Responses to Collaboration comments

Thanks to all the people who submitted comments. These have helped to improve the draft.  Please find the responses to the comments below.

Comments from JINR (Stanislav Vokal)

1) Page 3, line 40, „The cross section for bottomonium production is smaller than that of charmonium [8-10]...“, check it, is there any cross section for bottomonium production in these papers?

Answer: Both papers report a quarkonium result.  The PHENIX papers quote a J/psi cross section of ~178 nb. Our paper from the 2006 data quotes the Upsilon cross section at 114 pb. 

2) Page 3, lines 51-52, „compared to s_ccbar approx 550 - 1400 mb [13, 14]). ...“. It should be checked, in [13] s is about 0.30 mb and in [14], Tab.VII, s is about 0.551 – 0.633 mb.“.

Answer: In Ref. 13, the 0.3 mb is for dsigma/dy, not for sigma_cc.  To obtain sigma_cc, one has to use a multiplicative factor of 4.7 that was obtained from simulations (Pythia), as stated in that reference.  This gives a cross section of ~ 1.4 mb, which is the upper value we quote (1400 \mu b). In reference 14, in Table VIII the low value of 550 \mu b is the lower value we use in the paper.  So both numbers we quote are consistent with the numbers from those two references.

3) Page 3, line 78, „...2009 (p+p)...“ and line 80 „20.0 pb-1... “, In Ref. [10] the pp data taken during 2006 were used, 7.9 pb-1, it seems that this data sample was not included in the present analysis. Am I true? If yes – please explain, why? If the data from 2006 are included in the present draft, then add such information in the text, please.

Answer: That is correct: the data from 2006 was not included in the present analysis.  There were two major differences.  The first difference is the amount of inner material. In 2006 (and 2007), the SVT was still in STAR. In 2008, 2009, and 2010, which are the runs we are discussing in this paper, there was no SVT. This makes the inner material different in 2006 compared to 2009, but it is kept the same in the entire paper.  This is the major difference. The inner material has a huge effect on electrons because of bremsstrahlung, and this distorts the line shape of the Upsilons.  The second difference is that the trigger in 2006 was different than in 2009. This difference in triggers is not insurmountable, but given the difference in the amount of inner material, it was not worth to try to join the two datasets. We have added a comment to the text about this:

"All three datasets were taken with the same detector configuration.
Note that the data from our previous pp result was not added to this analysis because the
amount of material in the detector was different during 2006 than in all the three datasets discussed here, preventing a uniform data analysis."

4) Page 4, Fig.1, numbers on the y-axe should be checked, because in [10], Fig.10, are practically the same acounts, but the statistic is 3 times smaller;

Answer: The number that matters is the counts in the Upsilon signal.  In Fig. 10 of Ref. 10, there is a lot more combinatorial background (because of the aforementioned issue with the inner material), so when looking at the total counts one sees a similar number than in the present paper. However, in the case of the 2006 data, most of the counts are from background.  The actual signal counts in the highest bin of the 2006 data are ~55-30 = 25, whereas the signal counts in the present paper are ~ 50 - 5 = 45 in the highest bin. When you also notice that the 2006 plot had bins that were 0.5 GeV/c^2 wide, compared to the narrower bins of 0.2 GeV/c^2 we are using in Figure 1 (a), it should now be clear that the 2009 data has indeed more statistics.

5) Page 5, line 31, „114 ± 38+23-14 pb [10]“, value 14 should 24;

Answer: Correct. We have fixed this typo. Thank you.

6) Page 5, Fig.2, yee and yY should be identical;

Answer: We will fix the figures to use one symbol for the rapidity of the upsilons throughout the paper.

7) Page 5, Fig.2 – description, „Results obtained by PHENIX are shown as filled tri-angles.“ à diamond;

Answer: Fixed.

8) Page 6, Fig.3a, here should be hollow star for STAR 1S (dAu) as it is in Fig.3b;

Answer: Fixed.

9) Page 8, line 7, „we find RAA(1S) = 0.44 ± ...“ à should be 0.54;

Answer: Fixed.

10) Page 8, lines 9-12, „The ratio of RAA(1S) to RAA(1S+2S+3S) is consistent with an RAA(2S+3S) approximately equal to zero, as can be seen by examining the mass range 10-11 GeV/c2 in Fig. 4.“, it is not clear, check this phrase, please;

Answer: We have modified this phrase to the following: "If 2S+3S states were completely dissociated in Au+Au collisions, then R_AA(1S+2S+3S) would be approximately equal to $R_AA(1S) \times 0.69$.  This is consistent with our observed R_AA values, and can also be inferred 

by examining the mass range 10--11 GeV/c^2 in Fig. 4, 
where no significant 2S or 3S signals are seen." 

11) Page 8, line 26, „CNM“, it means Cold Nuclear Matter suppression? – should be explained in text; 

Answer: The explanation of the CNM acronym is now done in the Introduction.

12) Page 9, line 30-31, „The cross section in d+Au collisions is found to be = 22 ± 3(stat. + fit)+4- 3(syst.) nb.“, but there is no such results in the draft before;

Answer: This result is now given in the same paragraph where the corresponding pp cross section is first 
stated, right after the description of Figure 1.

13) Page 9, line 34, „0.08(p+p syst.).“ à „0.07(p+p syst.).“, see p.7;

Answer: Fixed. It was 0.08

14) Page 10, Ref [22], should be added: Eur. Phys. J C73, 2427 (2013);

Answer: We added the published bibliography information to Ref [22].

15) Page 10,, Ref [33] is missing in the draft.

Answer: We have now removed it. It was left over from a previous version of the draft which included text that has since been deleted.

Comments from Tsinghua

1) Replace 'Upsilon' in the title and text with the Greek symbol.

Answer: Done.

2) use the hyphen consistently across the whole paper, for example, sometimes you use 'cold-nulcear matter', and at another place 'cold-nuclear-matter'. Another example is 'mid-rapidity', 'mid rapidity', 'midrapidity'...

Answer: On the hyphenation, if the words are used as an adjectivial phrase, then those need to be hyphenated.  In the phrase "the cold-nuclear-matter effects were observed", the words "cold-nuclear-matter" are modifying
the word "effects", so they are hyphenated. However, from a previous comment we decided to use the acronym "CNM" for "cold-nuclear matter", which avoids the hyphenation.  We now use "mid-rapidity" throughout the paper.

3) For all references, remove the 'arxiv' information if the paper has been published.

Answer: We saw that published papers in PLB do include the arxiv information in their list of references. For the moment, we prefer to keep it there since not all papers are freely available online, but arxiv manuscripts are. We will leave the final word to the journal, if the editors ask us to remove it, then we will do so.

4) Ref. [33] is not cited in the text. For CMS, the latest paper could be added, PRL 109, 222301 (2012).

Answer: Ref [33] was removed. Added the Ref. to the latest CMS paper on Upsilon suppression.

5) For the model comparisons, you may also compare with another QGP suppression model, Y. Liu, et al., PLB 697, 32-36 (2011)

Answer: This model is now included in the draft too, and plotted for comparison to our data in Fig. 5c.

6) page 3, line 15, you may add a reference to lattice calculations for Tc ~ 175 MeV.

Answer: Added a reference to hep-lat/0305025.

7) Fig 1a, \sqrt{s_{NN}} -> \sqrt{s}. In the caption, |y| -> |y_{ee}|

Answer: Fixed.

8) For the dAu rapidity, the directions of Au-going and p-going should be explicitly defined.

Answer: We also realized that this was important to do. This is now done by adding the sentence: "Throughout this paper, the positive rapidity region is the deuteron-going direction, and the
negative rapidity region is the Au-going direction. "

9) Fig.2a, the label of x-axis, 'y_{ee}' -> 'y_{\Upsilon}'. In the caption for Fig. 2a, Ref. [21] should be cited after 'EPS09 nPDF'.

Answer: We moved the citation to the first part of the caption.

10) page 5, around line 28-29, please mention explicitly this result is for p+p 200 GeV.

Answer: Done. The text now reads "we calculate a production cross section in p+p collisions..."

11) page 7, line 33, add space after N_{part}

Answer: Fixed.

12) page 7, line 36, Fig. 5c -> Figure 5c

Answer: Done.

13) page 7, line 46, remove 'bin from'

Answer: Done.

14) page 7, line 55, 'the latter' -> 'the former' ?

Answer: Split the sentence into two, and explicitly stated "The level of suppression we observe for
|y|<0.5 stays approximately constant from dAu up to central AuAu collisions. " to make it clear.

15) Fig. 4 a, b, and c, '30%-60%' -> 30-60%, '10%-30%' -> '10-30%', '0%-10%' -> '0-10%' In the caption, |y| -> |y_{ee}|

Answer: Fixed.

16) Fig. 5, the label of the y axis better to be the same style as Fig. 2

Answer: Fixed.

17) Page 9, line 33, line 45, when quoting the RdAu and RAA, why omit the p+p stat. errors? Also the p+p syst. err. in line 34 is not the same as that in page 7, line 41, please check.

Answer: The p+p stat. errors are combined together with the Au+Au stat. errors because it is straightforward to combine stat. errors, and we just quote the combined stat. error. Syst errors are fixed.

Comments from UCLA

1. In the legends of Fig 1 and Fig 4, the line color for the like-sign and unlike-sign should be blue and red, instead of black.

Answer: Fixed.

2. On page 5, line 29, it is not specified whether this is for p+p or dAu.

Answer: Done. The text now reads "we calculate a production cross section in p+p collisions..."

3. The directions of the d and Au beams were not defined: which goes forward and which backward in y? It will be good to specifiy the direction, and briefly discuss the different physics we expect from the forward and backward regions.

Answer: We also realized that this was important to do. This is now done by adding the sentence: "Throughout this paper, the positive rapidity region is the deuteron-going direction, and the
negative rapidity region is the Au-going direction. "

4. Page 7, line 50, "Pb+Pb" should be upright.

Answer: Done.

5. Page 7, line 55-56, "the latter" should be the model, which doesn't look constant. It seems you are talking about the measurements. Then it should be "the former".

Answer: Split the sentence into two, and explicitly stated "The level of suppression we observe for
|y|<0.5 stays approximately constant from dAu up to central AuAu collisions. " to make it clear.

6. Page 8, line 13-14, "in d+Au to be $2\sigma$ from unity and consistent with unity in peripheral" -> "to be $2\sigma$ from unity in d+Au and consistent with unity in peripheral"

Answer: Done.

7. Page 8, line 22, "modeling"

Answer: There are two aims: to incorporate... and to model ... Since we use the infinitive form in the description of the first aim ("to incorporate") we also use the infinitive form ("to model") in the second aim.

8. Page 3, line 82, "pQCD" -> "perturbative QCD (pQCD)"
9. Page 5, line 6, "perturbative QCD" -> "pQCD"

Answer: Both are now fixed.

10. Page 5, Fig 2, the caption says "Results obtained by PHENIX are shown as filled triangles", but they are "diamonds", not triangles in figure.

Answer: Fixed.

11. Pg 4 Line 1 : Barrel Electro-Magnetic Calorimeter (EMC) - Barrel Electro-Magnetic Calorimeter (BEMC) and replace EMC with BEMC throughout.

Answer: Done.

12. Pg 4 Line 65 : |y_{\upsilon}| - |y|. In the following Figure 1, its |y_{ee}| < 0.5 in figure panels and |y| < 0.5 in caption. Inconsistency, if all of them are same.

Answer: Fixed.

13. Pg 5 Line 1 : The data are fit .. - The data are fitted ..

Answer: Both forms are grammatically correct. The past participle can be either "fit" or "fitted".
We kept the text as is.

14. Pg 5 Line 6 : via a perturbative (pQCD) next to leading order (NLO) - via a next to leading order (NLO) pQCD

Answer: Done.

15. Pg 5 Line 41 : ... with respect to ... - ... with respect to the ...

Answer: It is correct as written, usage: with respect to (something). One could also use "with respect to the" but then we would need to add another noun, for example as in, "with respect to the binary-collision-scaling expectation". We felt the original form was ok.

16. Pg 5 Line 46 : ... yield ... - ... yields ...

Answer: Done.

17. Pg 6 Line 25 : The present data ... - The present data in which figure ?

Answer: It is now made clear in the text that this refers to Figure 2b.

18. Pg 6 Caption for Fig. 3 : Use a) and b) instead of top and bottom

Answer: Done.

19. Pg 6 Caption for Fig. 3 : x_{F} in caption and X_{F} in figure  

Answer: Fixed.

20. Pg 8 Line 26 : when CNM first appears, it needs to be spelled out.

Answer: Done, it is now given in the Introduction.

21. Pg 9 Line 28 & 31 : The term B_{ee} \times is missing in front of d\sigma/dy

Answer: Done. 

Comments from Creighton

Page 3, Line 71. Why only p+p and d+Au? Why is the Au+Au cross-section not extracted?

Answer: We typically extract the yield per event in AA. This can be transformed into a cross section if we use the integrated luminosity. To get from a total number of minimum-bias events to an integrated luminosity all that is needed is the hadronic cross section for AuAu collisions, which is typically obtained using a Glauber model.  We typically don't quote it mainly because what the community wants to know is R_AA itself.  That is the quantity that the theorists typically calculate, and so we had received guidance to not include a cross section. (It was actually included in earlier versions of the draft.) Given this call for including it, we have now brought it back to the draft.

Figure 2. It might be more appropriate to include the description of the symbols in the figure caption rather than in the text. The legend might be reformatted so the description of symbols has the same structure for STAR, PHENIX, and Ramona Vogt. Why not use a consistent label for what we understand to be the same quantity expressed on the horizontal axis? (Figure 2a uses the rapidity for e+e- while Figure 2b uses rapidity for the upsilon.)

Answer: The caption now describes the symbols too. We left the description in the text also, to help the reader. 

Page 5, Line 4. The wording in the text makes it sound like the red line in Figure 2 could refer exclusively to the upsilon production.

Answer: We have reworded this part to:
"The data are fit with a parameterization consisting of the sum of various contributions to the

electron-pair invariant-mass spectrum. The lines in
Fig. 1 show the yield from the combinatorial background (dashed blue line), 
the result of adding 
the physics background from Drell-Yan and \bbbar\ pairs
(dot-dashed green line), and finally the inclusion of the \upsi\ contribution 
(solid red line)."

Page 6, Line 18. It might be more appropriate to discuss here why the mid-rapidity point is lower than the prediction (rather than later in the text).

Answer: In a sense, the next paragraphs and figures are meant to discuss this point being low. We use R_dAu to have more discussion of the model predictions (and show their uncertainties). We next compare our result to previous measurements, which show a similar suppression.  We added the sentence "To study this observation for \dAu\ further, we make a closer comparison to models and to previous measurements of \upsi\ production in p+A collisions. " to highlight this.

Page 7, Line 11/Figure 3b. It is unclear how the plot in terms of Feynman-x improves the comparison of rapidity coverage.

Answer: We added the x_F plot because the E772 data were given in x_F. We can massage our data to get x_F from rapidity making some estimates about the pT, which we can do because we have all the information on the Upsilon 4-momenta for our data, but we do not have this information for E772. So in order to compare to their result, it was best to not touch their data and massage ours, with intimate knowledge of ours, than to keep everything in y_Upsilon but having to massage their data without knowledge of their pT distribution so that we would only be guessing as to the correct y_Upsilon that would correspond to a particular x_F range.

Page 9, Line 30. This result in the conclusions does not seem to have been presented in the body of the paper.

Answer: This result is now given in the same paragraph where the corresponding pp cross section is first 
stated, right after the description of Figure 1.

Comments from WUT

Reader 1:
1. legend of Fig. 1b
I would rather put R_{dA}=1 (not R_{AA}) to be consistent with the figure caption and the main text

Answer: Fixed.

2. Fig 2a and discussion in the text
of the results for pp at positive and negative rapidities.
I found it a bit awkward that we are presenting results just after folding in data at positive and negative y.
Of course the physics for pp is symmetric wrt y=0,
but it would be better to present separately results
for -1 < y < -0.5 and 0.5 < y < 1.0 to show that indeed the results are consistent.
(Also as a cross check of correctness of including all experimental corrections, and nothing to hide)

Answer: We did check that the results were consistent for pp, but we wanted to maximize the statistical power of the data, given that we are still somewhat statistics limited.  Note that the acceptance and efficiency is lower for the 0.5 < |y|< 1.0 region, so that is why we wanted to add the two in pp, thanks to the symmetry, to show our best results.  For the d+Au case, as we say in the paper, we did leave the analysis in distinct rapidity regions because the system is not symmetric.

3. legend of Fig. 2a
For STAR and PHENIX points it would be more transparent,
if the legend would have similar layout as for NLO pQCD CEM.
I.e. 'STAR' in a single line followed by two lines
'pp' and 'dAu/1000' and analogously for

Answer: Fixed.

4. line 2 on page 7
"their deuterium result" => "their pd result"
would be more straightward statement
(I assume E772 had a liquid deuterium target to study pd collisions)

Answer: Done. And yes, we say in the text that they had a liquid deuterium target.

5. Fig. 4
The curves for combinatorial background should be made smooth
like for all other curves, not going in steps.

Answer: Fixed.

Reader 2:
page 4, line 1 and in further occurences: shouldn't it be BEMC instead of EMC ?
Answer: Done.

page 5, line 1: shouldn't it be "The data are fitted"
Answer: Both forms are grammatically correct. The past participle can be either "fit" or "fitted".
We kept the text as is.

Reader 3:
Overall it is a very well written paper and important results.

1. Acronyms in the introduction should be defined there (RHIC, LHC, pQCD or even QCD)

Answer: Done.

p. 3, l. 60: you use "cold-nuclear-matter effects" without defining what "cold" and "hot" nuclear matter is. It would be good to introduce these terms when you talk about QGP and then other possible sources of suppression (line 52-63)

Answer: Added short phrases to better define these terms.

p.8 l.26 - CNM should be defined

Answer: It is now defined in the Introduction.

p.8 l.44-48 - it is not clear from the text how exactly CNM and QGP effects were combined for the scenario 4.

Answer: We now state "For scenario 4), the expected suppression is simply taken to be the product of the suppression from scenario 2) and scenario 3)."

p.9 l.29 "with NLO" -> with "pQCD NLO"

Answer:  In the rest of the paper, we have used NLO pQCD, so at this point, it should be clear that when we are talking about
a Next-to-Leading Order calculation, we are implicitly talking about a perturbative QCD calculation (the fact that we are talking
about "orders" in a calculation implies 
that we are talking about perturbation theory,
and this entire paper deals with QCD), so it should be clear from the context.

Figures: Caption of Fig 2: " from EPS09 with shadowing" - "EPS09" is nPDF which includes shadowing already, maybe write "due to shadowing using EPS09"?

Answer: Changed the caption so it reads: "The dAu 

prediction uses the EPS09 nPDF which includes shadowing"

Fig 2 and Fig 6 - the contrast of the figures could be improved - for instance lines for models in Fig. 2 are barely visible when printed in black and white

Answer: Fixed.

Reader 4: Fig. 1 and Fig 4 - The information on pT range,
in which the signal is presented, can be added.

Answer: We added a sentence at the end of the "Experimental Methods" section to state: "For all results we quote, the Upsilon data are integrated over all transverse momenta."

Comments from BNL

The new p+p result is significant, why is it not in title?

Answer: We already have one paper that is all about the pp cross section. Our result in this paper is an improvement, but the new results on suppression are the highlight of the paper, and we felt they deserved to be emphasized in the title.  If we change the title to something like "Upsilon production in pp, d+Au, and Au+Au collisions at sqrt(s_NN) = 200 GeV" would include the pp result in the title, but it will not mention suppression.  We prefer to emphasize the suppression, as that is the new, important result. Since we are attempting to publish in Physics Letters B, we felt it was more appropriate.

The paper is not clear in many places, and would be helped from a re-­write keeping the audience in mind, i.e. not nesc. an expert in HI.  It was commented that in particular the introduction on page 2 line 56 to 66 has much expert knowledge assumed, but does cover the field. Some examples are given below in the individual comments.

Answer: We tried to make the introduction section a short review of the field so that a non-expert could follow.  We don't understand which expert knowledge is assumed in the introduction in lines 56-66.  We certainly have strived to make the paper clear, and we will look for the specific comments and suggestions below.

The different RAA values appears multiple places in text. We think it is important to present these in tabular form, particular since so many numbers are presented RAA |y| <0.5, 1 centrality and collision system. Noted by several readers. Page 7,30-­‐50 Page 8, 4-­‐20

Answer: A table with all the values has now been added to the paper.

The definition of RAA seems a bit colloquial, normally this is defined vs. e.g pt, but in the case of the Upsilon it is our understanding this is an integral of the cross section over all (or some) pt-­‐range divided by the pp . The paper should define this clearly.

Answer: We specifically wrote in the paper the equation used for R_AA.  This is as clear a definition as we can make.  We also now specify that our measurements are integrated over all pt.  

The abstract should reflect the conclusion of the paper, this does not at present.

Answer: The abstract includes the most central R_AA and the R_dAu values, which are some of the most important results of the paper.  We also state three of the most important conclusions we draw from the data:

Our results are consistent with complete suppression of excited-state Υ mesons in Au+Au collisions. The additional suppression in Au+Au is consistent with the level expected in model calculations that include the presence of a hot, deconfined Quark-Gluon Plasma. However, understanding the effects seen in d+Au is still needed before fully interpreting the Au+Au results.

 The most important observation, which is the unexpected observation that R_dAu is the same as R_AA for central events in the |y|<0.5 region, is the reason why we wrote the last sentence in the abstract.

The paper needs clarification in regard to the material budgets for the 3 running periods. The text alludes to differences, e.g. how its included in the fits. Why not summarize the rad lengths for pp, dAu and AuAu to be precise. If not, it is very hard to follow the different figures, and clearly different response functions for the Upsilon peaks.
Answer: This is now fixed. The sentence in question alluded to differences in the material budget, but for the three years there were no differences in the material budget. Only the differences in the detector occupancy and the detector calibrations affect the width.  In the new version, we also mention explicitly that the 3 running periods have the same material budget.
Page 6 Please define XF, how you used XF. It was not found in the analysis note, and we have problems to understand how we can reach XF~0.4 when measuring at mid-­‐ rapidity Xf= pz/pzmax normally, so are we seeing Upsilons with Pz=40 Gev in y<1? In any case its not defined.

Answer: Good catch! We made a mistake in the calculation for STAR, we accidentaly used the E772 value for the beam momentum. We were originally thinking of transforming their values of x_F to rapidity, but then when we decided not to move their data and change ours to x_F, we did not use our value for the beam momentum.  The figure is updated.  But the most important point which is at y=0 remains at x_F=0, so the comparison to the level of suppression seen by STAR and E772 at x_F=0 stays the same.
On page 8 line 7 it say RAA = 0.44+-­‐… where as figure 5 c clear as R > 0.5. Please clarify.

Answer: It should be 0.54, it was a typo, and is now fixed.
The discussion between the |y|<1 and |y|<0.5 is not clear cut, particular for the AuAu; It is surprising to have such difference. Is it possible this reflects un-­accounted systematic error or is it all statistical? It does take away from the final conclusions since for |y|<0.5 there is no suppression relative to dAu where as there is for |y|<1. This clearly translates into the interpretation of the interesting model comparisons presented in fig 6. Conclusions in the text are iffy. The data in fig 5 as given do NOT indicate any (significant) centrality dependence vs. Npart , only for RAA(1S). Is that the message that should come across?

Answer: We have discussed the differences in the |y|<1 and |y|<0.5 in the PWG, precisely to try to make sure that the results we are observing in |y|<1 and in |y|<0.5 are statistically consistent.  One of the results is a subset of the other, so one must be careful to take into account the correlations.  This study is in the technical note, in section 6A (page 33).  We concluded that the results are self consistent.  As to whether the result is statistical fluctuation, this is a possibility, but that is the case for any result, and the only way to remedy that situation is to run more dAu.  As to whether it could be a systematic effect, we have done the analysis in |y|<0.5, in |y|<1, and in 0.5<|y|<1 where for each we use the same methods for extracting the signal, for applying efficiency and acceptance corrections, for estimating the backgrounds, etc.  So if there is a systematic effect, it would affect the |y|<0.5 and the 0.5<|y|<1 region in the same way, and therefore it would not lead to differences between these two regions.  We do not think that this "takes away" from the final conclusions, because it is an observation that is not expected if there should be binary scaling in dAu, and it makes the result more interesting.  The reason why we included the E772 data was precisely because we observed such a striking suppression in dAu. So indeed, the fact that the data in Fig. 5b do not show a significant centrality dependence vs. Npart is one of the most important observations of the paper. And with the E772 data, we can point to a previous result that shows a similar level of suppression in pA.  Therefore, this paper will serve to exhort the community to take a closer look at Upsilon suppression in pA or dA.  We do not understand the comment about conclusions being "iffy". If there is a specific conclusion that does not seem to be supported by the data, then we can address that. 

The last sentence in conclusion seem exaggerated, and not documented from text just remove.

Answer: One of the main points of the paper is that in Fig. 5b, as we explain in the previous answer, there is no evidence for a significant centrality dependence of Upsilon suppression in dAu.  The models predict the level of suppression we see in AuAu, but one of the key results of the paper is the suppression seen in dAu. The GPC strongly advocated to include a sentence in the conclusions of the paper that cautions readers that one must understand the dAu suppression before any strong claims can be made. The last sentence was rephrased slighly to better reflect this.  

In abstract suggest the remove the sentence “Our measurements p+p…” and add to the text where relevant in the introduction. Not really relevant.

Answer: Done.

Individual comments:

Page 3 line 34: it is not at all obvious how the 2 statements (deconfinement and high temperature phase of lattice QCD where color is an active degree of freedom) in this sentence are scientifically connected.

Answer: The connection is that color Debye screening, which is the original effect proposed by Matsui and Satz,
requires a quark-gluon plasma where the color charges of the high-temperature plasma screen the heavy-quark potential that binds the bottomonium (or charmonium) states.  This is one of the key ideas in QGP physics.

Page 3 line 59 for a non HI guru this argumentation is basically impossible to follow. Also ccbar and bbar pairs are produced the same way through gg fusion so why should there be a difference.

Answer: It seems that the question arises because the inquirer did not follow that the arguments presented are about final state effects, since the comment about ccbar and b-bbar pairs being produced through gluon fusion is about their production in the inital state, not about the possible ways that they can be broken up in the final state.  The comment about 
the interaction cross section of the Upsilon with hadrons applies to the final state, once the hadrons are produced.  The size of the upsilon meson is much smaller than the J/psi meson, and the corresponding cross section of an Upsilon to interact with a final state pion (and then break up into a pair of B mesons) is much smaller than the cross section for a J/psi to be broken up by a pion into a pair of D mesons.  We will add a comment that the effects discussed in this section are final state effects.

Page 3 line 46. There is no reference to statistical recombination.

Answer: Added a reference to Thews et al.

Page 3 line 78 there is no issues using the 2008 dAu data even so other analysis claim they cannot publish because of the non perfect tpc alignment?

Answer: We put a lot of work to take into account the effect of the TPC misalignment.  This is discussed in the Technical Note in Section V.F, page 29. In particular, the 2009 pp data was originally processed with the same misalignment that the 2008 dAu data and the 2010 AuAu data both have.  The 2009 pp data was subsequently reprocessed with fixed calibrations, and we studied the effect that the distortions had on our invariant mass reconstruction on an event-by-event basis, i.e. comparing the mass obtained in the production with the misalignment and then with the misalignment fixed on the exact same event.  This allowed us to characterize the effect of the misalignment and to take it into account in embedding for the line-shapes and then in the extraction of the Upsilon yield via the fits using those line-shapes.  This was studied extensively in the PWG in large part because we wanted to make sure that any issues regarding the misalignment would be dealt with appropriately.  We cannot comment on other analyses, but if they can also study the differences in the two pp 2009 productions, that could help them to account for the TPC misalignment in their own analyses.

Fig 1 caption – comment to fit: the chi^2 of the pp fit must be horrible, any reason why the fit does not describe the data better.

Answer: The chi^2/NDF is 1.37 in the pp fit.  This is not something we would characterize as "horrible".  Given the statistics, there is not a strong reason to change the fit from using components we expect to have, namely the Upsilon states, the Drell-Yan and b-bbar continuum, and the combinatorial background.

2nd question: was the setup of STAR, especially the material budget, the same? If not, which I assume, how different are they?

Answer: The material budget was the same.  The TPC misalignment in dAu, and AuAu increases the width compared to pp. The higher occupancy in AuAu also contributes to a broadening compared to pp.  As noted above, we now explicitly state
in the paper that the material budget in all three datasets is the same.

page 5 line 6 (fig caption) ‘band’ -> box/square

Answer: The NLO calculations are shown as a band, and that is what is mentioned in the caption.

page 6 line 48: the effect at mid rapidity taking the systematic uncertainty into account is 2 sigma max. I think this is a number which needs to be stated.

Answer: We state the value of R_dAu with statistic and systematic uncertainties. We will also provide a table with all the R_AA and R_dAu values. The sentence we use in page 6 line 48 says that the suppresion is "indicative" of effects beyond shadowing, initial-state parton energy loss, or absorption by spectator nucleons.
Using "indicative" is usually warranted for effects that are of ~2 to 3 sigma significance, we certainly not claim a "discovery" (5sigma). 

Itʼs a bit hard to follow the various R_AA and R_dAu quoted in the paper. A table listing the R_{AB} for the various combinations might be more useful than scattering the values through the text.

Answer: A table is now provided.

Abstract: I realize that in the abstract you donʼt want to get too technical, but omitting the rapidity range and whether it is 1S or 1S+2S+3S makes the numbers not useful.

Answer: We added a short clarification in the abstract as to the result quoted being 1S+2S+3S, and in the rapidity range |y|<1.

p. 4: Lines 55-57: the tracking and electron identification efficiencies would be the same across the three datasets, but in the previous paragraph there was discussion about differences in efficiency. Needs to be made clearer.

Answer: The text is now clear that the main thing that was chosen to be the same was the electron identification efficiency.

Fig1 The N_{--} is unclear the – runs together with the N

Answer: Fixed

Fig. 2: Vogt band does not print well.

Answer: Increased the line weights and changed the colors to darken them so that they print better.

fig 2a needs ""Phenix"" in dAu/1000 (open diamonds)

Answer: Fixed

Fig 2: “are shown as triangles There are no triangles,

Answer: Done. It should be diamonds.

c) Fig 3a The label A^0.96 is not the actual black curve which is (A/2)^{-0.04) according" "to the text in pg 7. Maybe writting the A^{alpha} scaling of cross section in the figure may help.

Answer: Fixed

in Fig 4 where the CB in all three panels is not a smooth curve nor a histogram; it has an unusual "mexican pyramid" shape

Answer: What's wrong with Mexican pyramids? :-) The plot will now be a smooth curve.

The A to the 0.96 does not match the text in line 5 page 7

Answer: As noted above, the Figure will now display A^0.96 scaling to make clear that the line shown is not A^0.9, but 
rather derived from a cross section that scales as A^0.96.

Fig. 5: Are the shaded boxes systematics in the AB system? If so, needs to be in the caption.

Answer: Fixed

Fig. 6: "Our data is shown as a red vertical line with systematics shown by the pink box. There are two systematics (pp and AB). What was done with these? The pp is common to d+Au and Au+Au, so not clear, actually, what should be done.

Answer: The two systematics were added in quadrature for Fig. 6, we now state that in the paper. (Agree that it is debatable how to best combine them, but we should state what was done.)

.p. 6, lines 43-44: Do you mean y<~-1.2, rather than 1.2? Otherwise the argument doesnʼt make sense. And, where is the 1.2 from (citation)?

Answer: Correct, it should be -1.2.  We do give the reference (23) for this statement in the previous sentence.

p. 8, line 11: consistent with an RAA(2S+3S) approximately equal to zero. Would be better to quantify this as an upper limit. 

Answer: This section was reworded based on suggestions from another reader. The argument now starts with the hypothesis of an approximately zero yield of the 2S+3S, states what that would imply for the R_AA(1S) and R_AA(1S+2S+3S) values, and 
then notes that this is consistent with our data.

p. 9, line 1: at how many sigma was the exclusion? At 4.2 sigma, as quoted later?

Answer: The exclusion the "no-suppression" scenario had a p-value of less than 1 in 10^7 (better than 5 sigma) for all R_AA cases in AuAu. The R_dAu had a different p-value of 1.8 * 10^-5 (~4.2 sigma).

Line 18: result rather than effect reads better.

Answer: Done.

How were systematics taken into account in the quoting of “sigma”?"

Answer: The only time we quote "sigma" are for the exclusion of the "no-suppression" scenarios.  For R_AA, they would still
be excluded at better than ~5 sigma even including systematics.  For the dAu case, if the p-value is calculated with the systematic uncertainty shift we get 1.5 x 10^-3, which is about 3sigma.

a) The style of the paper is too colloquial for my taste, but I'm told that journals have relaxed their style requirements.

Answer: This is a style issue, we are certainly willing to discuss this with the editors of the journal if need be.

d) Reference [10] explains that the Combinatorial background is obtained by fitting the same charge sign pair distribution and that appears to be the case in this paper except in Fig 4 where the CB in all three panels is not a smooth curve nor a histogram; it has an unusual ""mexican pyramid"" shape.

Answer: The plots will all have a smooth curve.

Page 7 top (line)9 From the figs its not obvious there is 4.2 deviation, more like 3, can you cross check.

Answer: See previous comments on the deviations and statistical significance.

Clearly the difference between y 0.5 and 1.0 make the conclusion a bit waffly.

Answer: For dAu, in both scenarios we are excluding the no-suppression scenario. Both datasets are supporting this conclusion. Furthermore, the comment we make in about a 4.2sigma exclusion of the no-suppression scenario comes
from the |y|<1 measurement, which is the weaker exclusion of the two. The |y|<0.5 only serves to make this conclusion stronger.

The notation and fonts for RAA and Upsilon(1S+2S+3s) not not consistent across paper.
Answer: plots are now consistent (For Anthony).

Page 8 line 48 “ assumed a flat prior..” This reference to statistics may or may not come across well to the general reader,
Possible expand on this.

Answer: We have followed other papers in the Physics Letters B which use these same statistical techniques, and this usage was accepted.

One minor comment:" "In Fig.6, “CMN effects” should be “CNM effects”

Answer: Fixed.

Page 4 line 28&57, the three datasets” clarify to indicate “between the datasets from the three collisions systems”"

Answer: Done.

"line 57" "‘be the same” Really, should it not be “approximately the same".

Answer: Done.