Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EFFECTS OF PERSONALITY AND REARING-HISTORY ON THE WELFARE OF CAPTIVE ASIATIC LIONS (PANTHERA LEO PERSICA)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is relatively well-written, with some grammatical issues that could be addressed through the copy editing process if accepted. The information included from cited literature is sufficient to provide necessary background and context. The structure of the article is fine and figures, table and raw data are provided. In some cases, these materials need to be reviewed carefully to ensure legends are correct and provide enough information and that they add enough to merit inclusion (table 1 and figure 2 seem redundant). The results are relevant to the hypotheses.
Experimental design: There are stated hypotheses. However, the way in which these are descried in the discussion don't align very well with the way they are written in the methods. It would also be helpful to describe what is meant by more or less diverse measures of behavioural welfare (lines 244 and 246). Since behavioral diversity is one of the measures utilized, this wording is somewhat confusing. When stating focal sampling was used, does this mean all-occurence data were collected? Two of the behaviors listed as aberrant repetitive behaviors (ARBs) in the methods are not found in the ethogram, and one of the stereotypic behaviors in the ethogram (head bobbing) is not mentioned in the text about ARBs. In line 163, the ethogram is referenced as Supplementary table 2, but is labeled as Supplementary table 3 in the provided materials. Additionally, the personality traits table is labeled as Supplementary table 2 but referenced as Supplementary table 3 in the text. It is unclear how behaviors were categorized as bold or shy (see lines 199-200). The authors state that data were collected in one hour sessions followed by a 15 minute break during three 6-hour blocks, but it is unclear how many sessions were conducted during each of these blocks.In lines 191-195, the authors describe the personality tests administered, but do not state how many sessions were conducted (one per condition listed?). Since latency to approach a novel object was used to determine personality, it seems circular to also use this as a behavioral welfare measure. Explaining why this was used in both ways would be helpful.
Validity of the findings: Some of the tables and results mention age of the lions, but this is not described in the methods as one of the groupings in the methods.Table 1 and figure 2 seem redundant, one may be enough to accompany the results. Supplementary figure 2 needs a descriptive legend. Table 1 includes more information than listed in the legend, and this should be rectified. The legend for table 2 does not seem correct based on the life history parameters described in the methods and the data presented in the table. Spread of participation index is used to determine how much of the enclosure is used. However, lower scores mean more even use of space. That being said, how enclosure use is referenced in the results (e.g., line 339) is confusing, as a positive correlation would seem to mean high enclosure use is related to high levels of other measures tested. Based on the actual results, however, it seems the authors mean that SPI number is what is correlated, so a higher SPI actually means lower use of space and vice versa. There is no description of how the different areas of the enclosures may differ in resource availability, and this could impact use of space and should be mentioned in the discussion. It is also possible that time of year or social grouping could have impacted behavior and use of space and should be addressed as well.
Additional comments: Overall, this is an interesting manuscript describing how several different measures of welfare are impacted by individual characteristics. This is in line with the underlying understanding that welfare is experienced at the level of the individual and that captive animals should be managed according to individual needs.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EFFECTS OF PERSONALITY AND REARING-HISTORY ON THE WELFARE OF CAPTIVE ASIATIC LIONS (PANTHERA LEO PERSICA)
Review round: 1
Reviewer: 2

Output:
Basic reporting: I really appreciated this study, which was written clearly, with a professional English suited to the context. The introduction and the background are not too long but provide an adequate picture of the state of the art. Relevant prior literature is appropriately referenced. the structure of the article is conform to the Journal format. the Figures are relevant.  The completeness of the captions can be improved. Raw data are made available.
This article includes the results relevant to the hypothesis.
Experimental design: This article is definitely a valid step forward in the assessment method of the welfare of Asiatic lions hosted in zoos, and fits with the aims and scope of the journal. The research question is defined, meaningful and relevant. The investigation was rigorous and mets the requested ethical standard. The methods are well described.
Validity of the findings: The results of the work have never been published, and their validity is also supported by the number of subjects that the authors included in the study, which is very high for this species.
the conclusions are well stated and linked to original research hypothesis.
Additional comments: Line 134 to 136. please specify what the values in brackets refer to.
Line 176 to line189 - this part probably fits better in the Introduction section.
I have some suggestions, in order to make the method used in the study more immediate. I think the reading would be smoother and the understanding of the methods more immediate if the two paragraphs will be merged together.
from line 189 to line 200 and from line 270 to line 284: these two paragraphs should be unified, because they deal  with the same topic  (Personality assessment and latency to novel objects).
206-215 and from 285 to 289: same as above.
216 - 227 and from 299 to 307 - same as above.
228 -238 and from 308 to 313 - same as above.
 I have a question: were the animals defined as "captive raised" all hand reared? No cubs born in the zoo was parent raised? please make this concept clearer.
For enclosure usage, please specify if in the 1-9 different zones of the enclosure there were resources that could have determined a different use by animals, including structures in which to hide from view.
Were the history of the wild-rescued lions similar? could you specify their origin in more detail?


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EFFECTS OF PERSONALITY AND REARING-HISTORY ON THE WELFARE OF CAPTIVE ASIATIC LIONS (PANTHERA LEO PERSICA)
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors need to reconsider the organization of the manuscript.  The current organization leads to redundancy and confusion.  The methods particularly are in need of careful editing and reorganization.  Also, a great deal of necessary methodological detail is missing.

There is a fair amount of redundancy in the manuscript, particularly in the methods section.  Please describe procedures, processes, or rationale only once.   The authors might consider reorganizing the manuscript so they don’t feel a need to repeat.  For example, putting specific protocols described in the study design in a section describing how the specific independent variables (personality, life history, age, husbandry) were defined and in a different section describe how each dependent variable (response to novel items, behavioral diversity, enclosure use, and ARBs) was then measured.  Additionally, the authors use many of the same sentences in several different portions of the paper.  The abstract by its nature is entirely redundant, but no other section of the manuscript should be.

The entire document would benefit from thorough proofreading.  There are many, many grammatical errors.   They are usually minor but are quite numerous and distracting.  Unfortunately, some of the errors are of a nature that disrupts the flow and, possibly, the meaning of the text. I have identified several (but not all) of these errors at the end of this review. Aside from those errors, there are a number of inconsistencies and contradictions in the paper.  They are specified below.

The figures and tables are appropriate and the material presented easy to understand.  As stated in the section on experimental design.  There are significant flaws in the design.

It would be nice if the hypotheses as stated in the introduction matched the hypotheses as stated in the discussion.

The authors have an extensive and impressive reference list.  Never-the-less, there are significant issues with the referencing. First, some important references are missing. Second, some of the references in the text do not appear on the reference list.  Finally, and most significantly, some of the references are inappropriately used.  The authors often use references that don’t actually support (or are tangential to) the statements/concepts they follow.

As examples:
Line 83-83:  The two references used to support the preceding statement are inappropriate

Line 154-155:  Allport and Allport, 1921; Gosling and John, 1999  papers are not listed in the references.

Some key references the authors should consider :

Gartner, M and Weiss, A. 2013.  Personality in felids: A review. Applied Animal Behaviour Science, 144: (1-2) pp 1-13.

Gartner, M. C., Powell, D. M., & Weiss, A. (2014, August 11). Personality Structure in the Domestic Cat (Felis silvestris catus), Scottish Wildcat (Felis silvestris grampia), Clouded Leopard (Neofelis nebulosa), Snow Leopard (Panthera uncia), and African Lion (Panthera leo): A Comparative Study. Journal of Comparative Psychology. Advance online publication.
http://dx.doi.org/10.1037/a0037104

Marieke Cassia Gartner, David M. Powell & Alexander Weiss (2016): Comparison of Subjective Well Being and Personality Assessments in the Clouded Leopard (Neofelis nebulosa), Snow Leopard (Panthera uncia), and African Lion (Panthera leo), Journal of Applied Animal Welfare Science, DOI: 10.1080/10888705.2016.1141057

Watters, J. V. (2014). Searching for behavioral indicators of welfare in zoos: Uncovering anticipatory behavior. Zoo Biology, 33, 251–256.

Minor matters:

•    Line 31: Gender is a social construct.  I think you mean sex.  Please make sure you use “sex” throughout the document.
•    Line 76:  Change “it encompasses both physical and psychological well-being ”to they “encompass” both physical and psychological measures of well-being
•    Line 77:  Change “Significant” to “A significant”
•    Line 82:  The construction of this sentence is odd. Reconsider: the use of the word “either” (which is used when the choice between two things is required), the use of the word of, or the punctuation in the sentence.
•    Line 88:  Either “Asiatic lions (  ) are an” or The Asiatic lion (  ) is
•    Line 88: change “one such example” to “one example”
•    Line 89: Change the sentence to read:  “and are currently”
•    Line 101:  Change “across” to “among”
•    Line 147:  Maybe, using the word “fast” instead of “starve” would be a good idea
•    Line 161: Change “ethogram” to “ethograms”
•    Line 163:  Check the labeling of the tables (supplementary and otherwise).  I believe that Supplementary Table 2 should be Supplementary Table 3.
•    Line 188: I question the use of performance here. I wonder if you don’t mean cognitive style/approach.
•    Line 233:  swaying is not on the ethogram
•    Line 236:  Please change “valid” to “the cause could not be identified.” The animal's reason for executing a particular behavior or ARB may be perfectly valid.  But the validity may be unidentifiable to the human observer.
•    Line 242: please remove the word welfare
•    Line 244:  same as 242
•    Line 251:  include the full use of the abbreviation the first time it is used “spread of participation index (SPI)”
     Line 251: Same for Shannon-Weiner diversity index (SWI)
     Line 272: Change to “ascertain a personality”
•    Line 280:  no comma after personality tests
•    Line 306: Change “t-test” to “t-tests”
•    Line 331:  Change “enclosure use patterns” to “enclosure use.”  The authors really don’t report on usage patterns
•    Line 397: Change to “a diverse array”
•    Line 401:  Change “therefore” to “that is”
•    Line 420: Change “but” to “and”
•    Line 421:  change concept to concepts
•    Line 441:  change “which was supported by existing studies” to which supported studies by
•    Line 445:  Change Latency measure to The latency measure
•    Line 451:  Change was to were
•    Line 471:  Change “optimize” to an appropriate word
•    Line 478:  Galvanized in ethology or galvanized by
•    Line 483:  Change Modem to Modern

•    Throughout the manuscript:  I recommend limiting the use of such terms as urgent, must, optimized, dire.
Experimental design: The introduction could use some smoothing and better transitioning among concepts.  As currently written, it is a string of assertions rather than a well-considered and well-written argument.  The authors might consider moving some of the information contained in the document around a bit.  Some of the information in the methods and discussion sections would be better placed in the introduction.  Much of that information provides fundamental support for the study and is really not appropriate for the discussion anyway. For example, the authors need to establish the bold shy personality dimension as valid in felids (Lines 176-183: provide justification for the use of personality measures). The authors also need to provide justification for the importance of considering intraspecific variation when assessing welfare (Lines 422-437: provide justification for the importance of considering intraspecific variation).

Oddly, the authors never argue that this species of lion is not doing well in captivity, although presumably, they are faltering.  They do not reference behavioral, physical, psychological, or health issues. This leaves one wondering how welfare issues manifest in this species, if at all.

Materials and Methods

Subjects
A great deal more information and clarity is needed in all parts of the methods section.

The authors indicate the subjects to be genetically diverse. How have they determined the genetic diversity this of the population?

How long have the rescued individuals been at the facility?  What was the average stay at the facility?  How did they get there?  What is the “average” story of a rescued animal?

The management of the animals needs to be better described.  For example, it seems that it would be essential to know the constituency of each animal group.  It is conceivable, even likely, that the use of the enclosure by one animal would influence use by other animals sharing the space.

Also, more details of the enclosures need to be provided.  If supplemental figure one is correct, the enclosures differ quite a bit by size.  Enclosure size would very likely influence the animal’s behavior and use. What was the size range in enclosures?  How many individuals are in each size category.

A table that represents the important factors and demographics is recommended.

Study design
This section needs to be reorganized and streamlined. I recommend limiting the study design section to a description of your approach and strategy for the study. This is the place to clearly identify the independent and dependent variables as well as how they will be defined and measured. It would also be the place to acknowledge the confounding variables. This study appears to have many of each.

Unfortunately, it takes a bit of reading and rereading to deduce what the authors are attempting to do.

Within the body of the text, the authors first attempt to delineate their variables in the last paragraph of the introduction, identifying life history and personality (independent variables) and behavior based welfare measures as (dependent variables). Later, in the study design section of the Methods, they identify husbandry and management practices as another independent variable.  Later in the document, age is brought in as another independent variable. All of these factors need to addressed at the same time.

Additionally, there are quite a few other significant subject and husbandry variables in play and most have not been sufficiently described or accounted for in the methods. To name a few:

1.    Enclosure size (SML????)
2.    Social housing (0.2, 1.1, 1.2)
3.    Familiarity of cohabitating individuals to one another
4.    Time in captivity
5.    Time in the social situation
6.    Time in the enclosure
7.    Rearing history (hand-reared vs. mother reared)
8.    Differences (or lack thereof) of keeper style and practices
9.    Physical features of each enclosure
10.    Familiarity of the animals to certain practices like exposure to people, exposure to novel objects, etc.

 It is difficult to know if these factors would be significant because they are unaddressed in the manuscript. It seems clear that the factors of enclosure size, social housing, rearing history, and time in captivity would be very important to account for. Unfortunately, if the authors need to take all of the factors into account, the sample size (although impressive) would be too small.

Line 151: “assessed behavioural effects of husbandry and management practices on captive Asiatic lions.”  It is unclear what the authors actually mean by husbandry and management practices.   Do they mean to say that they measured the behavioral effects of standardized husbandry and management practices (since these did not vary during the study)?

Line 153:  Were interviews conducted or did keepers simply complete a Likert-scale based personality questionnaire, or both.

Line 180:  I question the use of the term “skills.” Does personality determine decision-making skills or does it influence the type of decisions (i.e., stay vs. go) an individual makes?

The authors do a good job detailing how they conducted personality tests.  I am curious to know if it was difficult to categorize some of the animals.  Were any of them consistently intermediate between bold and shy or did they all clearly fall within one or the other.

Behavioral diversity
This section is quite confusing.   In the Study design section, it was indicated that behavioral data were collected using focal animal sampling through video recordings to accurately measure durations of social, and aberrant repetitive behaviours. While in the Species-typical behavioral diversity section, it is indicated that one-minute scans were used to record behavioral states, zone in which the animals were located, social and aberrant behaviors.

It is unclear then how and when the event data (i.e., defecate, drink, groom, lick, mark, grab, roll, rub, scratch, sniff, vocalize, yawn, stalk;  See Supplementary Table 3) was collected.

I question the decision to categorize rescued and then hand-raised cubs in the same category as captive but mother-raised cubs.  There is just too much information on the impacts of hand-rearing on some species to do this without substantial justification.
Validity of the findings: The analysis appears conservative and appropriate for this type of data.  They are reported simply and directly.  The inclusion of the effect size was appreciated.

I would like to know why the authors did not use a multifactorial analysis.

In discussing variables, the authors indicate they divided the group into six categorical variables. They do not include age at this point, but it appears later in the analysis. This happens a lot in this manuscript. Age is a factor they often address and it should be described in the first paragraph.

What were the results of the two different keeper assessments of personality?

Again I am not sure why personality and latency to object are combined.

Lines 271-278: This content is both redundant and procedural, not analysis.

Line 301:  Please indicate why evenness is an important concept to measure and how it might be related to welfare.

Video recording.  Please describe the video recording, analysis, and data protocols.  What was done with the durational and directional data?  How did these data play into the analysis?

The analysis yields significant results and trends.  It is the interpretation of the trends that is the issue.

The authors need to exercise caution when discussing results.  For example, none of the study methods or design permit an assignation of causation.  So, the results are best discussed in terms of relationships.

With one exception the findings are consistent with the study hypotheses.

The authors try to explain the unexpected results from the wild rescued lions as a result of these adults being unable to perform a “diverse array of species-typical behaviors due to the lack of sufficient cognitive stimulus” in captivity.  If that is the case, it would seem that all of the lions would be so affected, especially those in captivity for longer periods. Contrary to their findings, wild-caught animals are often reported as being less impacted by captivity (inoculated) than animals raised in captivity. I think the authors need to speculate more widely.  Another, but unfortunate, explanation presents itself on line 389.  Where the authors state “We also found that most of the wild-rescued individuals have shy personality traits (n=12 63%), whereas a majority of captive-raised individuals have bold traits (n=14 88%).

Because personality traits are heritable one would have to speculate about why a large majority of captive lions had bold traits or why the wild-caught individuals were predominantly shy (not displaying both bold and shy traits more evenly).  Or, one could wonder if the trait in question was actually being measured.  It could be that environmental and procedural comfort/discomfort/habituation rather than the shy-bold personality trait was measured.  It could also be that the wild-caught animals were disproportionately in the smaller enclosures; or that the hand-reared lions influenced the measures in some way; or, the stress of finding one's self in captivity resulted in behavioral conservation; or,  animals needing to be rescued were traumatized, perhaps at the hands of people and, regardless of personality, a conservative response to captivity is reasonable. Because there are quite a few significant confounds in the study, it will be hard to say.

Finally, the statement “captive-raised lions with bold personalities are more resilient small changes in welfare conditions than shy subjects” needs some explanation. Precisely what small changes in welfare condition are being referenced?

Some of the information in the discussion could be moved to the introduction to better support the premise of the study.

It would be interesting if the authors discussed what they would do differently in executing this study.  What they learned about their lions and what they would do for them to enhance their welfare.
Additional comments: First, I congratulate the authors on attempting this study.  The sample size is also quite impressive.  These studies are quite complex, difficult to manage, and oh so important.  I wish I could give an unqualified endorsement.  Instead, I cannot recommend it for publication in its current state.  In my estimation, another attempt is needed.  It will not be easy and will require a total rewrite and rethink of the approach.

Unfortunately, it is my feeling that the study is seriously flawed.  The primary premise of this paper is that Asian lions with different personalities, ages, and life histories are being assessed through various behavioral indices indicative of welfare state within a backdrop of similar management and husbandry practices.  In fact, the management of the animals is quite different – to the degree that it could very well influence the various measurements.  Due to the size variations in enclosures, the varying social situations of the animals, and the widely different rearing histories; the validity of the various behavioral indices is questionable.  This includes enclosure use, latency to object, and behavioral diversity index. In my mind, it even calls in to question the determination of the personality trait of interest. To make matters worse, it is impossible to deduce because the authors do not do an adequate job describing the facilities, the management, or the animals.

A substantial reorganization of the manuscript should also be considered.  The current organization leads to redundancy and confusion.  The methods, in particular, are in need of careful editing and reorganization.  A great deal of necessary methodological detail is missing.

There is also a fair amount of redundancy in the manuscript, particularly in the methods section.  Please describe procedures, processes, or rationale only once.   Consider reorganizing the manuscript so there is no need for repetition.  For example, putting specific protocols for defining the specific independent variables (personality, life history, age, husbandry) in one section and describing how each dependent variable (response to novel items, behavioral diversity, enclosure use, and ARBs) was then measured in another.  Additionally, many of the same sentences are used in several different portions of the paper.  The abstract by its nature is entirely redundant, but no other section of the manuscript should be.

The entire document would benefit from thorough proofreading.  There are many, many grammatical errors.   They are usually minor but are quite numerous and distracting.  Unfortunately, some of the errors are of a nature that disrupts the flow and, possibly, the meaning of the text. I have identified several (but not all) of these errors at the end of this review. Aside from those errors, there are a number of inconsistencies and contradictions in the paper.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EFFECTS OF PERSONALITY AND REARING-HISTORY ON THE WELFARE OF CAPTIVE ASIATIC LIONS (PANTHERA LEO PERSICA)
Review round: 2
Reviewer: 1

Output:
Basic reporting: line 527 includes the term "zoochosis", however, the first citation listed does not refer to this term and the second reference is not listed in the reference section. An online search revealed one article by the authors that year, and that one also has no reference to zoochosis. This is a very specific term and should be referenced appropriately.
Experimental design: There is an issue with how personality traits were determined during the novel object tests. The researchers designated specific behaviors as representative of a particular personality trait, but do not provide any reasons or references for why/how these behaviors were selected. The way in which personality trait classification was done is also atypical, but might be okay if the authors at least provided results in the text relating to the tests.

The authors used latency to approach to determine personality, but provide no information in the text on the range or cut-off point they used to make the differentiation between shy and bold.

It is unclear if behavioral observations were conducted as focal or group scan sessions, as this is only specified for the novel object tests. This should be clarified.

It is unclear if all observations were video recorded, as this is only specified for the novel object tests. However, in lines 257-258, the authors state that video recordings were also used to fill in gaps for behavioral scans. If the videos were from novel object tests, they should not be used for regular behavioral scans.

It is unclear if the lions were tested socially for all three novel object tests. This should be clarified and addressed in the discussion.

How is interacting with their conspecific considered a novel object test?

Why was the effect of social grouping not included in the hypotheses, since this was one of the four categories used for comparisons?

In lines 324-325, the authors state that a behavior would be considered an ARB if there was no observer-discernible cause. What are examples of causes and how they were determined?

It is unclear why the enclosures were devoid of enrichment devices, as noted in line 161

Line 166 states that two cubs were orphaned and counted in the captive-reared group, and yet lines 215-216 state that it was three cubs.
Validity of the findings: In the discussion, the authors state that bold lions are more resilient to functionally barren housing (lines 486-487). However, the enclosures are described as resembling the lions' natural habitat earlier in the manuscript. It is unclear what is meant by functionally barren in that case, and how such a statement is supported by the findings.

Line 527 states that using their methods can help prevent zoochosis. The authors have not supported this statement using their results.
Additional comments: This revised manuscript is easier to read and the authors have addressed a number of the comments from the reviewers. However, a number of gaps in the methods remain. Making sure that the necessary information is included would really improve the paper and would address some of the methodological challenges present in the paper's current form.

The inclusion of multiple measures of welfare is helpful and promotes the use of such methods for others interested in assessing welfare.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EFFECTS OF PERSONALITY AND REARING-HISTORY ON THE WELFARE OF CAPTIVE ASIATIC LIONS (PANTHERA LEO PERSICA)
Review round: 2
Reviewer: 2

Output:
Basic reporting: Minor matters:
Introduction:  The introduction has been greatly improved, but could still use a smoothing and editing. For example:
Line 72: “Animal welfare is crucial for biopsychosocial health of captive animals and long-term success of ex-situ conservation breeding programmes.”  The term animal welfare needs a modifier (i.e. What kind of animal welfare?) or the sentence needs restructuring.
Line 96:  This is a complex sentence that should be simplified and punctuated correctly.
Line 164: The authors have provided very helpful information about the sizes and ranges of sizes of the enclosures. It is still pretty difficult to envision the spread of different sized enclosures and how many animals are in each.  Fundamentally, most of the animals are in smaller enclosures?

Materials and methods:
Line 245:  it seems like using “infighting” and “conspecifics” is redundant.
Line 261: change 19000 to 1900
Line 264:  Change to read-The same group of keepers carried out all husbandry work or the subjects on a rotational basis.  The rest of the sentence is unnecessary.
Line 410: This content is redundant
Line 417:  Change an to a
Line 425:  Change is to are
Line 429-431:  These lines are redundant
Line 437:  Supplemental table 3.  I wonder if this table should be in the manuscript and not supplementary
Line 445:  Change small to short.

Discussion
Line 910: The Webb, Hau, and Shappiro, 2018 reference cannot be found in the references.
Line 950: I would encourage caution with the use of the term “Zoochotic.” Please also include a referenced definition of the term, as this is the first, but not the last, time it has been used in this manuscript.

Lines 964-968: This text and much of the subsequent text in the discussion section was used earlier in the manuscript and is thus redundant.
Experimental design: The experimental design is generally well thought out.  However, I recommend some additional analysis particularly in regards to enclosure size and perhaps the interaction among Wild caught/Captive born and Bold/Shy categories.

There is a great deal of variation in the size of the zones among the various exhibits.  How can this be addressed? Because of the size difference in the zones, it is possible (and even likely) that an animal in a smaller enclosure  could traverse several zones in the same amount of time it would take an animal in the larger enclosures to traverse a fewer number of zones. At the very least, the authors need to determine if there is an enclosure size effect on the enclosure use data. It seems that they have the data to do that. If there no effect, they are good and can now make a stronger argument.

Additionally, the inter scan interval would have to be a lot shorter than 1/min in order to meaningfully capture rare and short duration behaviors - if the observers were following proper procedures for scan sampling.  The authors may need to abandon this statement. Recording all occurrences of rare behavior or events is the recommended data collection protocol.  Which, given the methods, is entirely possible.
Validity of the findings: The authors' approach a very difficult and important topic - one with lots of variables for consideration. There is ample research to support the importance of this research. The authors have appropriately operationalized the construct of personality. The large (relatively) sample size is impressive. They also do a pretty good job managing all of the moving parts.  I would still like to see greater external validity. If the authors would consider just how other facilities might integrate the approach laid out in the manuscript into the basic management of the animals in their care.  The issue with many facilities that manage captive animals is usually not that they don't want to do such work, but a shortage of time, staff, and resources.  My question to the authors is: how can this project inform the decisions of managers of captive wildlife and/or how might others use your approach/methods effectively and efficiently?
Additional comments: The authors did a fine job responding to most of the comments from all of the reviewers.  For the most part, the review concerns were well addressed and the rebuttals were well argued and to the point.  However, this reviewer considers the authors’ argument regarding enclosure size vs complexity and biological relevance to be weak and unsupported by the very literature they use as support.  Their approach to this issue should be reconsidered. It would be unfortunate if some of the statements in this manuscript were introduced into the literature without better context and support. There is still a fair amount of redundancy in the manuscript.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: LATE JURASSIC THEROPOD DINOSAUR BONES FROM THE LANGENBERG QUARRY (LOWER SAXONY, GERMANY) PROVIDE EVIDENCE FOR SEVERAL THEROPOD LINEAGES IN THE CENTRAL EUROPEAN ARCHIPELAGO
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors provide important documentation of (admitted) sparse fossil specimens that nevertheless increase our knowledge of the terrestrial vertebrate fauna of the Late Jurassic of central Europe. I would say that none of their results are particularly surprising for a Late Jurassic dinosaurian assemblage (although the possible neovenatorid is intriguing, as this would be stratigraphic range extension of the clade), but such confirmations are significant nonetheless: they help to fill in the map of the biogeography of the ancient world.

It is a shame the material is not more complete, but of course the nature of the recovery (specimens found after blasting) would preclude actual complete skeletons. Their presence, however, might spur future systematic collection in this or comparable quarries in hopes of the discovery of more complete and intact fossils.
Experimental design: No comment
Validity of the findings: The identifications seem very reasonable: they are consistent with observed morphology. Of course, given how fragmentary they are and given the existence of homoplasy, it isn’t impossible (although unlikely) these all represent the same taxon that belongs to only one or none of these clades. If the elements assigned to Neovenatoridae are properly identified, this would seem to be the stratigraphically oldest members of this (otherwise Cretaceous) clade discovered this far.
Additional comments: In line 550 the authors use “about 10 Ma older” to specify “about 10 million years older.” While it is certainly true that some use Ma for durations, many authors prefer the scheme in which Ma refers to a date and Myr refers to a duration. Berggren and Van Couvering (1979,p. A506, footnote) specified that the abbreviation Ma refers to millions of years before present, and this was adopted by various stratigraphic codes. A discussion of this issue can be found in Aubry et al. (2009).

Aubrey, M.-P., J.A. Van Couvering, N. Christie-Blick, E. Landing, B.R. Pratt, D.E. Owen & I. Ferrusquía-Villafranca. 2009. Terminology of geological time: establishment of a community standard. Stratigraphy 6: 100-105.

Berggren, W.A. & J.A. Van Couvering. 1979. Quaternary. In Moore, R.C. (ed.) Treatise on Invertebrate Paleontology, Part A. Introduction. A505-A543. University of Kansas Press, Lawrence, KS.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: LATE JURASSIC THEROPOD DINOSAUR BONES FROM THE LANGENBERG QUARRY (LOWER SAXONY, GERMANY) PROVIDE EVIDENCE FOR SEVERAL THEROPOD LINEAGES IN THE CENTRAL EUROPEAN ARCHIPELAGO
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors describe several new and interesting occurrences of theropod dinosaurs from the Late Jurassic Langenberg Quarry of northern Germany, which is a poorly known record and thus this work adds important information for our knowledge of Late Jurassic continental ecosystem of central Europe.
The manuscript is clearly written in professional, unambiguous language, the literature references are updated, the context is well described.
Experimental design: This is an original research, the questions are well defined, relevant and meaningful, the investigation is rigorous and the methods are described with sufficient detail.
Validity of the findings: The figures are high quality, well labeled, and described, and the conclusions are relevant and well stated. However, I think that the identifications of some of the described elements need to be better supported (please see general comments below).
Additional comments: I made some notes directly on the manuscript. Apart from these notes, I have some additional comments and suggestions:

- It seems to me that the attribution of the ungual DfMMh/FV1/19 to a neovenatorid theropod is hard to justify. The ungual (and other) phalanges beside usually not well described in the literature show frequently similar features among different groups, which makes the identification of these elements extremely difficult. I agree that there are general similarities with some neovenatorid taxa, such as Neovenator and Australovenator, but it seems to me that there are also some differences, including the wider groove surrounding the articulation surface, which gives to the surface a more constricted appearance and the position of the flexor tubercle seems much more distal in DfMMh/FV1/19. Besides and despite some isolated elements tentatively related to this clade, the presence of neovenatorid theropods in the Late Jurassic of Lausaria needs to be confirm based on more complete specimens. For all these reasons, I would suggest a more open identification for this element.

- The same argumentation may be used for the phalanx DfMMh/FV/343. There are some features in this element that I think should be better described and analyzed. For example, the overall aspect of the phalanx, with a stout appearance in dorsal and ventral view, but relatively narrow in lateral view and the near flat proximoventral surface seem to me very different of the strongly offset proximal articular facet typical of most allosauroids. However, this may be also due to distortion. Could you please comment something about it? Other feature that I would like you to comment is the absence (or seems to me by the figure) of a dorsal groove adjacent to the distal articular facet. This groove is generally present in all pedal phalanges of most theropods even the most proximal ones.

- The identification of the chevron seems to me less problematic despite I agree with your caution maintaining the possible relationship with megalosauroids open. I just would like that you develop a little more the discussion on the presence of the medial keel on the anterior surface. It seems an interesting feature. A similar keel is present in some theropods, but as far as I know, it is usually much lower. Could you comment a little about the distribution of this feature among theropods?

- In the description of the caudal vertebra DfMMh/FV/105 could you provide a description of the ventral surface?


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: COMPARATIVE ANALYSIS OF CHLOROPLAST GENOMES FOR FIVE DICLIPTERA SPECIES (ACANTHACEAE): MOLECULAR STRUCTURE, PHYLOGENETIC RELATIONSHIPS, AND ADAPTIVE EVOLUTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors report whole plastome assemblies for five Dicliptera species to contribute to the phylogenetic reassessment of the genus. The introduction gives enough background, however, as the title mentions structure and adaptive evolution a short review of the relevant literature to these should be included. This could give the background to the IR junction changes and the positive selection of ycf15.

PeerJ prefers separate Results and Discussion sections, so I would suggest that you reformat the paper to fit this. This could make the paper easier to read. I found the conclusions too long and it mostly just repeats what is in the abstract. It should focus on how this study moves our understanding forward.

The article in general is well written but I have included some comments below to hopefully improve the text.
Experimental design: The study fits well in PeerJ’s scope and the experimental design is suitable to answer the main question of the study.
Validity of the findings: No comment
Additional comments: Line 17: I think it should be: Here we would like to report
Line 18: the genus is misspelled
Line 38: There should be a full stop after the bracket not a comma
Line 50: Please include date for the Kiel et al. reference here and delete the citation from the end of the sentence.
Line 51: I think regions instead of sequences would be more accurate. Also, it would be useful to include here which chloroplast and nuclear regions the Kiel et al. study used.
Line 55-56: This sentences is too vague to be informative. I guess you mean that if has been used in many evolutionary studies. In any case this needs a reference.
Line 57: circular instead of circle. It is not strictly true, not all plastomes are quadripartite, e.g. ILC clade in Fabaceae
Line 59: I am unclear about what you mean “plants in ecosystem”
Line 69: 5 should be written as five
Line 82: including instead of include
Lines 88-104: You could delete all instances of software, it is redundant. Also, the styling of version (v. or version) should be consistent. Bowtie2 and PGA are missing the version information.
Line 102: GenBank instead of Genebank
Line 103: I don’t think the link for GenBank is necessary.
Line 107: Did you mean conserved regions?
Lines 113-114: I don’t think you need (mono-), (di-) etc.
Line 119: Do you mean you included only one IR per genome?
Line 122: Used would be better than hired here
Line 127: As far as I can see all the support values are above 50% and are shown, so this sentence is somewhat misleading.
Line 132: Do you mean PCGs or all coding genes?
Line 134: program could be deleted
Line 136: the second Yang & Nielsen should be deleted
Line 140: Do you mean that the average coverage of the assemblies varied?
Line 141: delete all
Line 151: You could delete “similar processed”
Line 155: In the abstract the GC content is reported as 37.9-38%. In Table 1 all GC contents are 38%. Also, above would be better than beyond.
Line 164: What do you mean moved backwards? Backwards compared to what?
Line 179: You should delete “In recent years”
Line 187: less variable would be better than more invariable
Line 195-196: It would be useful to include the Pi for matK, rpl16, and trnS-G here for comparison.
Line 201: should be “which accounted for”
Line 202: Why not a range? Given the size and IR junction variation between the plastomes I think the percentage of PCGs would also be a range.
Lines 207-213: I think it would be useful to mention here why A/U at the third codon position matters
Line 215-216: The definition of SSRs is not entirely correct here. Check Tautz & Renz, 1984; Jurka & Pethiyagoda, 1995.
Line 216: have instead of has
Line 218: this should be mono-, di-, tri, and tetranucleotide
Line 230-231: This is somewhat obvious given the numbers above and I think could be just deleted.
Line 233: is instead of was
Line 238: were instead of was
Line 246: drawn instead of drawed. Also, include date for the Kiel et al. reference here and delete the citation from the end of the sentence.
Line 254: Makalowski and Boguski is missing the publication date and is also not listed in the references.
Lines 261-263: This should be present not past
Line 264: It would be useful to cite any references here, if there are any, that reports positive selection of ycf15. However, I don’t think you can say that ycf15 plays a crucial function as we don’t know what its function is. Also, I am not sure what you mean evolution ecosystem.
Line 298: obtained instead of apply
Line 299: collected instead of collecting
Figure 2: I would delete the last sentence of the caption and add (Ψycf1) after ycf1 pseudogenes
Figure 8: I would recommend changing the X-axis labels so that it shows all genes. Also, the peak between ndhE and ndhG seems to be above 1.0, which makes the last sentence of the caption incorrect.
Table 1: I would suggest including a geographic region in the location if this is possible. What does assembly reads mean? The number of reads used for each assembly? In which case it should be assembled reads. Or all of the sequenced reads?
Table 2: I am not sure why rps19 and ycf1 are indicated to have two copies as neither are fully in the IR to have two full copies like for example ndhB.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: COMPARATIVE ANALYSIS OF CHLOROPLAST GENOMES FOR FIVE DICLIPTERA SPECIES (ACANTHACEAE): MOLECULAR STRUCTURE, PHYLOGENETIC RELATIONSHIPS, AND ADAPTIVE EVOLUTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors Huang et al reports the chloroplast genome of Dicliptera by selecting D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata. The article reports a novel work as this genus and its detailed chloroplast genomics have been overlooked. The authors shown that only one report is available at low level sequence analysis. Thus, suggesting that this work will further advance our knowledge to understand this genus. However, the manuscript suffer from various grammatical issues and typos. I would suggest to check it through a native speaker. The method part adapted for this work is a standard one. However, at some stage they say "five species sequenced" other places, its been shown only only D. acuminata (Fig 1). This has to be clarified. They can also make a combined circular map if they have really sequenced all the five species.

In addition, if you start with introduction, there is more need to emphasize on why only these five species selected, what were the bases of selecting only these say whether there are any taxonomical or morphological issues and sequencing could help to resolve that. A paragraph of rational is must to enlist the essentiality of this work. In addition, what is the importance of these species. I am sure if the authors come up with a photo of these species would be more attractive for the audience.

I think the authors can come up with more analysis to envision more insight from the available genome sequence data. A detailed phylogenetic analysis on the bases of shared genes in the five cp genomes will give a more detailed insight in the placement of the species. In addition, more set of phylogenetic analysis NJ, and MP would help to correct some instances.

Furthermore, I am not satisfied with the graphical presentations specially if you look at Fig 4, 5 6 and 8. Their quality and presentation style does not reflect much potential information. Similarly, if you see tables, table 2 and 3 can be moved to supplementary data. Table 1 is essential. However, some units are missing and for some species data has not been given.

A detailed expansion and contraction analysis of IR would be required to make sure how these species deviate. There are not much in depth analysis of repeats also made. They can use PHOBOS  for this purpose. In addition, how Missing and ambiguous gene annotations were confirmed by comparative sequence analysis after a multiple sequence alignment and gene order comparison were performed.
Experimental design: mentioned
Validity of the findings: Mentioned
Additional comments: The authors Huang et al reports the chloroplast genome of Dicliptera by selecting D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata. The article reports a novel work as this genus and its detailed chloroplast genomics have been overlooked. The authors shown that only one report is available at low level sequence analysis. Thus, suggesting that this work will further advance our knowledge to understand this genus. However, the manuscript suffer from various grammatical issues and typos. I would suggest to check it through a native speaker. The method part adapted for this work is a standard one. However, at some stage they say "five species sequenced" other places, its been shown only only D. acuminata (Fig 1). This has to be clarified. They can also make a combined circular map if they have really sequenced all the five species.

In addition, if you start with introduction, there is more need to emphasize on why only these five species selected, what were the bases of selecting only these say whether there are any taxonomical or morphological issues and sequencing could help to resolve that. A paragraph of rational is must to enlist the essentiality of this work. In addition, what is the importance of these species. I am sure if the authors come up with a photo of these species would be more attractive for the audience.

I think the authors can come up with more analysis to envision more insight from the available genome sequence data. A detailed phylogenetic analysis on the bases of shared genes in the five cp genomes will give a more detailed insight in the placement of the species. In addition, more set of phylogenetic analysis NJ, and MP would help to correct some instances.

Furthermore, I am not satisfied with the graphical presentations specially if you look at Fig 4, 5 6 and 8. Their quality and presentation style does not reflect much potential information. Similarly, if you see tables, table 2 and 3 can be moved to supplementary data. Table 1 is essential. However, some units are missing and for some species data has not been given.

A detailed expansion and contraction analysis of IR would be required to make sure how these species deviate. There are not much in depth analysis of repeats also made. They can use PHOBOS  for this purpose. In addition, how Missing and ambiguous gene annotations were confirmed by comparative sequence analysis after a multiple sequence alignment and gene order comparison were performed.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: COMPARATIVE ANALYSIS OF CHLOROPLAST GENOMES FOR FIVE DICLIPTERA SPECIES (ACANTHACEAE): MOLECULAR STRUCTURE, PHYLOGENETIC RELATIONSHIPS, AND ADAPTIVE EVOLUTION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The paper has improved from the previous version. There are a few corrections I would recommend before accepting the paper for publication. The adaptive evolution part of the introduction could be improved as it mostly consists of a definition.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Line 29: I would delete while
Line 41: Replace 'with' with 'from'
Line 48: This should be evolutionary studies
Line 75: Add the in front of five
Line 172-176: I would strongly recommend to change backwards and forwards to a direction in relation to plastome feature e.g towards LSC or towards ndhF. Backwards and forwards are ambiguous especially as isomeric versions of the plastomes are present in each cell.
Line 29 & 186: Please make sure the formatting of the tRNA genes are consistent through the text.
Line 194: should this be 78714-78747? 78715 is not divisible by three and 26238 * 3 is 78714.
Line 201-203: This should be in the discussion
Line 206-207: This should be in the discussion
Line 227-229: This should be in the discussion
Line 235-237: This is already in the methods, it does not need to be repeated here.
Line 237-239: This should be in the methods
Line 241-243: This should be in the discussion
Line 272: What does 'this' refer to?
Line 282-283: This needs a reference. Also, I am not sure this is relevant here, there are not any major rearrangements in these plastomes.
Line 289-290: Some requires more than one reference
Line 293: Significant should be changed to substantial unless there is a statistical test showing significance
Line 294: It should be paniculata
Line 311: Please check the in-line references
Line 321-324: Are there any morphological characters separating these species? The text is not clear enough to show this.
Line 333: I am not sure adaptive genes are the best choice here could just be deleted.
Line 335-336: This sentence needs a reference

Figure 7: I would recommend showing a tree with branch lengths instead of a cladogram, where all branches are equal length. Branch lengths contain very valuable information about sequence variation.

Figure 8: There should not be lines connecting KS and KA/KS measurements as this indicates changes that are not present, especially since the order of genes in the figure is alphabetical.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: COMPARATIVE ANALYSIS OF CHLOROPLAST GENOMES FOR FIVE DICLIPTERA SPECIES (ACANTHACEAE): MOLECULAR STRUCTURE, PHYLOGENETIC RELATIONSHIPS, AND ADAPTIVE EVOLUTION
Review round: 2
Reviewer: 2

Output:
Basic reporting: I have gone through the suggested revision you made. The MS seem improved. However, I still feel the manuscript must be submitted to a professional language editor to improve the flow and readability. Some of the sentence structures still need refinement.

The 2nd paragraph in introduction still fails to improve the rational of the MS. The author should emphasize on what specific taxonomical issues were there that they have considered doing the cp genome of five species. In addition, the last paragraph just explain what they have done, where, it must state clearly what was aimed to investigated.

In addition, I would suggest that table 2 and 3 can be moved to supplementary data, specifically table 2 as most of the genes have been reported elsewhere. The figure captions must be more elaborative to explain the figures well, e.g. fig 8. Fig 5; There is no A, B, C ... demarkation on Fig 1 (circular map), the visibility has also been reduced. I am sure you can come up with more higher quality figure. In results, the phylogenetic analysis need more explanation. In methods, more information are needed for taxonomic identification? how and who identified them? In addition, I assume if some pictorial presentation of all five species is made in revision would really improve the visibility of the manuscript.
Experimental design: N/A
Validity of the findings: N.A
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE NUTRITIONAL STATUS OF CHILDREN LIVING WITHIN INSTITUTIONALIZED CARE: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 1

Output:
Basic reporting: In general, it is an interesting article with a very specific topic. It is generally well-organized, but I think the discussion should be revised (see specific comments)
Experimental design: It is clear and the tables are very detailed.
Validity of the findings: More discussion about study limitations and some specific aspects about the micronutrients deficiencies and, importantly, the most common clinical problems in institutionalized children should be provided (see specific comments)
Additional comments: Introduction:
- paragraph 3 (especially from line 97 to 103) could be shortened or removed, as it contains information that are not essential for the study and its discussion, which is focused on nutritional issues in institutionalized children.
- paragraph 4 (line 104 to 127) should be summarized, by retaining the main concepts and information that are functional for the interpretation of the results and the eventual discussion.

Materials and methods are described appropriately.

Results:
- in addition to describe the output of the literature search in the text, I would suggest adding a Figure showing the flow chart of the extraction and selection process of articles, according to the PRISMA guidelines.
- line 393: define CWD; in general, define abbreviations at their first appearance in the text.
- Overall, the results section is quite clear.

Discussion:
- the first paragraph is quite interesting, as it seems that over the time the malnutrition of younger children can be overcome, since older children have fewer issues under this point of view. If we exclude some kind of bias (that I would recommend the authors to consider and discuss anyway), the authors tried to provide an explanation, namely the fact the most malnourished children may have higher likelihood to die, basically. By the way, in this regard, I suggest rephrasing this sentence “poorly nourished young children may also not survive to become older children in institutional settings”, by using the term risk and supporting this statement with additional references (e.g. Arch Public Health. 2018 Jul 16;76:28. doi: 10.1186/s13690-018-0277-1.; Am J Clin Nutr. 2013 Apr;97(4):896-901. doi: 10.3945/ajcn.112.047639.). Finally, the statement “Diet inadequacy, micronutrient deficiencies and illnesses or infections were also found to be prevalent”: where? In younger children?
- second paragraph: at some points, the discussion is difficult to be read and there are several repetitions, without addressing the main issue. For instance, specify the “reasons why IBC may offer opportunities of good nutrition”.  Moreover, the authors state “Our review also highlights several issues in this field of study, most notably a lack of well reported and standardized evidence”: which issues? Finally, “Despite Petrowski finding 140 countries with data on children in institution” should be rephrased.
- third paragraph: “Children with disabilities are disproportionately present in institutionalized care settings”…that may be another good reason to explain the greater prevalence of malnutrition in younger children, if we assume that a significant proportion may have neurological disabilities since birth. Can the authors retrieve data in this regard? If my assumption is correct, they may consider this observation in the previous discussion art paragraph one as well.
- paragraph #4: actually, this issue is partly discussed in this paragraph; therefore, I suggest the authors to go over and review the organization of the whole discussion, in order to follow a more linear logic line. Actually, clearly dividing and organizing the discussion in several section, as the authors did in the results and maybe following the same organization in the discussion as well, could be the best solution, in my opinion, in order to make the discussion clearer and easier for the reader.
- Similar observations can be made on all following paragraphs, in general.
- Additionally, I suggest the authors to consider additional paragraphs/section to discuss some specific health issues that occur frequently in institutionalized settings (e.g. diarrhea, respiratory infections, anemia). In this regard, the authors just mentioned also the concern about the medical care provided to these institutionalized children. Most papers come from developing countries: e.g. in Asia (which is the most represented country in this article, probably) common diseases, even not infectious (for instance, celiac disease, which is not rare, very heterogeneous clinically, but invariably associated with malnutrition and/or micronutrients deficiency) can be completely overlooked in healthy and normal settings and, then, the authors can figure out in institutionalized children (e.g. Medicina (Kaunas). 2019 Jan 12;55(1). pii: E11. doi: 10.3390/medicina55010011.; PLoS One. 2011;6(7):e22774. doi: 10.1371/journal.pone.0022774).
- the final part about the study limitations should be more concise, in my opinion, as well as the conclusion, whereby I would suggest avoiding references citations, since that should summarize the main findings and conclusions, already discussed in the previous sections.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE NUTRITIONAL STATUS OF CHILDREN LIVING WITHIN INSTITUTIONALIZED CARE: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 2

Output:
Basic reporting: It is really important paper given that so many children live in the context institutional care. It does a very good review of the existent literature. It has a great organization that allowed us to highlight the main areas such as: physical growth, disabilities, special health issues and nutrition. The discussion section provides us with main gaps and new directions.
Experimental design: very appropriate for the research question.
Validity of the findings: well identified topic and very focused on this topic analysis
Additional comments: Well written and very important paper to address challenges of sensitive children who live in institutional care.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE NUTRITIONAL STATUS OF CHILDREN LIVING WITHIN INSTITUTIONALIZED CARE: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 3

Output:
Basic reporting: see general comments section
Experimental design: see general comments section
Validity of the findings: see general comments section
Additional comments: Reviewer comments
Title: The nutrition status of children living within institutionalized care: a systematic review
Reviewer: Jude Thaddeus Ssensamba, MPH, MSc, FHSM
Date: 30/09/2019

Introduction
I thank you for giving me the opportunity to review this manuscript. With malnutrition still a major global health threat, this review is timely more so for more vulnerable populations like children staying in institutionalized settings.
The manuscript “The nutrition status of children living within institutionalized care: a systematic review” looks at existing data to paint a picture of the burden of malnutrition among children staying in institutionalized care. The study looks at both extremes of malnutrition (Under and over nutrition), and macro and micronutrient deficiencies.
The authors went ahead to look at the burden of malnutrition-related factors like gender, disability, age, and associated co-morbidities like HIV, skin infections, eye conditions, respiratory tract infections, genitourinary disorders, among others.
I commend the authors for putting this manuscript together; however, to ensure a clear understanding for readers, the authors should/could further clarify some points mentioned below:

General comments
The authors could consider defining the limits of what they describe as a child with regard to age. They could use international standardization.

Abstract
1.	Lines 42-47 in the results section seem to fit more in the methods section. The authors could consider effecting that change.
2.	The authors could consider using more specific wording in the abstract and whole manuscript. Words like “a few exceptions (line 55)”, “younger children (line 55)” may need to be clearly defined
3.	The authors could clarify the meaning and intent of the sentence: “High risk of bias was found” (line 57), and how this was ascertained.
4.	Being that the study did not intend to assess the extent of availability of information on malnutrition among children in institutionalized care, the authors could consider rewriting the conclusion (lines 58-67) to reflect the burden of malnutrition first and then maybe comment on limited data availability

Introduction
1.	Line 73, the authors could consider being more specific with regard to the “millions” of children affected. Let us have the absolute number.
2.	I appreciate the authors for painting a global picture of the burden of malnutrition among children under 5years. However, being that this study focuses on all children in institutionalized care, many of whom are above five years, the authors could consider giving a global view of malnutrition with a focus on all children (0-15 years) as using the under-five age to create a case for all children (0-15 years) may raise issues.
3.	Paragraph one (line 73-83) could be rephrased, and some sentences that may supposedly be hanging like line 81 may be changed to give it a good flow.
4.	Lines 84-85 could be rephrased as “Orphans and children living in institutionalized care are at a higher risk of malnutrition,” and a fitting reference included.
5.	Lines 91-95 could be rephrased to fit well with lines 84-90
6.	For consistency, the authors could choose to use either “Institutionalised care” or “residential care” throughout the manuscript
7.	The authors could add a reference to line 99
8.	Line 102-103 “these are rights for all children…” seems to be hanging. The authors could consider to modify it or put it into context with the whole paragraph.
9.	The authors may wish to be more specific with regard to the “numerous adversities” (line 104), and relate this well (sentence structure) with the whole paragraph.
10.	The authors could consider being more specific with regard to the use of the word “further adversities” (line 115), and for lines 116-117, the wording “impacted physical,” and the differences between infections and diseases may need to be clarified to the reader.
11.	Lines 124-126 could be rephrased and better punctuated to ensure proper flow

Methods
General comments
1.	In view of the already existing information on malnutrition among children in institutionalized care (already conducted studies), the authors may need to explicitly highlight herein the purpose of this review. More so that it is already known that children in institutionalized care have a higher risk of malnutrition more so younger children, the disabled, and those that were of low birth weight at birth. Otherwise, it may look like a global level interrogation of the extent of existing evidence on malnutrition in institutionalized settings.
2.	The methods section gives readers a detailed account of the “how” the study was conducted. For systematic reviews, we need to see how the data was aggregated, how the differences in study designs were reconciled, how the different measurements were compared, and any associated errors were accounted for. In line with this, authors may consider enriching their methods section to reflect this.

Other comments
1.	The fact that the review analysed data from different study designs and types (line 141) should be included in the limitations section
2.	The authors could include in the limitation section the fact that they only considered data for the period Jan 1990 to Jan 2019, given that other studies on malnutrition in institutionalized care had been conducted before 1990.
3.	Lines 141-157 could be rephrased and may be broken into two paragraphs where one looks at the “study type, the period of interest and justification, and criteria for inclusion of studies,” and the other, the variables of interest “anthropometric indicators, micronutrient status, presence of comorbidities, etc and the justification.”
4.	The tense used inline 148 “…these studies must address…” could be changed to reflect the past tense, and the whole paragraph rephrased to improve flow.
5.	Line 153, the authors may consider changing the use of “or” since head circumference for age cannot replace mid-upper arm circumference
6.	Line 158, could include a comma between “following which” and “full texts.”
7.	Line 159, Could replace “us” with “a.”
8.	Line 160, Include an “s” to discussion
9.	Line 164, In the methods section, the authors could be more explicit on the extent and meaning of “another measure.”
10.	Lines 165-166, the authors may highlight the differences between “reported disease,” “illness” and “infection” and how these were treated and reported during analysis

Results
1.	In the context of this study which is to investigate the burden of malnutrition among children in institutionalized care, lines 170-189 seem to explain the “how” the sample of interest, geographic distribution, types of studies, were ascertained. And this seems to fit more in the methods section. The authors may consider shifting this section to them methods section after improving its flow.
2.	Lines 181-182, The authors included a phrase that one study had no ages. This raises questions since age is a crucial determinant for one being a child or not. Authors should clarify how they treated this paper that had no age, and how they grouped it or could consider removing it from the analysis.
3.	The authors could clarify the difference between lines 182-184 and lines 187-188, or they could consider fusing them into one sentence
4.	It is of great importance that the authors highlight the disability aspect of the study (lines 191-199). However, since the primary objectives were to determine the nutrition status, the authors could consider sharing this first (lines 200-208) before they go deeper into other aspects like disability and malnutrition, clinical signs, etc.
5.	Lines 196-199 could benefit from rephrasing to make it easier for readers to understand.
6.	Lines 200-208, the authors could consider enriching this section by adding how malnutrition differed by gender, geography, and age groups(under 5years, 5-14 years[school aged children], and 15-18years), with specific statistics, and if this was not done during analysis, the authors could consider rerunning the analysis.
7.	Lines 210-211, the authors could consider changing the phrasing since HIV is not a clinical sign or symptom, and sections 210-212 could best suit the methods section.
8.	Line 213-214, the authors could be more specific with regards to “the higher prevalence” with regard to both groups so that readers can estimate the variance in prevalence. With
9.	Section 209-220 could speak more about what was the most prevalent signs/symptoms/diseases visa vie the number of studies that reported what
10.	Lines 215-216 the authors could clarify the meaning of the sentence “conditions associated with nutrition status were also noteworthy” or otherwise consider making it more specific or delete it.
11.	Line 223, the authors could include statistics to qualify this statement
12.	Lines 223-224 The limited funding aspect could be taken to the discussion section and referenced accordingly
13.	Section 221-233, could be rephrased to improve flow and coherence

Discussion

The authors highlighted key findings and their likely implications in line with existing literature. That said, the section could benefit from the following:
1.	Generally, the authors could consider restructuring the discussion section to discuss: malnutrition and IBC in general, then IBC malnutrition and age, IBC malnutrition and Gender, IBC malnutrition and disability, IBC malnutrition and HIV, IBC malnutrition and co-infections and infestations, etc. These could be small subheadings. This will make the flow better and reduce the risk of repetitions.
2.	Lines 237-238, the authors could consider changing the phrasing “of the 25 papers, all of them” to “all 25 reviewed studies…”
3.	Lines 235-248 could be rephrased improve flow and coherence
4.	Lines 247-248 could fit more in the result section. Perhaps the likely reasons for the deficiencies and illnesses could be discussed here
5.	 Line 249, the authors could provide a basis for saying this is the first systematic review (For example; based on a review of literature, to our knowledge…) putting in mind that many studies may have been conducted before January 1990.
6.	Line 251, the authors may consider using more specific language instead of “many reasons.”
7.	Lines 259-262 seem to suit more the limitations section; the authors could consider looking at it more closely
8.	Section 249-262 may benefit from rephrasing to improve the flow
9.	Line 263, the authors may consider being specific about the few studies by providing a statistic which may be a percentage.
10.	The authors could clarify lines 264-266 to answer the “so what” question
11.	Lines 269-270, a reference is needed for this assertion.
12.	Authors could consider to clarify sentence lines 277-279, and give them a reference
13.	The authors could consider revising sentence 283-284 “finally, becoming malnourished…), and to improve the flow of the whole paragraph.
14.	 Consider writing line 286 in reported speech
15.	Line 288 could benefit from clarification of “which status” at birth.
16.	The authors could consider revising lines 295-298 as them neem not to sync with lines 293-294
17.	The construction of the paragraph that covers lines 299-306 could be revised as lines 299-300 seem not to flow well with subsequent lines.
18.	For lines 307-309, the authors compared IBC malnutrition with global malnutrition among children younger than five years. Given that IBC covers different age groups comparing them with under-fives may need rethinking.
19.	For line 309, the use of words like “it may be” could be qualified with a reference
20.	Line 316, authors could consider qualifying the “six.”
21.	Line 322-326 could be another paragraph that talks about malnutrition and HIV, and the likely “whys.”
22.	Line 325, authors need to qualify “only eight.”
23.	The authors could clarify what lines 328-332 intend to portray to the reader in relation to the subject matter as it seems hard to comprehend.
24.	The authors could consider rephrasing line 340
25.	The authors could include a reference for the sentence that covers line 340
26.	The fact that the study only examined studies from 1990-2019 could be included as a limitation
27.	The authors could explicitly include the fact that reviewed studies were of different designs, which would make comparisons difficult and how this was overcome.
28.	 The authors could consider including some strengths of the study

Conclusion
1.	The authors could consider starting with the most important findings concerning malnutrition visa vie the extent of the presence of reviewed data, then would comment later on the scarcity of data.
2.	References are rarely in conclusions more so since conclusions are based on the general impression of the study.
3.	Line 381 the word “orphanages” seems new, the authors should clarify if orphanages also mean IBC settings/residential care and if yes, this needs to be defined in the introductory section

References
These were well written, and the authors are commended for this

Tables
Table 1:
The authors may need to clarify the rationale for the inclusion of some studies:
-	The author could clarify why Lesho 2002 was included in the analysis, given they did not know the age of the study subjects.
-	Pysz 2015 was included in the analysis though the age range was 7-20 years. The upper limit (20 years based on international standards) does not point to a child. How was this appropriated for? The authors could think of this.

Table 2: Okay

Table 3:
The inclusion of HIV rates as signs and symptoms (Braitstein 2013, Panpanich 1999, Nunnes 1999) could raise questions. The authors could consider including another column to specify “disease condition,” which could cater for specific diseases like Tuberculosis, HIV, etc.

After a thorough review of the manuscript, I thank the authors for bringing out the fact that malnutrition among children staying in IBC remains a challenge. The study highlighted the fact that few studies have been conducted in this area, an aspect that requires more rigorous studies. Given availed information, this manuscript would benefit from rigorous changes with regard to structure, flow, English, and content. I hope that the comments I raised herein will help the authors to make it better.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE NUTRITIONAL STATUS OF CHILDREN LIVING WITHIN INSTITUTIONALIZED CARE: A SYSTEMATIC REVIEW
Review round: 2
Reviewer: 1

Output:
Basic reporting: The paper has been significantly improved and the authors addressed most of my observations and comments.
Experimental design: Systematic research criteria and parameters are appropriate.
Validity of the findings: No major concerns.
Additional comments: There is only one point that I recommend the authors to address, mention and shortly discuss/emphasize in the discussion, as suggested in the previous review. See below the specific point and rebuttal.

Review #1
- Additionally, I suggest the authors to consider additional paragraphs/section to discuss some specific health issues that occur frequently in institutionalized settings (e.g. diarrhea, respiratory infections, anemia). In this regard, the authors just mentioned also the concern about the medical care provided to these institutionalized children. Most papers come from developing countries: e.g. in Asia (which is the most represented country in this article, probably) common diseases, even not infectious (for instance, celiac disease, which is not rare, very heterogeneous clinically, but invariably associated with malnutrition and/or micronutrients deficiency) can be completely overlooked in healthy and normal settings and, then, the authors can figure out in institutionalized children (e.g. Medicina (Kaunas). 2019 Jan 12;55(1). pii: E11. doi: 10.3390/medicina55010011.; PLoS One. 2011;6(7):e22774. doi: 10.1371/journal.pone.0022774).

Authors' reply #1
- Thank you for sharing, we reviewed this article and added additional information, line 122 on page

Review #2 (current)
- I think the authors should add in the discussion a paragraph or a few sentences mentioning the possibility that many medical conditions without acute symptoms or with blunted clinical manifestations can be easily overlooked in these institutionalized setting and, in particular, in low-middle income countries, which represent the provenience of most paper considered in this systematic review. The authors may consider several non-communicable diseases, but one very good example might be celiac disease (as suggested), which is probably the most frequent chronic disease (often pauci-symptomatic, manifesting with growth problems mainly) that can impair the growth and nutritional status in children (including the reported micronutrients deficiency) all over the world. Both articles previously recommended can be very useful to mention, discuss and emphasize this specific aspect in the discussion. The additional information provided in the introduction (line 122, page 4) does not address this specific observation/suggestion appropriately, in my opinion.  Indeed, table 2 (that is very detailed and informative) may indirectly suggest how chronic/no acute conditions are not considered in almost all available meta-analyzed studies. This issue of the under-diagnosis of medical conditions in settings with limited resources and/or poor awareness of specific non-acute diseases impairing the growth in children, should be mentioned.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE NUTRITIONAL STATUS OF CHILDREN LIVING WITHIN INSTITUTIONALIZED CARE: A SYSTEMATIC REVIEW
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I would like to take this opportunity to thank the authors for the great work done to make this manuscript what it is now. All comments i raised have been adequately responded to.

With the exception of a few areas that can benefit from editing services, I recommend that this article passes on to the next publication phase.

I just included a few comments on the attached PDF that authors can respond to at their discretion.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE NUTRITIONAL STATUS OF CHILDREN LIVING WITHIN INSTITUTIONALIZED CARE: A SYSTEMATIC REVIEW
Review round: 3
Reviewer: 1

Output:
Basic reporting: Clear and appropriate English Language.
Experimental design: Experimental design well defined
Validity of the findings: Results appropriately presented. The discussion might have been more improved and more focused, according to the previous suggestions.
Additional comments: No major concerns.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: OBAMA CHEZ MOI! THE INVASION OF METROPOLITAN FRANCE BY THE LAND PLANARIAN OBAMA NUNGARA (PLATYHELMINTHES, GEOPLANIDAE)
Review round: 1
Reviewer: 1

Output:
Basic reporting: Please see general comments to the author below.
Experimental design: Please see general comments to the author below.
Validity of the findings: Please see general comments to the author below.
Additional comments: Jean-Lou Justine et al 2019 PeerJ paper.

An interesting and valuable paper resulting from an extensive citizen science project. Publication is highly recommended, though some reorganisation and amendments are suggested.

I am not competent to comment in detail on the molecular part of this paper, though the conclusion seems reasonable.

Detailed comments follow.

Abstract
The Abstract could be much more concise without compromising the paper.
Is it usual to have sub-headings or even paragraphs in an Abstract?

Line 28. Delete “In this paper” and re-phrase this statement to something like:-
“A citizen science survey from 2013 to 2018 yielded 531 validated reports of the presence of O. nungara in 72 of the 96 departments of Metropolitan France.”
Rather than saying “over 500 reports” just give the number, 531.

Line 34: In English, Brittany is spelt with 2 ts.

Line 37: Pyrenees, not Pyreneans.

Line 45: Delete “The present findings strongly” Replace with “This suggests…”.

Throughout the MS: “O. nungara” after its initial mention unless at start of sentence.

Introduction
Much of the first paragraph is not needed.
Could start with something like:
“Obama nungara Carbayo, Álvarez-Presas, Jones & Rutort 2016 is one of several alien land planarian species found in Europe (Sluys, 2016).”

It is conventional to give the naming authority, Carbayo et al. 2016, after the first mention of the species. This should apply to all named species. Does this apply in PeerJ?

Lines 65-67. This is a conclusion, not an introduction!

Line 66: “land flatworm” not “land flatworms”.

Line 77: delete “the numerous”.

Line 81-2. Delete. This is a conclusion, not an introduction.

Line 90: Commas need inserting and removing to read as follows:  “… generally by email and, since 2018, from a dedicated web page…”.

Line 105: “side” not “size”.

Line 109: “…is unlikely” not “are unlikely”.

Results
Some re-organisation is needed. Results from the citizen science data should be presented and analysed in full, followed by the results from molecular analysis (or vice versa). As it is, the the molecular results splits the former.
I question the need for the section on Morphology since the specimens are identified as the species Obama nungara.
Line 185: The “Tiger stripes” described are the result of dorsal pigment overlying each dorsal testis.
Line 195: The section on colour variation is good but it would be good to have some numbers. For example, the dark brown form is stated as most abundant – how many and what proportion of the total? Ditto for other colour varieties. Give data.

Line 199: Delete: “are medium sized” to read: Living adult specimens ranged in length..’

Line 207-210: This should be the first sentence in the Results section.

Line 316 and following. This section should precede the molecular section. There should be a section purely on the citizen science results, sub-divided as appropriate, followed by the molecular results.

Line 317-322: Re-organise this section to something like: “Over the the 5½ years of the project, more reports were received in 2014 and 2018 than in other years (Fig 19). On a monthly basis, more reports were received in May and June and also in October (Fig 20).

Line 323-330. Consider moving this to Discussion

Discussion
Line 329. “…commented upon…”.

Line 333-358. Should this come much later in the Discussion? Discuss the distribution first, then the molecular results – in the same order as the Results section.

Line 360: It is sufficient to state that “Obama nungara has been found in 72 of the 96 Departments of Metropolitan France (Figs 13, 14).
Delete “As shown on the maps” and “has invaded a large part of Metropolitan France and.”. These are redundant words.

Line 373. Records from above 250 m altitude were “very rare”. How many and what percentage of the total? Fig 15 might be more clear with a logarithmic Y-axis. Alternatively give the data as a table including percentages.
Abbreviate Figure 15 to Fig 15.

Line 378. Insert comma after bracket to read: “…(369-458 m), below…”.

Line 380: amend to “...freezing, more likely at higher altitude”.

Line 383: “…is impressive.”

Line 434: (Fig 21) not (Figure 21).

Conclusions
This is more a Summary than Conclusions. It is almost a repetition of the Abstract.
Line 439: Suggest: “Records over five and a half years resulting from citizen science show that O. nungara has been recorded from more than two-thirds of Metropolican France departements, with the exception of mountainous areas. Hundreds of of specimens may be found in a single garden. It is estimated that potentially about 1000 individuals per day per hectare could be produced by sexual reproduction.”

Line 440. “two-thirds” not “two third”.

Line 443. Delete “and” between “per day” and “per hectare”.

Figures.
Generally excellent.
Figure 20. Could error bars be included – or some indication of the difference between years? Perhaps the X axis could be months from start to finish over the 5½ years.

Table 2 Small amendment suggested as follows:
Ireland	2009	H. D. Jones, personal communication (col. & ID: R. Anderson).

Table 5. It is usual to give Mean ± standard deviation.