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: ASSOCIATION BETWEEN MATERNAL PRE-DELIVERY BODY MASS INDEX AND OFFSPRING OVERWEIGHT/OBESITY AT 1 AND 2 YEARS OF AGE AMONG RESIDENTS OF A SUBURB IN TAIWAN
Review round: 3
Reviewer: 2

Output:
Basic reporting: None.
Experimental design: None.
Validity of the findings: None.
Additional comments: I have no further 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: EVALUATING THE UTILITY OF CAMERA TRAPS IN FIELD STUDIES OF PREDATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: I reviewed a previous version of this manuscript and was pleased to see that the authors have made improvements between iterations. I maintain that this is an excellent idea that represents a potentially useful and informative advancement on replica studies. The writing is clear and unambiguous, throughout.

However, the Introduction requires a short paragraph on the ecology of snakes and, specifically, the snake replicas used in this study, to provide much-needed background information that would inform subsequent inferences. For example, are any highly venomous? If so, this could have implications for the assessment of ‘predation’ where it is instead recontextualised as disabling a potentially dangerous snake. Further, the Discussion is poorly referenced, with few calls to existing literature.

The structure of the article is appropriate, but the Results section is, unfortunately, extremely thin.
Experimental design: The study is original and within the scope of PeerJ. The research question is acceptably defined, though there are no explicit hypotheses and the context of 'predation' is contentious (see Validity of the findings). The experimental design is appropriate, though a number of relevant details are missing from the Methodology. The novelty of the study is clear and there were no ethical issues.
Validity of the findings: No statistical analyses were carried out, despite many potential avenues of investigation. Nevertheless, the findings were broadly valid. The structure of the data provided in Supplemental Information made assessment difficult and I would recommend revision of that particular document. The Conclusions are appropriate. However, both the Discussion and Conclusions are let down by their narrow scope. There is little consideration of how this methodology could be of benefit and fill knowledge gaps beyond simple making artificial prey studies ‘better’.

I am not convinced by the author’s loose definition of ‘predators’ and ‘predation’ as it is not clear that all detected species truly constitute predators of the snakes, or replicas thereof. Further, there is no discussion of the relevance of species’ traits and ecologies and how this informs interpretations of observed behaviours. I suggest that the paper is re-cast, reconsidering the validity of statements about predators and predation.
Additional comments: Abstract

L29-30: The use of the word ‘prey’ confuses things. I suggest replacing with ‘replicas’. Further, ‘unmarked’ has no prior context in the abstract and requires explanation
.
L36: I don’t think the authors need to mention subsets in the abstract – this is a methodological note that can be brushed over, here.

L39-40: This is a broad statement and I’m not convinced that it is supported by the findings. It would be more appropriate – and accurate - to say that videography can be used to study artificial prey experiments and associated predator behaviour.

Introduction

L67: The reference can be removed from this sentence as it is invoked for each of the three noted shortcomings.

L104-108: These are methods and shouldn’t be placed here. This section also requires hypotheses, if any were generated (I’d assume that they were).

Materials and Methods

L119: Which species, specifically? Table 1 notes phenotypes but also “4 Micrurus species”. The authors should provide pictures of the real snake vs the replica in Supplemental Information to facilitate reproducibility and synthesis. What impact does using various morphs have in multi-species communities (e.g. might some be seen as a greater threat/more viable prey than others)? How many replicas were placed in each location? If this varied, why? How far away were replicas from cameras?

L132-143: Was camera placement random or according to certain features, e.g.  paths? If the latter, what impact does this have on detection probability by certain species? What was the average distance (± SD) between cameras?

L144-149: Were obvious redetections also omitted? For instance, if a herd of peccary leave the area on 29 minutes and more peccaries turned up – from the same direction in which the others left and with the same number of individuals – on 31 minutes, was that counted as a new detection?

L152-153: There’s a big difference between ‘capable’ and ‘likely to’. Also, this is playing with the definition of ‘predator’. Predators prey on other species. Is a lethal interaction between a bird (where predation has not been previously observed) and a snake where the snake is not consumed or carried off truly predation? Perhaps the authors should reconsider recasting the paper as an exploration of interactions with replicas, rather than a study explicitly focused on predation.

L155: Table S1 appears to be incomplete. There is no information for Tiputini Biodiversity Station, Orellana, Ecuador.

L155-156: Why were markings left by these species omitted? The authors already use a loose definition of ‘predation’. Were any of these markings particularly damaging or potentially lethal? Was recorded behaviour indicative of precautionary or otherwise aggressive behaviour? If so, there doesn’t seem to be a good reason to leave them out of the manuscript.

Results

While the authors state that “predators were more often observed to avoid replicas…”, there has been no attempt made to quantify this statistically. There are many models that could be explored with these data, including: mammals vs birds (attacks); mammals vs birds (cameras); damaged vs undamaged; attacks vs avoidances; differences between sites; differences between replica morphs within sites; etc.

There are also more fundamental metrics and associated plots than could be described and provided. For example, what was the time-to-detection for each putative predator (and, for the Discussion, how might this be influenced by local population densities and detection probability)? How many detections of each putative predator? This is in Supplemental Information, I know, but this is relevant information that should be described here, along with bar plots (a,b,c for each site). What was the temporal pattern of interactions (perhaps a kernel density plot for each site)?

There is also an apparent discontinuity between attack counts. For example, 170 attacks were counted from clay markings compared to 6 from cameras, across 54 detections in Mexico. How were clay marks counted? Further, the authors state that gray foxes, opossums and armadillos were the species identified as interacting on camera footage while clay marks showed avian attacks. This should be acknowledged and discussed – were bird attacks simple not captured by the cameras?

L184 & 204 & 228: I don’t see the relevance of pointing out how many cameras did not detect interactions.

L195-197: Why wasn’t the area searched more thoroughly in the first instance? 4m is not a great distance.

L197-200: The field categorisation is incorrect, as-read as it seems that the replica sustained damage. There is a big difference between ‘not attacked’ and ‘we could not identify the attacker’.

L220: Redundant; delete.

Discussion

L263-270: The authors note that their findings have ‘implications’, but are there any beyond increasing statistical power? What about ecological interactions between species?

L275: Rephrase, avoiding the implicit suggestion that the bias might be trivial.

L281-282: This is unconvincing. Just because a predator appears from a different direction, that does not mean that they did not detect scent. Also, predators can follow human paths, regardless of scent.

L288: “… would [likely] increase…”

L291-293: This is based on the assumption that real, mobile animals are encountered by apparently oblivious species as frequently as immobile replicas. Further, while I agree that previously unobserved interactions between species may be important in shaping morphology, etc., it is a bit of a stretch to suggest that a species that ignores a replica is a candidate for shaping the anti-predator behavioural repertoire of the real thing.

L299-303: Combine costs and present one figure per site. Batteries and SD cards are essential, after all.

L308-312: This invites a question regarding the cost and feasibility of DNA analysis. The authors also need to provide a more thorough justification for camera traps, e.g. conservation relevance, developing new questions, etc.

L316-317: Why might this be?

L321-322: Was this done during the current study? It might be useful for the authors to provide information on the costs of their study with and without camera traps.

L324: The use of transects should be mentioned in the Methods.

L325-328: This is also detail missing from the methodology.

L330-341: This can be abbreviated by recommending field trials for appropriate camera settings.

L334: How did new captures and a full SD card cause the loss of previous data? This doesn’t make sense.

Conclusions

L364-366: I agree, but this doesn’t logically follow from the findings of this 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: EVALUATING THE UTILITY OF CAMERA TRAPS IN FIELD STUDIES OF PREDATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Camera trap videos have been underused in predator-prey experiments and could contribute a great deal towards our understanding of how prey characteristics influence predator response. The authors use data collected as part of three experiments from Ecuador, Mexico and the USA to demonstrate the superior ability of video footage to characterize predator behavior, when compared to the traditional methodology.  Overall, this manuscript is well written and topical.  However, the authors have included some extraneous information, which provides context and site-specific details, but is unnecessary for delivering the overall message that the use of videography in aposematic/mimetic model experiments greatly improves the ability of investigators to study predator-prey interactions in multi-predator systems. The authors should spend some additional time editing the discussion and Table 2 with an eye toward eliminating any unnecessary details.  I have included some specific comments below.

30: “unmarked prey” word choice—easily confused for mark-recapture nomenclature—perhaps something like “prey replicas that have not been damaged by predatory attacks.”
129-130: Need full names of museums—either in text or supplementary materials
163-164: Clarify
204-207: Need to some clarification of these numbers of detections/attacks reported here.  There were only 54 events were predators were detected on camera, but there were 92 attacks made by mammalian predators and 78 attacks by avian predators.  It is not clear how these numbers add up.
229-231: See previous comment
298-303: Discussion of the cost of cameras at scale of entire experiment is unnecessary.  It would be sufficient that say that for some experimental designs the cost of cameras may be prohibitive.
317-322: Discussion of additional set-up time/transportation costs is also unnecessary.
323-341: This paragraph may also be unnecessary.  While specific use-case suggestions may be helpful to some readers, these details are tangential to the main message of 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: SUCCESS OF CONCRETE AND CRAB TRAPS IN FACILITATING EASTERN OYSTER RECRUITMENT AND REEF DEVELOPMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is an interesting manuscript investigating the use of two different substrates for oyster reef restoration. The results from this study are highly applicable to scientists and restoration practitioners in the Nature Coast. Although the Introduction provides context for the research question, there are quite a few typing errors, missing references, use of extra words and lack of flow between topics and paragraphs that could easily be fixed with a few more rounds of rigorous editing by the authors. The Figures and Tables are relevant and easy to understand but see specific comments and suggestions below.
Experimental design: This article presents original primary research and the methods are easy to understand. The methods are provided with sufficient detail and information to replicate. See additional comments below.
Validity of the findings: The Discussion of this paper is quite strong and results are linked to previous research. The impact of these findings could be improved with further explanation of key research areas that are the foundation to this type of research (i.e. long history of testing oyster reef restoration substrate materials). Specific comments included below.
Additional comments: Major comments:
There is a large body of literature investigating oyster recruitment and reef development in response to a variety of substrates. There is some discussion of substrates in the second paragraph of the Introduction (lines 61-75) but this is mainly to do with reef restoration over longer time scales when in this study oyster recruitment and growth were monitored over a 22 month period. The authors should provide further background on the mechanisms (i.e. shading, chemical cues) that might influence initial oyster recruitment to concrete or wire substrates as these initial differences will have a large impact on overall community development.
Similarly, further justification for the decision not to control substrate material (by dipping crab traps in concrete) is needed. There is reference to a few research chapters that have done this (though one reference is missing, see below) but without further description of the results from these other studies, the results from this study seem premature. For example, did the other researchers find similar recruitment to and growth on concrete coated crab traps vs concrete blocks or concrete coated crab traps vs bare wire crab traps?
Generally, there are a few key concepts in oyster reef restoration, oyster settlement and growth that should be further described. They are: the impact of substrate type on recruitment and reef development; how chemical cues of other substrates (i.e. non oyster material) influences oyster settlement; oyster recruitment on shaded vs open surfaces; and how the vertical height of reefs and restoration material may influence oyster feeding, growth or susceptibility to disease. Additionally, statements about the longevity of using bare wire crab traps rather than concrete dipped crab traps would help make the results of this manuscript applicable to restoration practitioners domestically and internationally. The authors mention that the wire crab traps survived a hurricane, but realistically how long do these wire traps stay intact inter or subtidally? Derelict crab trap clean up programs might be able to help estimate this duration. Where solid concrete, or rip rap based structures are generally good foundations for oyster reef restoration, information about the durability of crab traps as the foundation of reefs will allow scientists and practitioners to determine if this in fact a suitable alternative.
Some references that might be helpful are: Dunn et al. 2014 “Effect of substrate type on demographic rates of Eastern oyster (Crassostrea virginica)”; Soniat et al. 2004 “Vertical structure and predator refuge mediate oyster reef development and community dynamics”
Line 31: Missing “the” in “However, due to relatively open structure”
Lines 56-59: This sentence should be restructured or split in two to improve flow between the previous sentence and the next paragraph.
Line 60: Try to not to start sentences, let alone paragraphs with “Because”
Lines 62-63: Check for consistency in spelling of referenced author “O’Beirn”
Line 64: Are there references to support this sentence? References from the previous sentence likely mention these material so the two sentences could be restructured.
Lines 106: change “low costs” to “low cost”
Lines 108-110: Further explanation of this concept needed. How does dipping crab traps in concrete enhance their surface area? Does it strengthen it? Provide chemical cues more similar to oyster shell? Improve the longevity of the structure? Etc.
Line 110: Kingsley-Smith 2012 is a very critical citation that I tried to find but it is missing from reference list
Line 115: Based on the introduction it appears that evaluating the use of crab traps in oyster restoration is an unexplored field. Why limit the applicability/findings to the Nature Coast?
Line 127: If I am interpreting this hypothesis right, “intraspecific” should be changed to “interspecific”
Line 130-131: This statement should not be part of the hypothesis and could instead by included in the abstract or conclusions.
Line 143: The deployment date and experiment duration is hidden in this sentence but should be more clearly stated, especially if these results will be used to inform restoration projects. I suggest re-working this first paragraph of the Methods section to state “We deployed this field experiment in August 2015 on five offshore... for a period of 22 months…” to improve clarity. Also, I would recommend stating the number of months into the experiment the region was impacted by Hurricane Hermine rather than “mid-way”.
Lines 146-168: This paragraph could be split into multiple paragraphs.
Line 170: Rather than stating just the actual dates monitoring was conducted, the number of months after deployment would also be useful.
Lines 248-250: I find this sentence a bit confusing. Aren’t you more interested in the oyster percent cover? Why this focus on barnacle cover? I agree that barnacle cover is likely to increase if oysters aren’t present but this study was investigating the use of structures to facilitate oyster growth & reef development.
Lines 265-270: I would prefer to read these results within the text rather than a Figure. The percent change in oyster reef volume and final oyster biomass could be presented as in-text values.
Line 308: There is reference to “main factors influencing oyster and barnacle cover” that were identified elsewhere in the Results or Discussion. What are these?
Lines 324-333: There is a large focus on the production of market-sized oysters in this section. However, is the deployment of these restoration structures (concrete or crab trap) intended to provide harvestable oyster populations or instead provide healthy oyster populations that can supply larvae to nearby harvesting reefs? If these restored reefs aren’t intended to be harvested, then we should instead be interested in when oysters reach sexual maturity (i.e. in the juvenile oyster size range) rather than market size. If these reefs are intended for harvesting, then this should be clearly explained in the introduction. This would also lead to further questions I have about the durability and longevity of using wire crab traps if they must also withstand hand-harvesting pressures.
Line 333: remove “however” at the end of the sentence.
Line 360: This sentence starts to address some of the questions I have about the differences in vertical height between the concrete and crab traps and how this influences reef development and oyster survival, but is not fully explained. Rather than just referencing other papers that have discussed how elevation or vertical reef height influences oyster settlement, mortality and growth rates, can you also provide some explanation as to why? Is it because of increased temperature or desiccation stress? Altered water flow or wave exposure? This could perhaps be discussed in a separate paragraph within the Discusison.
Line 491: La Peyre et al. 2014 reference out of place.


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: SUCCESS OF CONCRETE AND CRAB TRAPS IN FACILITATING EASTERN OYSTER RECRUITMENT AND REEF DEVELOPMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: I congratulate the authors on a well constructed manuscript, which I found pleasant to read and easy to interpret. The language was unambiguous, but at times a little long-winded. More concise, active voice would make parts of the introduction more engaging.

Comments by line:
Line 55 – as written it is slightly ambiguous what Grabowski’s evaluation relates to here. I would say something like “services which are collectively valued between…”

Line 56-57 – wow that is impressive!

Line 60-61 – true, hard substrate availability is the major limiting factor to recovery where there remains high spat fall (such as the southern states), but at many sites water quality, disease and limited spat fall restrict recovery. Suggest you clarify you are talking about a system where spat is not the limiting factor, at which sites provision of hard substrate is the primary strategy for restoration.

Paragraph starting line 76 – this paragraph is very region specific and of limited interest to the broader readership. I think generally discussing the environmental change/threats that are relevant to oyster decline in this area (i.e. changing freshwater flows, sea level rise) may appeal to more readers. You can then discuss the local context later in the introduction, and how this region is an area where these threats must be mitigated.

Line 106 – low “cost”, no plural

Line 106-108 – more concise language could reduce this sentence by about 10 words. E.g. “Repurposed crab traps are cost-effective structures for oyster restoration because their expense is limited to transportation and installation costs”.

Line 115 – “never been valued in the Nature Coast”. Again, these paragraphs are very site specific, which will limit the ever growing international readership interested in oyster restoration.

Line 120 – I am glad you monitored intraspecific recruitment of barnacles, but can you extend this to other fauna? One of the primary concerns of deploying substrate/structure in the environment is whether it unintentionally facilitates “undesirable” species, namely invasives. Surveying the complete faunal assemblage recruit to each structure could address this. Furthermore, from a restoration viewpoint, where we are trying to enhance the fitness of the oysters, I would be particularly interested in whether these structures facilitated oyster predators, such as crabs, which could negatively impact oyster performance.

Line 144 – that is a positive result if the concrete structures can withstand hurricane forces. Did the hurricane not impact the crab traps? As hurricanes are a persistent issue in the region and you inadvertently examined their impact on restoration structures, do you discuss this further?

Line 157 – “likely similar to other concrete-based materials”…a point of reference for what you expect will be similar to other concrete structures. Oyster abundance/m2?

Line 333 – remove “however”

349-341 – I am glad you mentioned this. To my mind this is a missed opportunity for your study, because quantifying predation (structures attracting predators vs provision of a predation refuge – inside the crab trap looks like a good place to live!) would allow restoration practitioners in different systems to apply this knowledge to their known compliment of predators.

368 – I think it’s tricky to talk about “sustainable materials” – perhaps true for abandoned crab traps, certainly not for concrete production. I think “opportunistic materials” is more appropriate.

Line 371-372 – “…recycled for oyster restoration as long.” As long what? Advocating hauling concrete from demolished buildings to place in the intertidal for restoration sounds like a hard sell. There may be opportunities from time to time, but not as a environmental management strategy.

Line 374: “obstuct” . Also, couldn’t they potentially trap fauna once they partially erode?

Figures could be sharpened up a little by greater distinction between colours on the bar graphs, and fewer tick marks on the x-axis of the Fig. 2. In the legend for Fig. 2, should it say “5 treatment replicates”, as it is the substrate treatment that is replicated. As it reads it suggests there are 5 treatments per substrate type.
Experimental design: I think the design and execution is fine if purely interested in oyster-structure interaction. But I feel not collecting more biological (facilitated species assemblage, predation rates) or environmental data (temperature differences between the intertidal structures, sediment scour/erosion impacts of structures) is a missed opportunity to expand the relevance of this study to other habitats and biological systems.

Line 163-164 - A short explanation as to why all crab traps were not the same size would be good.

Line 170 – I’m a little confused about the sampling frequency and dates. On line 143-144 you state the experiment ran from Aug 2015 till May 2017, though you sampled after this in June 2017 (line 171). I am struggling to see a defined pattern for your sampling frequency, so a little clarity on this would be good. Personally, I find specific dates like this distracting. I would be more inclined to say something like “After establishing the experiment in August 2015, we initially collected data after one month, and then approximately every 12 months until it’s completion in …”

Line 175 – that is 6 quadrats were replicate concrete structure? Please clarify
Validity of the findings: The results section and data discussion are clearly written. I am satisfied with the data and information provided in the supplemental materials. The statistical approach is well reasoned.

Conclusions are clearly stated. I particularly like how they hypotheses were partitioned first in the introduction, which help me interpret the results later.
Additional comments: I have two major concerns with this work. The first is the extremely narrow focus on the circumstances of the Nature Coast. Yes the local circumstances drove the design and opportunistic use of crab traps, but the introduction and overall focus needn't be so site specific, which disengages those unfamiliar with your system. I suggest that the discussion of using alternative materials to those typically used to restore oysters (i.e. shell) takes center stage, and your site and region are described as the vehicle to test these materials.

The second issue, and the more limiting, is the missed opportunities to quantify other biological and/or environmental responses to the structures. I believe this is important because environmental restoration efforts should be underpinned by evidence based reasoning. The authors pay little mention to how each structure influenced the surrounding abiotic environment, some impacts of which may be negative. For example, wave action around the intertidal concrete structures would likely scour the surrounding sediment, potentially altering the immediate benthic environment or impacting downstream sites. Further, little attention is paid as to how the two structures provide extremely different environments for the oysters. For example the concrete would likely store substantial heat when exposed to the sub-tropical sun, such that substrate heat stress would impact the oysters. Meanwhile, the crab trap would likely provide a predation refuge from larger predators (i.e. fish and crabs), but it may also facilitate meso-predators (who may also benefit from the predation refuge of the trap. My overarching concern here is, if we advocate the re-purposing of disused concrete (i.e. from demolition sites: line 371) to place in the marine environment, we want to be very sure there will be no negative environmental impacts (e.g. navigation hazard, chemical leaching, facilitating invasive species), otherwise it is more environmental vandalism than restoration.


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: SUCCESS OF CONCRETE AND CRAB TRAPS IN FACILITATING EASTERN OYSTER RECRUITMENT AND REEF DEVELOPMENT
Review round: 1
Reviewer: 3

Output:
Basic reporting: Overall the manuscript is well written, but in some places the English is a little awkward and could do with some improvement - e.g., lines 42 to 48 - over dramatic language and clunky description of the issues involved - could be streamlined.

Referencing is appropriate and breadth of literature well used

Article structure is sound and self contained.
Experimental design: Fits within aims and scope of journal

Research question is well defined in terms of a knowledge gap, however, it is very unfortunate the experiment did not include a comparison with traditional oyster restoration materials, such as bags of shell so that an appropriate comparison could be made to provide broader relevance.

In terms of the experimental design - the 5 replicate structures for all treatments were all in a relatively confined area so it is hard to assess whether the results have wider applicability other than for this localised site.

One crab cage was a different size and it is not clear how this possible influence on the results was dealt with in the experimental design.

The duration of the experiment is relatively short so the persistence of the structures would be interesting to follow especially at the crab pots were likely to be breaking down.

Ethically I have concerns about altering the natural coastal environment with concrete and waste crab traps- are these zinc coated wire traps which would leave a toxic residue in the marine environment, or plastic coated, which would leave plastic waste in the marine environment. This requires some commentary at least, as in my part of the world dumping concrete and waste crab traps in the coast environs would be unacceptable and would not be permitted by regulatory authorities.
Validity of the findings: The results have value for oyster restoration, but are somewhat limited in scope in my view by the lack of measurement of the results over a wider spatial scale to confirm they are consistent, and not a localized phenomenon. Furthermore, the lack of comparison with oyster shell limits any assessment of the comparative performance with traditional enhancement approaches.

The data is well collected and the analyses look entirely appropriate to me. The results would benefit from reporting of more information on the scale of measured comparative differences in results.  e.g., "Similar to oyster cover, barnacle cover also did not vary
between landward and seaward sides of the structures." - we don't actually know what the amount of measured cover is for each of the structures at different heights.

Conclusions are sound and well founded on the data presented.  The conclusion I found quite long given the extent of the research results and its relative significance.
Additional comments: This is a well presented manuscript that is of some relevance to oyster restoration efforts.  I have outlined some of my points in preceding sections of the review and these should be shared with the authors.


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: TUMOR MUTATIONAL PROFILE OF TRIPLE NEGATIVE BREAST CANCER PATIENTS IN THAILAND REVEALED DISTINCTIVE GENETIC ALTERATION IN CHROMATIN REMODELING GENE
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: It is not clear which material was used in the study: primary  tumor tissues and/or metastatic lymph nodes?

It appears that lines 173-178 should be transferred to the section Study Population.
Validity of the findings: The study result showed that Thai TNBC has higher tumor mutation burden than previously reported data (ref. 10-12).  But the authors compare their results with data from three other studies that have a different design. The analysis in those studies was carried out with the involvement of not only tumor, but also healthy tissue (matched tumour/normal pairs). In this way, germ-line genetic variants could be distinguished from somatic mutations and excluded from analysis. Moreover, in the at least one study (ref. 12) the frozen tumor material was studied. In the other two articles, unfortunately, data on the material is not presented. Formalin fixation leads to significant changes in DNA. Do the authors believe that such differences in design could lead to a higher tumor mutation burden?

I can’t fully agree with the statement lines 223-226. A large number of examples have been described when synonymous mutations are significant for carcinogenesis and lead to the synthesis of mutant proteins. So they can create neoantigens and trigger immune response too. See Cell. 2014 Mar 13;156(6):1324-1335. and EMBO Mol Med. 2016 May 2;8(5):442-57.
Additional comments: Line 156: It is necessary to clarify the abbreviation.


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: TUMOR MUTATIONAL PROFILE OF TRIPLE NEGATIVE BREAST CANCER PATIENTS IN THAILAND REVEALED DISTINCTIVE GENETIC ALTERATION IN CHROMATIN REMODELING GENE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Structure article and English language conforms to requirements
Experimental design: Experimental design is standard for this kind of research
Validity of the findings: The results are consistent with previously published data and complement them with new ones. The limitations of study  have been described honestly.
Additional comments: The surgically removing  primary breast tumors and lymph nodes is standard treatment described in the "Methods" (lines 112).  In order to avoid misunderstanding I recommend the authors to describe in more detail which samples were analyzed (primary tumors or lymph node metastases).


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: TUMOR MUTATIONAL PROFILE OF TRIPLE NEGATIVE BREAST CANCER PATIENTS IN THAILAND REVEALED DISTINCTIVE GENETIC ALTERATION IN CHROMATIN REMODELING GENE
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: Thank you.
I am satisfied with the answers and agree with the corrections.


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: TUMOR MUTATIONAL PROFILE OF TRIPLE NEGATIVE BREAST CANCER PATIENTS IN THAILAND REVEALED DISTINCTIVE GENETIC ALTERATION IN CHROMATIN REMODELING GENE
Review round: 2
Reviewer: 2

Output:
Basic reporting: Structure article and English language conforms to requirements
Experimental design: Experimental design is standard for this kind of research
Validity of the findings: The results are consistent with previously published data and complement them with new ones. The limitations of study have been described honestly.
Additional comments: Comments taken into account. The manuscript made all the necessary amendments. Article recommended for printing


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 NARROW LINEAR CLEARINGS ON MOVEMENT AND HABITAT USE IN A BOREAL FOREST MAMMAL COMMUNITY DURING WINTER
Review round: 1
Reviewer: 1

Output:
Basic reporting: In general, the author used clear and unambiguous, professional English throughout the paper. However, it was not as concise (i.e. short and to the point), as I would have liked to see. Sentences were unnecessarily long.
Abstract: Very interesting findings, but it reads like a discussion. I suggest adding structure to your abstract – 2 lines for intro, methods, results, and discussion. Followed by a conclusion of preferably one line that tells your reader why these findings matter within a global / conservation context.
Structure – the article will benefit from added structure throughout the paper. I have mentioned specific points and suggestions in the sections below
Introduction – Take care to put your most important word / phrase first in a sentence. Most readers do not read entire sentences, but only skim over the most important pieces, which they think should be in the first part of a sentence. For example, the first paragraph of the intro is about fragmentation. Hence, I suggest starting the first sentence of this paragraph with the word – fragmentation. Similarly, the second paragraph is about how type of linear clearings influence animal movement. Hence, I suggest starting this paragraph with ‘Different kinds of linear clearings …’ or something similar.
Last paragraph of the introduction – please start with an overall aim, and then list specific hypotheses / objectives of the study. For example, ‘the overall aim of this study was to determine how non-road linear clearings affect mammalian species of different sizes and trophic levels. The specific hypotheses were 1) that large predators will use linear clearings more than small predators, 2) …’
Results – improve structure with sub-sections addressing each of your original hypotheses listed in the last paragraph of the introduction. Suggestion: 1) SL vs. forest transects: effect on species and different functional groups, 2) SL vs. forest transects: mode of travel (approach vs. cross vs. linear travel), and 3) SL vs. forest transects: effect on snow surface.
Figures and tables – all of the information is there. It just needs a bit of reshuffling.
Table 1 – where it was not possible to discern among species’ tracks within a group (e.g. weasels), and the group comprises of more than one species, list the species as follow: X, Y AND Z. Do this for deer too. Then, refer to the specific group (e.g. weasels and deer) in the main text, and not to the individual species (e.g. termed mule deer and white-tailed deer) within that group. Remember to refer to the supplementary tables in the main text.
Figure 1 – I suggest separating Fig 1a and 1b, and writing a caption for each figure. Key – symbols and words should be in the same line. Figure 1a and 1b – the ‘a’ and ‘b’ should be in the upper left corner of each map. Symbology for Fig 1a – use ArcMap (or a similar package) to change the different elements e.g. seismic lines, pipelines, roads, etc. This will reduce the clutter in the graph. The north arrow should be on the map to which it applies. It cannot go underneath the key, as it does not inform the reader whether it applies to Fig 1a or 1b.
Figure 2 – suggestion for caption: a comparison of mammal movement and habitat use between linear clearings and forest habitat for different species. Add species to the x axes of all graphs. It would have made sense to only label the bottom graph if this figure did not take up the whole page. However, as it is, I have to scroll up and down to see where significant differences lie.
Figure 3 – apply suggested caption for figure 2 to figure 3, but for functional groups. Habitat use intensity – please correct the y-axis. It will be kind of hard to fit in 2000 meters into 1km.
Figure 4 – please change font size of x-axis and y-axis. Add labels (a and b) for moose/elk and shrew.
Raw data shared – shared and it opens without problems
Consistency: Please be consistent in the use of terms, e.g. linear clearings and seismic lines. I realize that seismic lines are one kind of linear clearings, but you have to pick one term and use it throughout the manuscript to prevent confusion.
Terminology: I suggest using the term ‘species’ instead of ‘taxa’. Reason: a taxonomic group can be any group of species or genus or family, depending on your point of interest. It is too general.
Literature – I found it strange that the author did not refer to the papers by Fahrig 2003 (http://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.34.011802.132419), Fischer and Lindenmayer 2007 (http://onlinelibrary.wiley.com/doi/10.1111/j.1466-8238.2007.00287.x/full), or Forman 1995 (https://pdfs.semanticscholar.org/1c15/77b4520d6baadb01857877b9714f6858873d.pdf) about the process and effects of fragmentation. In particular, Forman discusses roads (or seismic lines) as dissection of the intact landscape. I suggest placing the article within the context provided by these papers, or providing good reasons why the author chose not to do so.
Experimental design: Pseudo-replication. The size of the study region was ~ 4000 km2, which is 142 km x 28 km. Seismic lines at a density of 2km/km2. There were 14 replicates. Thus, one replicate roughly every 10 km. Large mammals walk further than 10 km in one day. How did you control for the possibility of spotting the same individuals at different localities (i.e. pseudo-replication)?
The research paper falls within the Aims & Scope of the journal – Biological Sciences.
Formulation of research questions needs attention, as mentioned above for the introduction under 'basic reporting'.
Knowledge gap identified: how non-road linear clearings influence mammals. however, I find it difficult to see at a first glance whether studies cited refer specifically to forest habitat, or rather other habitat types. Please clarify, as communities in forest habitat might respond differently to linear clearings than those in grassland.
Reference to species – refer to them first by their common names and then their scientific names (e.g. weasels (Mustela spp.). Thereafter, you may only use the common name.
Lines 80-83: Very valid hypothesis. How did you come to this ‘general observation’? Is it from literature cited earlier, or is it one of the hypotheses that you wish to test? If it is the hypothesis that you wish to test in this paper, move this sentence to the last paragraph and identify it is a hypothesis. For example, ‘we hypothesize that …’
Methods - all important points covered in sufficient detail to allow for replication. However, this section is very long. I think it can be reduced in length by about one third.
Line 110-112: Did you use the same study area as Pattison et al. 2016? If so, state explicitly. In addition, please add a map of your study area. Note that Fig 1a is not a map of your study area, as the caption mentions that it is just an example of a site.
Validity of the findings: Replication – this is my greatest concern for the whole paper, and I am not sure how to deal with it. If the authors could not reliably differentiate among different weasel and deer species (which I completely understand), I do not see how they could have distinguished among individuals of the same species. Therefore, it is possible that they might have counted tracks of the same individual multiple times. This is especially the case, seeing that they worked with non-primitive animals that can have learned behavior. One wide-roaming individual might have contributed significantly to the data recorded.
Statistical analyses – please mention the software used to conduct analyses.
Data distribution - Did you consider data distribution (normal vs. Poisson)? If so, please state explicitly in the text which variables had a parametric and non-parametric distribution. Because you have count data, I would expect your data to have a Poisson distribution. Repeated measures ANOVA is suitable only for parametric data.
All-in-all, I find the data analyses sub-section of the method section to be too simple. Have you considered using Generalized Linear Mixed Models (GLMMs) in R statistical software? It allows you to define the distribution of each variable, incorporate random variables (e.g. kind of forest, days since last snow storm, etc), and then use a standard approach to compare linear clearings vs. forest transect for 1) habitat use, and 2) type of crossing for each species and functional group. Please add references to papers in which statistical methods were developed or tested.
Control sites were sufficient, as it was a paired design, with linear clearings = treatment and forest transect = control / reference group.
Discussion – very well researched, but very long. It is not always clear when you refer to your own work, and when you refer to someone else’s work. Structure your discussion in the same way that you structured your results i.e. same order as your hypotheses. In addition, 1) start each paragraph with your own findings, 2) which contrasts or agrees with person x’s work, and 3) phenomenon Y might explain this finding. Then, you can mention your snow compaction findings, as a potential reason why species (or functional group) Q use linear clearings more often than forest transects.
Additional comments: This paper has potential to contribute to the growing body of knowledge regarding how animals of different sizes use fragmented landscapes, or alternatively – which kinds of animals are most sensitive to fragmentation. In particular, it focuses on non-road linear clearings where animals respond to the shape of a landscape element, rather than to a threat associated with this landscape element (e.g. traffic on roads). As such, it poses a new perspective of dynamic fragmented landscapes, which could be useful for landscape ecology and landscape management.


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 NARROW LINEAR CLEARINGS ON MOVEMENT AND HABITAT USE IN A BOREAL FOREST MAMMAL COMMUNITY DURING WINTER
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors conducted field work in a presumed remote, difficult to access study area during a time of year (winter) when data collection can be logistically difficult.  The study effort was likely high.  However, the paper as written does not clearly articulate the study design or validity of results.

- Terms were not defined and inconsistent with the literature.
- References appeared selective, but I did not check these extensively
- Findings and raw data seem unrelated to biologically meaningful results.  For instance, there are 36 occasions with >100 red squirrel tracks.  Assuming some territoriality, each of these occasions likely represented 1-3 squirrels within a kilometer.  Using tracks as an index of use should have careful study designs, standardizing or accounting for time following snowstorms.  For instance, Halfpenny (1994) recommended all tracking be conducted within 72 hours of a storm.  Also see notes and suggestions within general comments.
Experimental design: - Experimental design and site selection was not explained.
- Research question defined, but data not collected to a high technical standard as explained
- Methods do not contain enough detail to replicate study (see notes within general comments)
Validity of the findings: - Data does not appear statistically sound.
- Conclusions are not consistently linked to data or results.
Additional comments: Introduction in general:
There are several words that have meanings in the literature that are either odd or incorrect throughout the manuscript.
I’d either further explain, or tone down the functional group concept for which most of the paper is based on.  You lumped species by size and whether or not they were plant vs meat eating essentially.  In each category, those classes should not behaviorally similar.  For instance, large predator (grizzly bear, cougar, gray wolf, coyote, lynx) encompasses every strategy, e.g., cougars are sit and wait predators, wolves are social pack animals, lynx are solitary specialists.  You would expect each species, based on the literature, to use seismic lines differently.  You’re ignoring behavior (and the “functional” group) and testing whether species by size and diet class is more influential.  You explain this in paragraph 66 stating that functional groups might not be the best approach and focus your paper accordingly BUT you use the term functional group in your abstract (line 27), suggesting that these are functional groups – they are not.
You often use the word habitat to mean vegetation or patch.  Habitat could be defined as:
•	a distinctive set of physical environmental factors that a species uses for its survival and reproduction that produce occupancy (Hall et al., 1997; Krausman and Morrison, 2016)
•	“the resources and conditions present in an area that produce occupancy, including survival and reproduction, by a given organism.  This includes more than vegetation structure, but the sum of specific resources” (Krausman, 1999)
•	“the set of resources necessary to support a population over space and through time” (McComb, 2007)

Here, there is no information on survival, reproduction, long term resources, nor do the data ever have this capacity.  As such, the term habitat seems inappropriate.  The term “habitats” is nonsensical.  The term functional habitat (e.g., line 29) is confusing and even more incorrect, confusing the reader with the functional group phrase (neither are functional or defined as such). In short, these diverse animals are not using habitat (e.g., seismic lines) unless you can convincingly determine that each species is using the area for increased reproduction or survival – movement is different.  We can swim across a lake, traveling entirely across or entering briefly and exiting.  Neither event would make the lake human habitat. Consider forest, patch (and define patch), or the actual description of what you’re describing.
You are sampling animal movement trajectories during winter in areas that differ in forest cover and configuration.
Specific comments:
Line 23: First line – “internal fragmentation” does not make sense. Fragmentation obviously increases the number of patches and reduces the amount of “core” area, but here it is not defined.  Is “internal” something that is >5km or 50m from any disruptive feature?
Line 57: “Open habitats” is an incorrect use of the term habitat (please see Krausman and Morrison 2016, Hall et al. 1997).  Similar issue line 62, 93, 146,   .

Line 80: Define mammal functional groups.  Is large predator a functional group?  This premise is unclear within the paragraph and throughout.
Lines 116-119: This would be a good location to describe a seismic line for the reader – how wide?  How long?
Lines 122-130: How were the 14 replicates selected?  Were these a random sample, stratified random, or selected?  How did you account for differences in seismic width?
Lines 132-135: Here, you suggest that sites were maximizing spatial dispersion (ave = 6km distance, maximum = 12km).  However, for all large and mid-sized carnivores and larger herbivores it would be easily conceivable for the same individuals to occupy multiple transects.  I’d consider a new Figure 1 with panels – one that shows the locations of these sites spatially and a demonstration of how the surveys were conducted.
Line 135: what is original coniferous forest cover?
Line 136-9: Can you more clearly define what you mean by average forest cover affecting sites?  I’m assuming that you mean your sampling estimate of forest cover.  Even so, it’s not clear why you would mention this and what it’s in reference to.  Are 2 sites with linear seismic lines covered in 6m high trees and thus are no longer open?
Lines 143-146: I think I can understand what you’re saying here, but it’s not clear.  You have 2 treatments: open seismic line transects and perpendicular forested transects, presumably with fairly closed canopy which is why you mentioned 98% canopy cover (line 138).  I’d strongly recommending spending more time on the study design and purpose, clarifying your two treatments with clear and consistent diction.  For instance, you can set up
-	Where sites were chosen
-	How sites were stratified – are all similar, or are you accounting for width and type (e.g., you mentioned seismic lines with propane)
-	How did you pick your direction and placement of the perpendicular forested transects?  Are these always central, creating a “T”?  Do they always stem to the west like shown in figure 1?
-	What were the conditions of the open and forested transects
o	Canopy cover
o	Tree size
o	Tree height
Lines 147-152: Can you further explain your snowtracking methods?  Did you use suggestions by Halfpenny (e.g., Halfpenny 1994)?  How was the snow measured?  Was the survey medium the same during all 6 surveys?  What was the duration between storms?  Do you expect any difference in detectability between surveys?
-	Since you did repeated surveys within a season, were they at the same locations?  For instance, did you resurvey the 14 sites EACH time (9 surveys x 14 locations = 126 tracking opportunities) or did you go to some of the sites on each survey?
o	If you went to different sites each survey, how are you accounting for differences in timing?
o	If you went to the same sites each time, could you use an occupancy model to verify that your detectability was high?
Line 154: How was an observer trained?
Line 158-160: This might be better clarified in the introduction with citations why you chose these categories.  Can you use these data to compare to other studies and test their predictions?  It seemed like the introduction was moving towards larger hypotheses, so it would be helpful to explain why and how.  It’s also odd – why wouldn’t large herbivores also be >10kg to match the predators?  Why are mid-sized predators and herbivores different sizes?  Seems like you had a plan… but explain for the reader.
Lines 163-168:  Explain to the reader why 10m?  Why is this relevant?  You’re using the same methods for diverse species but that seems odd.  10m to a shrew is much different than 10m to a wolf.  10m to a wolf is 2-3 strides, perhaps 10 seconds of the animal’s day.  Does it ecologically matter to a wolf whether during that moment it was moving along or across?  It might, and it would be great to explain how you are accounting for size (aside from clumping groups by size). In pondering, the way that you would be able to increase meaning is by increasing sample size.  If the animals are similar across all 14 sites, or across 100 sites… then you have a pattern.  Here, it’s not clear why you are collecting data and what pattern you expect to see.
Line 179: here is the first time you mention the width of a seismic line.  That is WAY too late and offhanded for a paper founded on the study of seismic lines.  Incorporate in the introduction or early methods.
Lines 176-182: These metrics seem mostly logical, but also created.  Are there no movement metrics in the literature that could be compared or used?  Did you take path measurements to calculate turn angles for instance?  I’d justify these methods a bit more.  Because they are logical, I think you can make a case.  I’d also write in the active voice.  Instead of “crossing propensity was calculated as” say “we estimated an index of crossing propensity as”
Line 185: clearfell forest harvesting is not defined or cited.  It’s also unclear why harvesting reduced your transect length?  Do you mean you created a forest transect and during the study the forest was cut – thereby decreasing your ability to survey?
Line 189: Can you define (earlier) your fundamental unit of measure?  Is a track a footprint or a path?
Line 190: Ah… snow measurements.  I’d put this section earlier during the tracking portion.  This is great, but it’s not clear how and why this is used in the analyses.
Line 199: How would a repeated measures ANOVA tell you differences by taxa?  Wouldn’t it merely show a difference in time and not by subject (species)?  Or did you do this separately by species?
Line 201 – this suggests you resurveyed each of the 14 sites each year, but your methods suggest you had 2 surveys in year 1, 4 in year 2, and 3 in year 3.
Line 207: Paired t-tests seem okay if you have a single response variable for a single paired question, but you likely have correlations between species within site at between sites.  I suppose you can do a multiple comparison correction (e.g., Tukey, Bonferroni) but I’m assuming that a generalized linear mixed model would be more appropriate.  Since you’re not interested in either survey time or site, both could be random effects.  Your fixed effects could be as simple as vegetation type (1 degree of freedom), snow depth, and species.  You have 3 response variables.  You could also test for assumptions of heteroscedasticity and ensure your results are valid.  Recall for any of these tests – your sample size is 14.
Line 218: I’m confused here.  You traveled a total of 1 kilometer, but you’re measuring distance up to 570m.  Please explain in the methods as I’m assuming there was additional landscape variables calculated?  Also, your sample size is still 14, correct?  I’m not clear how some distances would have a sample of 36 and others with 60 with the further distances having increased samples.  Perhaps an additional figure and description of how sites were chosen should be included.  If you do have this many crossings, then you’re likely not accounting for landscape level variation, which has been significantly influential in other research (e.g., the percentage of patches, the size and core area, etc).
Line 225: You’re differentiating between voles, mice, and shrews… I’d either report how you can do so in the methods or lump your small mammals.
Line 233: I’m assuming based on your table, that your 95% confidence in the figures are based on the number of tracks and not the number of sites.  If so, that would be pseudoreplication and inappropriate.  Please define in the methods and change accordingly.
I stopped line edit suggestions here due to a lack of time and inability to decipher results.
Paragraph 270: ANOVAs will provide information as to whether one group is significantly more or less – but not which group.  Also, see evidence and study designs to assess small mammal use e.g., Rosenberg, D.K., Noon, B.R., Meslow, E.C., 1997. Biological corridors: form, function, and efficacy. BioScience, 677-687.
Paragraph 280: Your statement in line 283 about statistical power is concerning.  Your sample size is 14 and you do not demonstrate that those locations were random – this is a very small study to be making such statements.  Please reassess.
Paragraph 294: Your study did show an effect on shrew movement (assuming you can differentiate shrew tracks accurately).  This paragraph seems to stray from your results.

Figure 1: See notes within.  I’d have a study area map, then inset with a transect set up and the designations for crossing/linear travel.  Your figure 1a isn’t exactly clear.  Can you use a different icon for roads?  Are seismic lines and non-forest different?  If so – as expected if created from differing processes, I’d suggest other colors/textures.  Lastly, on your legend, please put the symbol to the left of the feature.
Figure 2,3: I’d change the forest to be grey and the seismic lines (open) to be white.  It’s counter intuitive currently.
Figure 2, 3: define each response.  What’s a habitat usage intensity?  Also, see note above – this is an incorrect use of the word habitat by definition.  I suggest changing to vegetation or seismic line throughout.  This paper doesn’t address habitat


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 NARROW LINEAR CLEARINGS ON MOVEMENT AND HABITAT USE IN A BOREAL FOREST MAMMAL COMMUNITY DURING WINTER
Review round: 2
Reviewer: 1

Output:
Basic reporting: Writing is generally okay, but some of the definitions are not common or correct in ecological literature.  Specifically, I am still concerned about the use of "habitat" and "functional groups".  Mostly, I suggest the word habitat is removed as no formal analyses of predicted habitat were completed nor do the authors demonstrate data or capacity to evaluate predicted habitat.  Functional groups of mammals were classified by weight, ignoring ecological aspects of each species.  My suggestion is to remove the entire mention of functional groups and the associated figure. The information will be more transparent and biologically meaningful without that distinction.

The introduction highlights novelty of this study evaluating communities within non-road linear features, which may be a novel assertion for seismic lines.  Authors fail to consider the breadth of information/literature from utility lines, which are also non-road linear features.  Otherwise, there are only minor changes suggested.  I was only able to read through the methods and results.  I suggest major revisions before another review.

Raw data are shared, but I was unable to replicate any of the information and tables and it's unclear that the analyses were appropriate.  It is unclear how the raw data were used to create the data summaries (elaborations in the validity of findings section).
Experimental design: The paired design between seismic lines and forest interior is helpful, as the authors are taking into account local conditions over time.  This work comprises a huge field effort but, unlike the authors argue, is modest to small in terms of sample size.

First, data were not randomly collected.  This is an observational study and results can be applied to these areas during the time of the study, as verified by the authors in their response: comment 47 "Regarding site selection, some revisions to the text have been made, but we have avoided giving the excessive rationale now provided below, because these types of issues are very common in ecological studies that use multiple sites, and it is not usual practice to attempt to describe them in detail. Sites were not selected randomly or systematically in space because random selection without attention to the distribution of possible factors that affect habitat use can result in confounding between independent variables of interest with some other related but unknown factor (Hurlbert 1984; Fahrig & Rytwinski 2009)."  Non-random selection is common in ecology due to logistics and safety and this should be made more clear in the methods (paragraph beginning line 128).

I'm curious about the response to comment 58. "Finally, we reject the premise that increasing sample size would address this issue."  I suggest using your observed variation in data between sites and conducting a power analysis to better understand if you have enough data to draw conclusions.
Validity of the findings: Raw data are shared, but I was unable to replicate any of the information and tables.  It's extremely unclear that the analyses were appropriate.  It's unclear how a particular value (which should be within 1/10 of a segment) was used to derive percentages in the figures or supplemental tables.

Based on the methods, I presume the data include the number of tracks by species within 100m.  Authors provide the site (n=14), the treatment type (forest, seismic line), the  portion of the transect within 100m segments, the type of movement activity (crossing, approach, linear travel along transect), and a count for each species.  I assume the distance the number of meters traveled.  In this case, it would be helpful to know results by year and time.

Linear distance is unclear and how a measurement is represented by the other data.  There should be an opportunity to clearly summarize use and intensity.
- As an example, within a 100m segment of a portion of a site, there was a linear distance of 4162m for coyote (site = 14, type = Seismic, subtransect = 1).  Does that mean within a single 100m segment one or more coyotes traveled >4km during 3 winters?  For this same region there was 6 crossings and 0 approaches.  The methods suggest that there's a net longitudinal displacement calculation, but this is not shown.

Because I was unable to understand the linear values, I went through the raw data more.  Some clarity is needed.  As an example,
Site = 1
Type = Forest
Subtransect = 1

For deer, you record 1 approach, but you have 10 crossings.  Does that mean a single deer approached and crossed 10 times within 100m?

I attempted to repeat your formula for crossing propensity for hare.  By transect, I summed your raw data in a pivot table by each treatment.  Then, I calculated your cross propensity using your formula and I think I was able to obtain similar estimates to Figure 2a.  My average crossing propensity appeared similar, but not the same as yours with 96 and 87% for forest and seismic lines.  My standard error was low, suggesting a difference. A paired t-test in excel suggested P<0.001, similar to your figure. Nonetheless, here your data is suggesting (I think) the number of footprints differed which doesn't make any sense to me.  If you assume a hare has a home range of 100m (or even half that), then you would be more interested in a count along the transect and a frequency along transects.  If you do the same test with the count data (Excel Sheet from your raw data, Hare Cross Tab) then there is no difference between hare crossing propensity between the forest and seismic lines (P = 0.41).  This is an example of why the reader cannot directly take your thought process (as developed in the introduction), methods as written, raw data and come to similar conclusions.

I would strongly suggest that the authors walk the reader through, step by step how data were analyzed either in the main body or a supplemental guide.  Further, if possible, I would use an R script or a word document to describe how data were altered for each summary and analysis.

Further, there may be some evidence that the authors have looked at the data more thoroughly.  In the response comment 26, authors suggest "Friedman tests were conducted where residual plots indicated a non-parametric distribution."  After describing how data were used, I would include these preliminary plots as supplemental information.
Additional comments: There are some scientific opportunities within this paper and I applaud the authors for this field effort.  I'm still very unclear about the validity of the analyses, summaries, and results.  Before I can understand the discussion and context of these findings in the literature, the analytical methods and results would need to be clarified.

In general, I don't feel as if you respected the suggestions by your reviewers and this made the paper difficult for me to approach.  It seemed like you spent time providing arguments, but not I'm not convinced that your arguments were scientifically valid.  For instance, the other reviewer suggested reviewing and summarizing the data differently (comment 27) and provided opportunities to do so.  Your response that the analyses were appropriate for the research questions seem incorrect, especially since it's very unclear what you actually did with your data.  In some (like comment 42 regarding habitat), you provide citations that cited Forman 1995, a book on land mosaics ignoring the wealth of information on the term and correct usage for the word habitat.  Although I could spend time working through the paper pointing out many discrepancies, I highlight only a few.

You may have an interesting data set, but it's not clear how you're reporting results and why you're summarizing data as described.  See some of my comments within the pdf.


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 NARROW LINEAR CLEARINGS ON MOVEMENT AND HABITAT USE IN A BOREAL FOREST MAMMAL COMMUNITY DURING WINTER
Review round: 3
Reviewer: 1

Output:
Basic reporting: The authors improved the manuscript for this version considerably.  I found the introduction to read better and provide additional clarity for the reader.

- Habitat: the authors revised much of the introduction to remove the word habitat with a vegetation class.  That was appreciated and the manuscript reads more accurately.

- Functional groups: I would suggest replacing the term "functional group" with their own category as used in the caption for Figure 3: "groups based on body
size-diet combinations", adding within the abstract/introduction/methods hereafter "size-diet groups". To me, "functional group" seems like a key word search to allow the impression of broader impacts.  I disagree that a function group can be condensed by weight and diet.  With an extreme example, a great horned owl, large mouth bass, and house cat could be considered a "functional group" within the author's use (size/predators), but that's not correct due to differences in behavior and obvious differences in mobility.  Here, these species also differ in their movement and how they would perceive linear features.

I'm not a fan of Wikipedia for definitions, but this is the first paragraph, emphasizing a functional group with characteristics linked to a niche and fitness [Accessed 31 Oct 2018]:

"A functional group is merely a set of species, or collection of organisms, that share alike characteristics within a community. Ideally, the lifeforms would perform equivalent tasks based on domain forces, rather than a common ancestor or evolutionary relationship. This could potentially lead to analogous structures that overrule the possibility of homology. More specifically, these beings produce resembling effects to external factors of an inhabiting system.[1] Due to the fact that a majority of these creatures share an ecological niche, it is practical to assume they require similar structures in order to achieve the greatest amount of fitness. This refers to such as the ability to successfully reproduce to create offspring, and furthermore sustain life by avoiding alike predators and sharing meals."
Experimental design: I'm concerned that the authors are arguing but not thoughtfully addressing potential issues within their response:

For example Comment 8, Reviewer 2 rebuttal: "We stand by our original statement and reject the premise that increasing sample size would address the comment (above) because this was not a research question posed by this study. With respect to the current comment which refers to “conducting a power analysis to better understand if you have enough data to draw conclusions.” We believe that this is unnecessary for the following reasons:
1)	“Statistical power is a measure of our confidence that we would have detected an important effect if one existed.” (Quinn & Keough 2002). Since we detected an effect for several taxa and functional groups, power was sufficient in those cases.
2)	With respect to non-significant results, we accept that the reviewer may be concerned about our conclusion that mammal movements across transects were either unaffected by seismic line clearings or restricted only slightly. However, we have included figures, mean values, measures of variance and statistical test results in the current manuscript. It has been demonstrated that p-values and power are inversely related and that low p-values mean higher power and high p-values mean lower power (Thomas 1997; Hoenig & Heisey 2001). Since we have included p-values, the addition of post hoc power calculations would not add new information to the manuscript.
3)	In addition, the manuscript’s figures and supplemental tables provide the necessary information for readers to draw conclusions. For example, Figures 2a and 3a show that there was very little difference in crossing propensity between seismic line and forest transects (i.e., a small effect size). Therefore, irrespective of the power of the statistical test, the figure shows the reader that mammal movements were restricted only slightly, or not at all because a) there was little difference in crossing propensity between the 2 types of transects (i.e. forest versus seismic line) and b) seismic line crossing propensity was high, as 89% of tracks approaching seismic lines, subsequently crossed them. A power analysis would not change this finding."

Certainly, few studies have the fiscal capacity to achieve a desired sample size. Here, the authors failed to conduct a power analysis and its not clear if they have data of sufficient capacity for proper interpretation.  This is an observational study, and therefore descriptive.  Given what I've read, I'm hesitant to believe the first statement in their discussion is appropriate:

"Most taxa in this boreal region showed no difference in crossing rates of seismic line clearings compared with forested control transects: these non-road linear forest clearings did not create strong barriers to movement."

This statement could have profound implications for conservation and the data are not robust (in my opinion) to clearly state whether or not linear clearings were barriers.  Track data during winter and the analyses within this manuscript allow for hypothesis generation.  There are potential implications from these data, but the evidence is not sufficient as the manuscript (and supplemental materials) are written.

Please see my comment within the validity of the findings.  Using the argument that because the authors report p-values, having sufficient statistical power is unnecessary is incorrect.
Validity of the findings: - Supplemental tables:  The authors negate many of the concerns in the last review by providing additional supplemental tables.  "We have also created a supplement to describe the process used to calculate the results shown in Figures 2 and 3 and Supplementary Tables 1, 2 and 3 and to address concerns which were raised regarding the nature of the analysis (points 5, 9-14, 16, 17 and 19)." [1st comment to the editor.]

The authors suggest that Supplemental table 1 addresses concerns on 11 occasions.

These supplemental tables are NOT providing me with reassurance that data were properly assessed.

First, the Supplemental tables do not address the reviewer concerns or it is unclear how they do so.

Second, the tables provide t-tests for all species, groups, and they test each possible transformation (Footnote: "Transformations were applied to data sets prior to conducting paired t-tests. 2nd indicates square root transform, 3rd is cubed root, etc. Log applied as log(x+1).").  The P-values require a Bonferroni correction or a correction for false discovery like the Benjamini-Hochberg procedure.

From a free online bio-statistical handbook [http://www.biostathandbook.com/multiplecomparisons.html, Accessed 31 Oct 2018]:  "Any time you reject a null hypothesis because a P value is less than your critical value, it's possible that you're wrong; the null hypothesis might really be true, and your significant result might be due to chance. A P value of 0.05 means that there's a 5% chance of getting your observed result, if the null hypothesis were true. It does not mean that there's a 5% chance that the null hypothesis is true.

For example, if you do 100 statistical tests, and for all of them the null hypothesis is actually true, you'd expect about 5 of the tests to be significant at the P<0.05 level, just due to chance. In that case, you'd have about 5 statistically significant results, all of which were false positives. The cost, in time, effort and perhaps money, could be quite high if you based important conclusions on these false positives, and it would at least be embarrassing for you once other people did further research and found that you'd been mistaken.

This problem, that when you do multiple statistical tests, some fraction will be false positives."

Because the authors are interpreting their data within a scientific publication, it seems that each piece of evidence should have assumptions clearly stated and the analysis most fitting to the data. These data could be incorporated within a generalized linear mixed model or tests could be completed with a multiple comparisons adjustment.

- Raw data and repeatability: there was no apparent effort made to refine data or allow readers to repeat calculations as per my prior review comments.  Please reformat the supplemental materials to address prior concerns.

- Figure 4:  This is extremely confusing: "Effect of distance from seismic line (SL) clearings on habitat usage intensity within forest transects, for (a) moose and (b) shrew which were measured repeatedly in sub-transects located various distances from seismic lines (n=36, 44, 60 for 0-50 m, 51-150 m, 151-570 m respectively) in 14 sites (subjects); results of ANOVA test shown (+P<0.1, *P < 0.05)."

Is the graph a mean and confidence interval, or output from an ANOVA?  Please clarify. An this analysis of variance test would only show whether or not there was a difference between populations (I'm assuming distances).  Further, an ANOVA is for independent data that is normally distributed and has equal variance.  In the caption, it's clearly stated that these data are not independent; there is no mention of a Levene's test for equality... I'm fairly certain this is an inappropriate test.
Additional comments: I apologize for the extended time of this review.  I have recently transitioned jobs and am attempting to juggle two positions simultaneously.

I believe this study required a remarkable amount of field effort.  I would consider these and prior comments carefully. I don't feel that many of my original concerns were addressed. I am disappointed to be in a place of argument rather than collaborative improvement. I feel this manuscript could benefit from transparency, and thoughtful interpretations with clearly stated caveats, and ideally the assistance of a trained statistician. The discussion, as written, leans towards confident opinions and I am skeptical that your data and evidence are appropriate to make strong claims.  There is great opportunity reporting your results in a peer reviewed journal and I applaud your tenacity.  Please consider revisiting this paper, ensuring the evidence is correctly portrayed and your interpretation matches the weight of the evidence.  Also consider the wealth of literature moving away from p-values and stressing the importance of effect size, an issue not addressed within.


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: EMERGENCE OF VISIBLE LIGHT OPTICAL PROPERTIES OF L-PHENYLALANINE AGGREGATES
Review round: 1
Reviewer: 1

Output:
Basic reporting: All the formal criteria are met.
Experimental design: Though testing of the impact of intrinsic fluorescecne to the ThT signal is meaningful, I have several questions about the experimental design, which are described in the General Comments section. The authors have to answer this questions before the paper is published.
Validity of the findings: The main conclusion of the paper is that ThT fluorescence can be enhanced due to gelation, but not to fibrillation of Phe. I agree with this fact, as well as with the potential overlap between dbAF and ThT.
Additional comments: 1. The authors test the oxidation hypothesis suggested by Tikhonova et al. by using filtration of the samples. However, Tikhonova et al. used mush lower concentrations of Phe to minimize aggregation of the sample. Hence, this comparison is not totally correct.

2. In Figure 1 authors demonstrate the band in EEM, which is an obvious aftefact (second order of difraction, see the peek centered at ca ex = 250/em = 550 nm). Why?

3. During long incubation of Phe (15 days) even at 60C bacterial contamination is possible, which may lead to fluorescence signal close to dbAF of Phe or its aggregates. Hence, sodium azie is used. Please, explain why you don't consider the possibility of bacterial contamination – the structure of bands in EEM is more typical for bacteria than for dbAF of Phe or proteins.

4. "The appearance of optical properties could be the result of chemical modifications that occur to
Phe upon incubation at 60 °C(Tikhonova et al., 2018). In order to rule out such a possibility, we
attempted to remove the aggregates using filtration through 0.22 μm filters" - as can be seen from Table 1, this possibility was not ruled out, but proved - filtration didn't remove 310/419 nm fluorescence, which doesn't originate from Phe. Please, indicate this in the text in a more clear way.
And, once again, see the comment 1 – much higher concentrations are used in this study compared to Tikhonova et al.

5. The FRET hypothesis is speculative now and coud be tested e.g. by titration of Phe aggregates with Phe. However, as a hypothesis it is ok.

6. Please indicate what is the baseline (solution parameters) in Fig. 3.

7. Conclusion: "These findings show that Phe does indeed form aggregates". Please explain, which data in the paper illustrate this fact. I have no doubts that at 100 mM concentration there will be aggregation, however, it is not clear from Fig. 1-2 or Table 1, where the maximum change is 40% at 3kDa filtration. For instance, this conclusion would be much more clear if you show e.g. DLS or other scattering data.


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: EMERGENCE OF VISIBLE LIGHT OPTICAL PROPERTIES OF L-PHENYLALANINE AGGREGATES
Review round: 1
Reviewer: 2

Output:
Basic reporting: Review on Manuscript Submitted to PeerJ
Manuscript: 32513-v0

Manuscript Title:
"Emergence of visible light optical properties of L-phenylalanine
aggregates"

Authors:
M. Ziaunys, V. Smirnovas

I have read the paper with a great interest. On  the one hand it considers well known experimental biomedical research of formation of amyloid fibrils.  On the other hand it teaches the researchers how to avoid false conclusions relying on misleading data based on visible photon emission.
Two kinds of visible luminescence techniques (effects, methods) allowing to detect and monitor nucleation and growth of amyloid structures are considered. The first one is visible autofluorescence created by hydrogen bonds of -sheet secondary structure. The second method applies visible dye imaging labels such as ThT and Congo red which are the major assay to observe Phe amyloid fibril formation.
The authors conducted good and reliable experimental research.
Their studies  of the excitation/emission properties of the Phe solution spectra show that the Phe-specific emission bands overlap with the aggregate specific excitation wavelengths.  This could cause false-positive ThT assay results and give an inaccurate impression of amyloid fibril formation, despite it being π-aggregate assembly. The  results also directly indicate that in the case of Phe aggregates, ThT could acts as a fluorescence quenching agent and actually hinders the detection of these structures.

My opinion: It is a good methological work. It can be accepted and published as is.
Experimental design: no comment
Validity of the findings: no comment
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: EMERGENCE OF VISIBLE LIGHT OPTICAL PROPERTIES OF L-PHENYLALANINE AGGREGATES
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is well written. Literature references and background information are fine.
Experimental design: Overall the design is solid and the methods are fine. One question I have is the difference in fluorescence intensities between Fig. 1 and Fig. 2. Were the Phe concentrations or other conditions different? It is not clear from the manuscript.
Validity of the findings: The results are fine but I think the authors may be overstating their case somewhat. It is clear from the manuscript that Phe forms some kind of aggregates in the conditions used and these aggregates are auto fluorescent. But it's not clear what is the relationship between these aggregates and any previously reported ThT-positive aggregates of Phe. As it is well known, depending on the conditions proteins and peptide can form a variety of aggregates and only relatively few of them bind ThT effectively. I think the authors could clarify this.
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: EMERGENCE OF VISIBLE LIGHT OPTICAL PROPERTIES OF L-PHENYLALANINE AGGREGATES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed my major concerns in the revised manuscript. Some additional remarks can be found in the "General comments for the author" section.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: 1. "Normally we would consider not including the region beyond 2nd order Rayleigh scattering as it is almost always filled with 2nd order artefacts, however, the 230/418 band (which is likely a FRET band) extends slightly into the region beyond 2nd order Rayleigh scattering and its extent into this region varies after the reduction of the newly appeared bands (see included Fig. R1), hence we feel like it should be included. Which means the artefacts that happen to be in the scanned region also get included."

This could be due only to higher scattering in the "control" sample compared to the "filtered" one, you can check this by comparing the intensities at 460 nm (230/460).

2. "Nevertheless, we prepared Phe samples with 0.1% sodium azide. As expected, the spectra were slightly affected by sodium azide, but non-phenylalanine bands were still present (Fig. R3) as well as was the overlap with ThT specific emissions at 440/480 nm."

The authors did not provide the incubation time and the conditions of the experiment. Their results thus can not be critically analyzed. The EEM in Fig. R3 is definitely different from Fig. 1 in the manuscript and this has to be commented.

Also I strongly suggest to the authors to include the optical density spectra for the incubated Phe samples to show the inner filter effect influence on the presented data – it seems that it would be quite high.

3. Conclusions
"These findings show that Phe does indeed form aggregates, as was demonstrated on multiple
occasions, however, aggregates generated under the conditions used in this work have optical
properties that give rise to a false identification as amyloids when applying ThT assays."

Better correct to "false identification of Phe-based fibrils", as the general statement about amyloids is out of scope of this 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: EMERGENCE OF VISIBLE LIGHT OPTICAL PROPERTIES OF L-PHENYLALANINE AGGREGATES
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Overall, looks good.


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 IMPACT ON LIFE CYCLE CARBON FOOTPRINT OF CONVERTING FROM DISPOSABLE TO REUSABLE SHARPS CONTAINERS IN A LARGE US HOSPITAL GEOGRAPHICALLY DISTANT FROM MANUFACTURING AND PROCESSING FACILITIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: Using an anticipated life expectancy of 41.7 years for reusable sharps containers seems unrealistically long in a high use clinical unit e.g. operating theatre, oncology / chemotherapy ward. I would be interested to see calculations using a more realistic life expectancy e.g. 5 years, 10 years, 15 years.
Validity of the findings: No commnet
Additional comments: no comment


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 IMPACT ON LIFE CYCLE CARBON FOOTPRINT OF CONVERTING FROM DISPOSABLE TO REUSABLE SHARPS CONTAINERS IN A LARGE US HOSPITAL GEOGRAPHICALLY DISTANT FROM MANUFACTURING AND PROCESSING FACILITIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: This paper addresses the environmental implications of changing from disposable to reusable sharps containers. This is a relevant topic, because sustainability in a hospital context is an underdeveloped theme. The study uses life cycle assessment (LCA) as a method, which is appropriate because there is a trade-off between the impacts of production and treatment from disposable containers and the impacts of decontaminating from reusable containers. Moreover, PeerJ is an important journal in the medical world, so messages broadcasted through PeerJ have the potential to be received, and may change hospital practice. As such, I appreciate the manuscript.

From another side, there is much to comment on. I have 25 years experience in the field of LCA, and the paper violates many basic rules of good LCA practice. The standard for clear reporting as outlined in the ISO standards 14040-14044 is not followed. This implies that many important choices and issues are addressed in a limited or obscure way. For instance, "allocations for emissions were as follows ... electricity generation (kWh); water supply and treatment (litre)": I have no idea how these allocations were done in detail, and I would have difficulty in reproducing the study. The purpose of the ISO standards is to make studies transparent and reproducible. Another example: I have no idea which greenhouse gases were included (CO2, CH4, N2O, etc). The online supplementary info states a "GWP emission factor" for different plastics and transport activities, a highly unusual way of reporting, given the widely-endorsed preference of separating inventory analysis and impact assessment. A third example: it is a usual practice to include uncertainty analysis, offering ranges or distribution of outcomes rather than point values. Most LCA-software nowadays features Monte Carlo analysis for this.

The paper does offer some statistics, on line 174, but this p-value doesn't seem to be based on repeated sampling. Or is it? I do understand the 65,3% reduction, but I have no clue how this translates into p-value or an RR. Perhaps this is a good novelty, but it is uncommon in LCA, so please report how it was done and what it means.

Line 244 discusses "other impacts" besides global warming (by the way, the impact is global warming, not global warming potential or GWP; GWP is calculated by IPCC, not by you). But it doesn't mention other environmental impacts. LCA studies should not be restricted to global warming, but usually include acidification, toxic emissions, and many more impacts. Please check http://eplca.jrc.ec.europa.eu/uploads/ILCD-Handbook-LCIA-Framework-Requirements-ONLINE-March-2010-ISBN-fin-v1.0-EN.pdf or another contemporary document on LCA. Inclusion of a broader range of impacts mught affect the results quite a bit, either strenghtening the conlusion or weakening it.
Experimental design: Basically, no experiments were done, this work is based on a calculation model (LCA).
Validity of the findings: The validity is difficult to check; see my points made above.
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 IMPACT ON LIFE CYCLE CARBON FOOTPRINT OF CONVERTING FROM DISPOSABLE TO REUSABLE SHARPS CONTAINERS IN A LARGE US HOSPITAL GEOGRAPHICALLY DISTANT FROM MANUFACTURING AND PROCESSING FACILITIES
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Overall the article is well structured, the experiments and analysis are appropriate, the discussion and conclusion are solid and convincing. I have one question on a tiny detail in the article

line 163 to line 167 discusses the 'worst-case' lifespan of RSCs, from the evidence it seems in the 'worst-case' scenario, the RSCs are used 360 times in 19 years, that's 360/19 = 17 times/year, which is above the average of 12 times/years (line 162). My question is

How does the lifespan is correlated to the reuse times per year?
and
How does 17 times/year accountable for the worst case?

This question doesn't affect my decision, it's up the author to answer this question for me.


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 IMPACT ON LIFE CYCLE CARBON FOOTPRINT OF CONVERTING FROM DISPOSABLE TO REUSABLE SHARPS CONTAINERS IN A LARGE US HOSPITAL GEOGRAPHICALLY DISTANT FROM MANUFACTURING AND PROCESSING FACILITIES
Review round: 2
Reviewer: 3

Output:
Basic reporting: Some of the information in the introduction is outdated. US GHG emissions e.g. Chung and Meltzer US GHG estimate of 7.6% in 2009 has been updated by Eckelman and Sherman to 9.8% in 2016 publication, and should be updated to the most recent. Further, while the NHS publication notes more than half of GHG emissions stem from procurement, this is not reflected in either Chung or Eckelman since the data is aggregated differently. Thererefore, please remove the Chung citation from line 53.

Abstract/discussion: “..sharps wastes….can account for up to half of total medical waste” is not supported by the citations noted. Either support this claim or remove.

Lines 181-183 require an original citation.
Experimental design: In terms of waste management, for sharps without pharmaceuticals, treatment is not necessarily simply autoclaving and landfilling. Rather such sharps waste must be rendered both non-infectious and non-recognizable (i.e., no longer sharp) in several states (and I believe this includes California where this study takes place). The latter treatment is at higher temperature than standard autoclaving. The authors should clarify and cite their state regulations, and correct their calculations if necessary.
Validity of the findings: Original data and reproducibility acceptable.
Additional comments: Overall, this study is well done, but is VERY similar to the study, Grimmond T and Reiner S, 2012 study. The only difference is that this study is performed at a different hospital in a different state, thus the transportation and waste volumes are different.