for your PhD defense."

That is total nonsense of course. I've already published and the data analysis - which I am now spending most of my time doing - has gone great. I'll be publishing some of the tools pretty soon too. The problem is that if I stop killing mice, my boss is going to really make things miserable for me for the next two years - and the end result of that might even be I'm asked to stop working on the PhD. I don't know exactly how or through what mechanism I would get kicked off the PhD, but my boss/PI is obviously a lot more senior than me and he's paying me every month (which he reminds me of, every month), and we both know if I don't kill the mice, some one else is going to have to.

What should I do?

EDIT: Out of respect for the German PhD system, I should point out that my supervisor isn't German - and I'm confident that another supervisor would have handled the issue very differently. Whilst I'm not confident it is an isolated case, I don't think in this scenario there was anything the Institute (or affiliated University) could have done better/differently.

Honestly, the take home message for me is that I wish I had asked this question sooner, had received all of the kind and encouraging words earlier, and then maybe I would have had the courage to do the right thing before it grew into something more difficult. Thank you all so much!

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    Can you talk to the department head? Or even better, a university ombudsperson (aka a neutral 3rd party who can discuss your options with you)?
    – tonysdg
    Apr 29, 2016 at 12:40
  • 94
    And yet if you continue killing mice, you're bound to hate your field so much that you'll eventually have a PhD in something you can't even stomach. Not to mention the damage you'll likely do to your psyche in that time. I don't have a good answer for you - though my heart hurts for you :( I will say this - the knowledge you've gained over this time, and the publications you've made cannot be taken away from you. So even if you leave and start again elsewhere, you won't have nothing. Remember that as you move forward.
    – tonysdg
    Apr 29, 2016 at 12:50
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    As a biologist, I'm amazed by this story and I have a hard time believing something. To use animals in experiments, you need a kind of approbation by an animal care board (maybe called something else in Germany). It's doubtful you can publish without saying you have this approbation. It's more doubtful you can get an approbation without a careful and respectful plan of how you're going to euthanized animals. How did you publish without this?
    – Emilie
    Apr 29, 2016 at 15:08
  • 81
    Forgot to mention this in my earlier comment, but - if you are feeling depressed/mentally exhausted/emotionally distressed, do not hesitate to go see a mental health counselor/psychologist. They are trained to help you in these scenarios.
    – tonysdg
    Apr 29, 2016 at 21:32
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    I believe that your institution is also at fault. Under FELASA (european animal science association) guidelines, you are supposed to receive training in both the relevant legislation in your country as well as practical training (on post mortem animals) before doing anything on live ones -- here is a german example. In the UK, your supervisor (and you) would potentially have committed crimes, and your institution could lose its animal research licence. I would report this incident and seek advice. Good luck.
    – Landak
    Apr 30, 2016 at 23:37

12 Answers 12


tonysdg asked in a comment

Can you talk to the department head? Or even better, a university ombudsperson (aka a neutral 3rd party who can discuss your options with you)?

and you replied

I don't know - I'm studying in Germany and I can't speak German.

While it might be a good idea to learn German, you most probably don't have to know German to contact your university's ombudsperson.

Universities tend to be very international environments, and English being the predominant language in middle and western European international research, the ombudsperson is likely to know English and maybe even some other foreign languages. If they don't (or if they don't know English well enough), they can probably get hold of a trustworthy interpreter/translator.

More importantly, I absolutely cannot do anything that results in my PhD coming to an end. If my supervisor gets in trouble, it hurts both of us.

Similar to medical practitioners, priests and attorneys an organization's official ombudspersons are usually required to grant confidentiality to all who come to them for seeking advice or for filing complaints. They might be trained in de-escalating hairy situations of power abuse by superiors in scenarios of dependency like yours. Usually, they will not take any action that you didn't agree to, unless they are required by law to do so (which isn't the case often) or when the situation requires escalation to stop severe harm (e.g., if others are in danger by someone's action).

The exact rules might differ from organization to organization, but it is neither rude nor is there any shame in asking the ombudsperson what rules apply to their role before even deciding whether to confide in them. So if you don't make public that you're going to see the ombudsperson, doing so should pose near-zero threat to you and your PhD project.

Having said that, I will definitely look into it

Please do. Even if your university does not have an official ombudsman or ombudswoman, there might be unofficially assigned persons of trust in the institutes fulfilling a similar role and playing by similar rules. (If there are, again, ask what the rules are before proceeding.)

Your university's website probably has more information on this. If it's a larger university (and by the type of research you do, it probably is) the website and that information is likely available in both, German and English.

You can also ask your head of department, head of institute, the university's headmaster or any other of your boss's bosses, who the ombudsperson responsible for you is. If you ask them, you can (and probably should) do so without mentioning that (and why) you want to see the ombudsperson.

If you have problems finding an ombudsperson

I did a web search myself and found there is an official German organization called "Ombudsman für die Wissenschaft" (ombudsman for science), appointed by the renowned association DFG (Deutsche Forschungsgemeinschaft e.V.). The organization's website seems to be entirely in German, but they do have an English inquiry form for reporting conflicts and suspected violations of "good science" rules / suspected scientific misconduct.

They seem to be more focused on "good science" rules and scientific misconduct investigations than on conflicts, but according to their own examples in these presentation slides, they do consider "Inadäquate Doktorandenbetreuung" (inadequate / unsatisfactory support / supervision of PhD students) a violation of those "good science" rules, not just plagiarism, made up data, skewed results etc.

They also publish a "Liste der Ombudspersonen an deutschen Hochschulen und Forschungseinrichtungen" (list of ombudspersons at German universities and research facilities). I'm not sure how up-to-date that list is, but the people on it are probably still around. If they aren't active ombudspersons any more, they can probably tell you who's in charge of their chair nowadays.

Whether you confide in a local ombudsperson at your university or send an inquiry to the "Ombudsman für die Wissenschaft" organization is up to you. The DFS's white paper that lead to founding "Ombudsman für die Wissenschaft" is explicit about this:

Hochschul- oder Institutsangehörige werden ihre Probleme in der Regel bevorzugt einer örtlich erreichbaren Instanz mit Kenntnis der lokalen Verhältnisse vortragen wollen. Sie sollen dazu aber selbstverständlich nicht verpflichtet sein, wenn sie es vorziehen, sich unmittelbar an den [...] überregionalen „Ombudsman“ zu wenden.

(My translation: University and institute members will usually prefer to bring their issues forward to a locally available entity with knowledge about the local circumstances. Of course, they shall not be required to do so if they prefer to address the [...] supraregional ombudsman directly.)

  • 27
    Wow this is such a fantastic answer - thank you das-g! I have started drafting out an e-mail to the DFG about my situation. Even if they tell me there's nothing practical we can do, I think just having someone to talk to will help immensely, which also goes in the same direction as what tonysdg said. Thank you both! Apr 30, 2016 at 9:15
  • 2
    You're welcome. I hope this helps you to get further advise. You might prefer to write to the "Ombudsman für die Wissenschaft" organization founded by the DFG instead of to the DFG itself. The DFG is AFAIK a large association with various activities, so if you write to the DFG, it could take them some time to get your inquiry to the right person. Also, while the DFG has most likely people willing to help, they are probably not trained in how to handle requests like yours and could (without ill intend) violate confidentiality or such.
    – das-g
    Apr 30, 2016 at 9:25
  • 9
    Also, while the DFG is reknowned, your inquiry could get into hands of people with ill intend. Any large enough organization can have some rotten apples. Ombudspersons on the other hand are selected for their trustworthiness and follow an additional code of conduct. (E.g., they have to step down from a case if there is a conflict of interest for them.)
    – das-g
    Apr 30, 2016 at 9:30

On the basis of the information you've given, I think you should look for a new supervisor as soon as possible. Regardless of whether you manage to adapt the focus of your work, your current supervisor does not sound like someone you want to work with.

I couldn't get anyone to teach me at the time, so the whole experience was pretty traumatic

No one should have to figure out how to humanely kill animals by trial and error.

he tells me quite bluntly - "this is what you are required to do as part of your PhD"

This is your project, and if you can find an alternative way of addressing the aims of the project then you are entitled to.

he's paying me every month (which he reminds me of, every month)

It sounds like he wants a technician, not a PhD student. Doing a PhD is not about unquestioningly doing the bidding of a supervisor.

Other answers have made good suggestions about how to make sure that you don't just have to throw away the progress that you have already made. But find another supervisor to continue your work under!

  • 81
    Agreed. It sounds like a toxic environment, best avoided. - "figure out how to humanely kill animals by trial and error." Honestly, it doesn't matter that it was killing animals. For any technique that's important to your Ph.D. research - even pipetting - you should be trained on how to perform it properly, or at the very least given the appropriate resources to teach yourself. You shouldn't potentially botch your data with trial and error mistakes if you don't have to. (e.g. Does stress change assay results in those tissues? If so, untrained hands have possibly confounded the experiment.)
    – R.M.
    Apr 29, 2016 at 17:56
  • 9
    I found this answer to be immensely helpful to me personally, thank you. Even though I marked another as the accepted answer, I just want to say thank you again. May 1, 2016 at 10:02
  • 1
    No problem at all, glad to be of help. I hope you manage to resolve the situation! May 2, 2016 at 9:37
  • 3
    @CarlWitthoft That's not been my experience, but perhaps I've been lucky. Though I don't think it's controversial to say that there should be more to a PhD than just following instructions. May 3, 2016 at 19:25
  • 6
    @CarlWitthoft no they are not. Many are, yes, but that's because their supervisors are, quite simply, bad mentors. A PhD should be a collaborative effort between the PhD student and the supervisor. Abusing a PhD student as a lab technician who has to follow orders instead of allowing them to go where their project leads them is unacceptable. Yes, it happens. Yes, it happens more often than it should. That does not make it OK and it doesn't make it normal.
    – terdon
    May 4, 2016 at 8:57

You are two years into a four-year PhD, or perhaps you have completed four years out of six. It may seem long, but it's still early in your academic career. It's not too late to quit and restart, and you might even be able to jumpstart into a new PhD position using the work you've already done.

That might be your best option. Stop your current PhD. Not abruptly, but accept you will have no more data, finish and submit publications in progress, and meanwhile search for a new supervisor/plan where you don't have to kill your conscience. Your papers exist, and you have a valid explanation for a possible gap.

Change while you still can.

  • 20
    as a person that, 2 years into a 4 year PhD, has changed, I wholeheartedly subscribe the above.
    – Federico
    Apr 29, 2016 at 13:26
  • 2
    Based on an older answer, OP is in the 4th year of a 6 year Ph.D. Apr 29, 2016 at 16:49
  • 4
    ...which doesn't really change that you are probably right in your suggestion...:) Apr 29, 2016 at 17:13

I'm going to assume that this question is for real – that important research is being done, and live mice must be killed in order to conduct the research.

(Sorry for that caveat, but there's something rather fishy about this question, especially in light of Emilie's comment. If the O.P. was a newer user, I'd guess we were being trolled.)

Your question ends with:

we both know if I don't kill the mice, some one else is going to have to.

So why not have someone else kill the mice?

Part of this problem seems to stem from the early trauma you experienced by not being properly trained in the first place. So, lesson #1 for the research team would be to not make that mistake again. The advisor should admit that his callous attitude was a wrong one, and then help you solve the problem so that you can get on with your research.

Next, find someone who can kill the mice for you – perhaps even a student at the university. Train them to do it humanely. Explain the advances your research is expected to accomplish. Be more understanding than your advisor was with you. You might even consult with your university's psychology department, asking them for advice in training someone for such a grotesque undertaking.

If this course of action fails, then I'd be inclined to follow some of the other suggestions listed here: change advisors, find a new topic. But I wouldn't follow those routes until you at least tried to fix the problem in more constructive ways first. Otherwise, some unfortunate student is likely to follow in your footsteps and end up asking this same question two years from now, and then be even more shocked to find the question being closed as a duplicate of this one.

  • 4
    In many cases it would be unethical not to kill the animals after the experiments have been conducted. For example, some neuroimaging techniques involve injecting a virus to the animal's brain.
    – mmh
    Apr 29, 2016 at 15:56
  • 5
    There is a course that scientists can take called the FELASA, however at the time I started my PhD (and I dont know what the details are now) it was not a requirement to simply kill mice, and then work with them postmortem. The more invasive experiments, the ones that really bothered me, well - I don't know. I dont know what is and is not legal. But all that aside, you make a really excellent suggestion - teach the new students to do it, under the knowledge that I really hate it and one day they will take over from me. My boss cant argue if I dont do it so someone else can get experience... Apr 29, 2016 at 17:34

Explore whether you can salvage some of the work and not completely start over.

Given that you have completed a substantial amount of work, you might be able to somewhat shift your project focus and complete it.

I would start by discussing this with your advisor. Communicate that you just can't continue to kill mice, and you will have to stop your PhD and start over on a new topic if it comes to that. However, you want to explore if there was any way you could shift the focus and complete the PhD. This request is really quite understandable, given that your work has shifted to something quite different than what you expected to do.

So far your advisor has not been very flexible on this point, but he might become more flexible once he realizes he may lose you from the project.

I would also ask your advisor if you could continue related work under a new supervisor, if he remains unwilling for you to change the focus while working for him. This would require finding a new, supportive supervisor,.

Another option to explore is PhD by publication

This is quite common in Europe. If you can get several good publications out of the work you have done so far, you might be able to switch to a different project, add a couple more papers, and get a PhD based on that.

The challenge here is that the work has to be somewhat related. However, it doesn't have to be on exactly the same topic.

Ultimately, you may have to start over.

As gerrit's answer states, it is probably worth it if that is your only option. However, I wouldn't quite give up on salvaging your current PhD yet.


This isn't an answer for everyone in this situation, but it seems very much an answer for you.

As you present it, you have skills in bioinformatics and don't like wetlab work (my wife is a vegetarian who had to do lots of work with mice during her PhD, so I very much understand the view). These two facts alone seem to present a reasonable solution. Having spent time in the bio-science world, my understanding is that bioinformatics is in much higher demand than wetlab experience. It is hard for me to imagine that there is not another PI at the university that would be extremely happy to have a full time bioinformaticist, who never even entered the wetlab, in their group.


First of all, let me tell you that I'm sorry this happened to you. Animal experiments are a necessary evil, but this is not the way to go about them. And when you are so desperate as it comes across from your question, remember: your first duty is to yourself. Not to your PI, and not even to your PhD project.

Before you look for any other solution, take a step back and look at the big picture. Is this line of work (still) good for you?

Do this when you have a bit of time for yourself, in a calm environment (go to the forest for a walk, do some sport first or mediate. Don't do it while stressed in the lab and thinking "I can't take one more minute of this"). Imagine yourself in 5 years. You have finished your PhD, you are a successful bioinformatitian, and you picked a position where you never have to touch a mouse again. You sit in a clean office doing gene pathways analysis on a computer, say. And every time somebody brings you an Excel sheet with data from n=20 mice, you know that for each of these quadruple mutants, they had to kill 200 littermates because they did not have the right genes. Will you be able to distance yourself sufficiently from this information that you can still do your job without it flashing traumatic images back with you and eating away at your happiness day after day?

If your head wants to go on, but your gut is churning every time you see preclinical data, you can try to solve this conflict by exposing yourself to the other end of the matter. Your university probably has a clinic attached - try to find out if there is any way to meet patients (maybe volunteer to help with some tasks in a clinical trial under the guise of acquiring more understanding about translational research) or look up stories and videos on the Internet about people healed by novel medicine. It was palpable contact with mouse suffering which traumatized you, and palpable contact with the positive outcome, seeing gleaming patients who would have died if not for animal research, has the best chance of calming your revulsion.

Assuming you want to stay in the area, your best option is probably to change advisors. It would be administratively easiest to see if you can change to another PI within the same group (assuming he's not the prof himself), but might still bring some friction on the people level - it is up to you to know if there is a suitable other PI, how are his connections with your current PI, is your current PI a resentful person, etc. Else you may look into other groups at the same university, or even move to another institution - may be very well worth the hassle, and as a bioinformatitian, you are in demand, you should be able to find a position easily.

Why change advisors? You accepted an answer suggesting an ombudsman, and this may be a good route short-term so you don't leave in bad blood. But 1) if somebody outside your group forces your advisor to concede something he doesn't want to (e.g. allowing you to stop the experiments, or to write the PhD based on your current work only), he will be angry and resent you, making your work with him extremely difficult. And 2) He has clearly shown that he cares more about his experiments than about the wellbeing of his coworkers, even when the situation gets as extreme as yours. This is the epitome of bad management - really, you deserve a better boss than he is.

If you conclude that you will always have trouble if you continue in the job, do not despair. I know, at first it feels like a failure, having to let go of your dreams is very painful. But the sunk "costs" of 1-2 years of working on something you don't finish as planned are not worth suffering for the next 35 years of your worklife. And they are not that much of a cost, if you factor in the experience you gathered even without getting this PhD as planned. Also, if 10 years later you realize you need to change careers, you will be biting yourself in the ass for not having changed now.

Stop focusing on this one path (staying in this PhD as it is) and trying to endure the raging inner conflict. The immense stress in situations like yours frequently leads to tunnel vision. Look at all the other options and allow yourself to accept them as viable options. Don't fall into the trap of "I have to finish this PhD, but I can't continue as now, so how do I change this project to fit my desires" and your boss resisting each of your tries to change it. If you find a way to change it - and it needs to be a good way, not out of the frying pan into the fire - great for you. If you don't, get out of the project and do something which brings you forward, even if not in the direction you imagined until now.

I wish you best of luck!


My sympathies as I cannot imagine doing what you had to. If you are open to starting mostly from scratch as you'd still like a similar academic career, on top of bioinformatics that was recommended elsewhere, consider looking into computational neuroscience.

Your wetlab experience would ease your work with the experimentalists greatly, and should count in your favor when applying elsewhere. Commonly, all you do is take experimental data, and try to explain it (typically, from a stochastic or machine learning angle). In particular on the ML side, you'll code and run your suggested models to produce a fit. You never touch a mouse, and this doesn't change in the different stages of your career: as a Ph.D. student, you work with your primary (theory) adviser and experimentalist faculty who provides your data; as a Postdoc, you typically are the theoretician attached to an experimental lab (or join a theory lab); and as faculty, you are the theory adviser of the Ph.D. student stage.

If you followed the deep learning success this year of a computer beating go, say, the firm who did this is rather keen on those students who drop out of their academic career in computational neuroscience (be it as a Ph.D., or a Postdoc). Facebook is another example of a place to target neuroscientists; and within Google, there are other groups too, not only DeepMind. So there are also exciting outside options should you eventually decide against being an academic for life.

Best of luck!


The past experience has left you traumatized. Yes, you learned to cope somewhat, but you really haven't gotten over the experience either (it is apparent from your speech and actions). It is probably not a big deal, but having to keep at the same work is wearing on you.

In Biology, lots of above board but could-be unsettling things are done in the pursuit of knowledge. Biology researchers and professors have to deal with the outrage against these unsettling things till they get jaded. Since you self-selected this field initially, odds are there is a bit less sympathy (right or wrong).

I suggest you leverage your school counseling system. A licensed therapist can help you with coping strategies, and if that is not enough, can help you sort out the core issues which might permit you to have clarity and certainty before continuing or changing your current academic path.

Once you can decide if you can cope through your PhD (which might be a possibility with better coping tools), it is easier to leverage that degree in areas that don't require the data collection techniques you are performing now.

From your statements, it seems that the professor has indicated that getting off this path at this time jeopardizes your PhD. Odds are that professor is right, and despite how the professor delivered the message, the fastest path to your degree is likely to continue what you are doing.


I am sorry I didn't see this question before; the accepted answer is excellent, and hopefully you've gotten everything straightened out by now. I do want to add two additional ideas, for you, if things are still up in the air, and for others who may come across your question.

  1. There are telephone translation services. So, if you're ever in a situation where you need to talk to someone in a language you're not fully comfortable with, and you can't find a friend or colleague to interpret for you, don't hesitate to use a translation service. In the U.S., hospitals, banks, courts, etc., have a contract with companies that handle a wide variety of languages. Your university may be able to supply an interpreter at no cost to you (either in-person or by phone).

  2. It sounds like you've had a traumatizing experience. If you were in the U.S., it might make sense for you to see a doctor for an evaluation; if a problem, such as post-traumatic stress disorder, is found, it might make sense for you to get this documented with the university's office for students with disabilities; at the end of this big chain of IFs might be some accommodations, and some assistance with working out those accommodations with your advisor.

    I don't know what the analogous procedures and structures are in the EU. But I bet there's something analogous.

    I once asked about this on SE and never got an answer. Maybe it's time for a bounty....


All of these answers are well thought, cogent remarks. But what remains missing is a very straightforward question that you and your advisor should discuss:

Data collection aside, is this activity (sacrificing mice) critical to meet your academic and career goals? I had a similar, (yet decidedly more revolting) requirement, but argued successfully that my career goals did not necessitate that I personally do the job. There were others that could, and were happy to, assist.

If your advisor is difficult, he/she very well may remain adamant that you do the sacrificing. But, if you sit down and calmly state your moral/ethical objections, alongside an argument that it is not integral to your academic development, you might be able to turn the tables.

Remember that most PIs seem to think that their students will become some kind of clone of themselves, and they want to prepare you to operate a lab just like their own. From that perspective, of course you need to be able to sacrifice mice - that's part of the daily routine. His/Her statement that "this is what you are required to do as part of your PhD" perhaps anticipates this bias.

If you are unable to come to an agreement with that argument, I'd assume the only argument would be 'shortage of labor'. But if there are others willing to complete this necessary evil in your behalf, I can't see a compelling reason why it must fall on you.

As for: OK, but "you won't have enough data for your PhD defense." -- at the end of the day, if its between quitting or lobbying for a reprieve -- double down. Your PI has a vested interest in you completing the work, as you are most closely connected with it, and may bend upon ultimatum. He or she may elect to take a deal rather than lose you once all cards are on the table.


If the project is important for the professor, one may ask a labor technician just to kill these mice, you taking over the remaining procedures. Of course, this is a high luxury to have a labor technician as an assistant for a PhD student, but should be possible if they do understand the need.

You can also ask to make this a shared project with some other PhD student. While it is not possible to get PhD degree just for killing mice, maybe that partner could also take over few other tasks and you would have the shared publication later.

Finally, as the competence of the professor is not questioned by this problem, it should be relatively easy to change the project, even by moving the to adjacent laboratory.

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