Responses to Collaboration comments

• Comments from JINR
• Comments from Tsinghua
• Comments from UCLA
• Comments from Creighton
• Comments from WUT
• Comments from BNL

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:

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 

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".
http://en.wiktionary.org/wiki/fit#Verb
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

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
PHENIX/

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". 
http://en.wiktionary.org/wiki/fit#Verb
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 

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.

Responses to GPC, April 2014

 Thomas:

1. General: with the new text (in red) there's no a wild mix
of Au in roman and italic in normal text and in super/sub-scripts. Since Au is a chemical symbol I would put it all in roman
consistently.

This sentence doesn't say a lot and as I already mentioned that
I do not think the feed-down pattern is any more complex
than that in the charmomium sector. I attached a schematic
diagram. Replace Y with Psi and chi_b with chi_c and h_b with h_c
and that's it.

Why not simply saying here that the amount of feed-down into
the Y(states) is not measured at RHIC energies and then give
numbers of the next closest energy (which is Tevatron I guess).

3. Fig 1,: I already mentioned that I suggest to turn this
into a table. The plot doesn't really provide any new insight.

4. Page 9, line 13.
"*" -> "\times" or just leave it out

5. Page 11, Line 18.
I wonder if one should add one sentence mentioning the Y suppression
in high multiplicity pp events seen by CMS. Fits in the context.

6. Page 11, line 50.
Delete "However".

7. Fig. 6. The font size of the legend is a bit on the small side.
There's enough room to make it a tic bigger.

8. Table II.
Can we really say that d-Au is 0-100%? That would be zero bias.
Wasn't there a min-bias mixed with the Y trigger. To my knowledge
we never quoted anything above 80/90%. What about simply saying
min. bias instead of 0-100%.

Lanny:

P3 L30 -- remove "complex" (it is an unnecessary adjective here)

P4 (new) Fig.1 and red text lines 50-51, 65-69:  The efficiencies are
about the same for the 30-60, 10-30 and 0-60 at each rapidity bin.
This information probably should be in the text since HF reco. eff.
are useful to know by others in the business. I recommend putting
this information in the text in place of the above Figure 1 and lines, e.g.

   "The $\Upsilon$ acceptance $\times$ efficiency for three centrality
bins (30-60%, 10-30%, 0-60%) are XX, XX and XX for respective
rapidity bins |y|<0.5, |y|<1.0 and 0.5<|y|<1.0. For the 0-10% centrality
the corresponding total efficiencies are reduced by approximately XX%."

Please check that the various uses of "total efficiency", "reconstruction
efficiency", "acceptance times efficiency" etc are used consistently and
avoid extra such terms if possible.

P5 Fig2b -- The legend "p+p x <Ncoll>" is misleading and may be what ref.2
is asking about. The grey band in 2b is not simply the red curve in 2a
multiplied by a constant (Ncoll).  There are resolution effects as discussed
on P6. The caption should say, "The grey band shows the expected yield if
RDAu = 1 including resolution effects (see text)."

P5 L8 -- Are b-bbar pair backgrounds NPE from open HF meson
decays (B-mesons)?  Just curious.

P5 Tabel I -- I assume momentum resolution effects are included in
the line shape entries.  Ref.1 is concerned about p-resolution and in
addition to the response, this table caption should note that p-resol.
is included in the line shape errors if that is true.

P5 L17-28 -- I did not find any discussion in the paper about the
use of max likelihood fitting. This turned out to be a big deal and
will be discussed in the response. This parag. would be the place
to say, briefly how the fits were done.

P6 L6 -- "miscalibration" sounds scary. Can this issue be explained
in the text, and more so in the responses, so that neither referee nor
the readers are put-off by the statement and dismiss the paper's results?

P6 L26 -- I recommend against arguing with the referee over simple
wording changes that have equivalent meanings.  Is there a subtlety
here that I don't recognize?

P6 Fig.3a -- The referee is asking that the legend "Upsilon -> e+e-"
say explicitly "Upsilon(1S+2S+3S) -> e+e-".  But also change to l+l-.
She/he wants the states listed explicitly.

P8 Fig 5c caption - same issue as above with the grey band. The
last sentence in the caption should read: "The grey band ... number
of binary collisions including resolution effects (see text)."

P9 L8 -- Referring to Fig. 6c, the 10-30% RAA is consistent with unity
also. This sentence should say, "..consistent with unity in peripheral
to more-central Au+Au collisions..."  BTW, "events" is jargon which we
all use, but I think it is better to say "collisions" here and throughout
the paper unless we are specifically discussing a triggered event in
DAQ.

P10 L8 -- "With two possibilities.." implies that CNM and QGP are
the only possibilities for reducing yields.  There is at least the
possibility of modified fragmentation of HF quarks in a
dense system.  I recommend saying "Considering two possible
sources..."  which more accurately reflects what was done; we
considered these two effects and not others.

P10 L37-39 -- Isn't the "QGP only" preferred in Fig. 8b? Why
mention the other as "consistent" and not also mention the

Responses to PLB Referees

 Responses to Reviewers' comments:

We would like to thank the referees for the insightful and constructive comments. We discuss below our detailed replies to your questions and the corresponding explanation of changes to the manuscript. But before we go into the replies to the comments, we want to make the referees aware of changes to the results that were prompted via our studies of the systematic effects on the yield extraction.  Since this paper deals with cross sections and with nuclear-modification factors, both of which involve obtaining the yields of the Upsilon states, this change affects all the results in the paper. We therefore wanted to discuss this change first. Please note that the magnitude of these effects do not change the overall message of the paper.

We wanted to alert the referees up-front about this important change before we proceeded into the detailed responses.  This study was indirectly prompted by one of the questions from Referee 2 regarding systematic effects from yield extraction.

In the process of investigating the systematic difference between extracting the upsilon yield through simultaneous fitting compared to background subtraction as requested by the referee, we also studied the effects of chi^2 fits (specifically of Modified Least-Squares fits) compared to maximum-likelihood fits. We used chi^2 fits in our original submission. We were aware that extracting yields using a chi^2 fit introduces a bias (e.g see Glen Cowan's "Statistical Data Analysis", Sec. 7.4). The size of the bias is proportional to the value of the chi^2 of the fit.  In the case of the Modified Least-squares fit, when fitting a histogram including the total yield as a fit parameter, the yield will on average be lower than the true yield by an amount equal to chi^2.  The relative bias, i.e. the size of the bias divided by the extracted yield, goes to zero in the large yield limit, which is why for cases with large statistics this effect can be negligible.  We had attempted to mitigate the effects of this bias by using the integral of the data, since this removes the bias completely in the signal-only case.  But a bias remains in the case where there are both signal and background present. For our case, the yield extracted from the fit for the background is also biased toward lower values, and since we used this background estimate to subtract from the integral of the data in the extraction of the Upsilon yields, these biased the Upsilon yields towards higher values.   Through simulation studies, where we include signal and 3 background components as in our analysis, we were able to quantify these effects. Given that in some cases the biases could be of order 10-20%, the fits needed to be redone in order to remove the bias. The solution is straightforward since the extraction of yields using a maximum-likelihood fit is unbiased.  We have studied the difference of a modified-least squares fit and a maximum-likelihood fit and confirmed that the yield extraction in the latter method is essentially unbiased. We therefore have redone all the fits to extract the Upsilon yields via maximum-likelihood fits. The revised results are now quoted in the paper. The overall message of the paper is not affected by these changes.

We proceed next to answer the specific points raised by the reviewers.

Reviewer #1: This paper reports results on Y production in pp, dAu, and AuAu
collisions at top RHIC energy. It contains original and important
results and clearly qualifies for publication in PLB. However, there
are many aspects of the paper which need attention and/or improvement
prior to publication. They are detailed below:

1. the introduction is carelessly written. For example, the value
quoted for the pseudo-critical temperature near mu = 0 of 173 MeV is
taken from an old publication in 2003. Recent lattice results from the
Wuppertal-Budapest group (PoS LATTICE2013 (2013) 155) and the Hot QCD
Collaboration (Phys.Rev. D81 (2010) 054504) imply much lower T values
near 150 MeV and are far superior in terms of lattice sizes and spacing.

furthermore, statistical recombination is not a 'complication' but a
direct measure of deconfinement. And the smallness of off-diagonal
terms in the recombination matrix does not imply absence of
recombination as the diagonal terms can be substantial.

Also the newest results on p-Pb collisions from the LHC are entirely
ignored, see, e.g., arXiv:1308.6726.

2. section on experimental methods

no detail is given concerning the crucial momentum resolution but it
is stated at the end of this section that cuts were adjusted for
different systems such that 'tracking and electron id would be the
same across the 3 data sets'. On the other hand, already in Fig. 1 we
see a strong dependence of the mass resolution on the system even for
low multiplicities as in pp and p-Pb. The effect must be much stronger
in Pb-Pb as is indeed visible in Fig. 4. Especially in view of the
importance of resolution for the separation of excited Y states this
referee has to be convinced that the systematic errors are under
control for momentum and pid measurements as a function of
multiplicity. Also how the systematic errors for the separation of Y'
and Y'' from Y are determined as a function of multiplicity needs to
be demonstrated explicitely.

3.  Fig. 2b  

even at y = 0 the difference between data and models is less than 2
sigma, taking uncertainties due to the pp reference into account and I
don't believe it makes sense to argue about effects beyond shadowing
and initial state parton energy loss in these data. 

4. in Fig. 3 the size of the systematic errors should be indicated.

5.  in Fig. 5 it is demonstrated that the observed suppression near
midrapidity is independent of system size (N_part). This could imply
that the higher Y states are already disappeared in dAu
collisions. This is mentioned briefly in the conclusion, but could be
stressed more. 

6.  At LHC energy, the anisotropic model of Strickland reproduces well
the centrality dependence of R_AA but not the rapidity dependence,
see, e.g. the final session of the recent hard probes meeting in South
Africa.

7.  The presentation in Fig. 6 on the quantitative evaluation of
different model assumptions compared to data depends again strongly on
the size of the systematic errors, see the comment in section 2.

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Reviewer #2: I have read the manuscript PLB-D-13-01645 submitted to me for review.
The authors present a detail analysis on the suppression of Y production in d+Au and Au+Au collisions at sqrt(s_NN)=200 GeV using the STAR detector at RHIC. The article is very well written and deserves publication. However, I would like to suggest considering the following remarks to improve the understandability of the article:

1. Page 1, column 1, paragraph 1: The now accepted value for the critical temperature (chiral transition) is Tc = 150 - 160 MeV (depending on the exact definition of the observables). Reference 3 is outdated and should be replaced by more recent publications, i.e. arXiv:1005.3508 [hep-lat]

2. Page 2, column 2, paragraph 1: Please quantify the corrections due to the trigger bias w.r.t. the event centrality. Same for the tracking efficiency as a function of N_part. How does acceptance times efficiency for detecting Y as a function of rapidity and N_part looks like?

3. Page 3, column 1, paragraph 1: statement "some information will be lost" is too general! What are the systematic uncertainties arising from the different methods (same-event like-sign CB, fit to the CB) of the combinatorial background subtraction? What is the signal significance, in particular in the d+Au measurement? How does the signal looks like after CB and physical background subtraction? Systematic errors should be clearly mentioned.

4. Fig 1: It would be easier for reader if the range of the y axis would be the same in Fig 1a and Fig 1b. Why is the explanation of the grey curves in the figure discussed in this complicated way, to my understanding the gray band simply shows the pp yield scaled by the number of binary collisions? If so, the label could read simply pp*<N_coll>.

5. Fig 1a: From where the line shape for pp comes from? It seems NOT to fit experimental data, i.e. all data points around 9 GeV/c^2 and below. Is it then evident to take as a cross section the integral of the data points?

6. Page 3, column 2, paragraph 1: How was the measured Y(1S+2S+3S) yield transformed to cross section?

7. Page 3, column 2, paragraph 3 (wording):  "Hence, averaging between forward and reverse rapidities is not warranted as it is in
p+p." -->  "Hence, averaging between forward and backward rapidities is not justified as it is in p+p." sounds more understandable.

8. Page 4: Try to arrange the placement of Figs such that there will not be a single line of the text within one column.

9. Fig 2: also here Fig a and Fig b could be presented with the same range on the Y axis, e.g. from -3 to 3.

10. Fig 2a : what is shown here is Y(1S+2S+3S), moreover PHENIX results on Y -> mu+mu- are shown in the same plot, that is why the figure label should be changed, i.e. Y->e+e- should be replaced by Y(1S+2S+3S)

11. Page 4, column 2, paragraph 2: <N_coll> (not <N_bin>) is commonly used as notation for the number of binary collisions. Sigma_AA is sigma^tot_AA (same for pp). It is important to indicate in the text the values for the total inelastic cross sections in pp, dA and AA and <N_coll> used to calculate R_AA.

12. Page 4, column 2, paragraph 3: In view of the discussion would it be helpful to also show R_AuAu vs. Rapidity?

13. Page 6, column 1, paragraph 1: Which function has been used to fit the CB - exponential? Again, what are the systematic uncertainty arising from the different methods (same-event like-sign CB, fit to the CB) of the combinatorial background subtraction. See also comment 4. concerning the label.

The function used to model the CB is now discussed in the text. Systematics from the fit methods are summarized in Tab. I.

14. Page 6, column 1, paragraph 2: The statement "Similar suppression is found by CMS in PbPb collisions (37)" should be moved to the paragraph 4 where the authors discuss Y(1S) suppression. Actually, for the same value of N_part=325 R_AuAu=0.54+-0.09 as for R_PbPb=0.45

Done.

15. Page 6, column 1, paragraph 4: How did the authors derived: R_AA(1S+2S+3S) = R_AA(1S)*0.69?

16. Page 6, column 2, paragraph 2: What are the uncertainties on Drell-Yan and bbbar cross sections and how does it influence the significance of the signal.

Various normalizations are used in the fit. This is accounted for in the correllation

17. http://arxiv.org/pdf/1109.3891.pdf reports on the first measurement of the Y nuclear modification factor with STAR. It is probably worth to mention this work in the ms.

18. The R_AA of J/psi (p_T > 5 GeV), Y(1S) and an upper limit on the R_AA (2S+3S) was obtained in STAR. I would like to suggest to add a plot showing R_AA as a function of binding energy as a summary figure (also as a key figure to the long discussion on the extraction of the upper limit on R_AA(2S+3S)).

In summary, this ms. contains very interesting results and I propose publication in Phys. Letter B after the authors have taken care of the remarks above.

We thank the referee for her/his comments and remarks, which have helped improve the paper.  We hope that we have addressed the issues raised, and adequately answered the questions posed, and look forward to the publication of the paper.

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