Review Reports

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The manuscript by Grigorean et al. is an extensive work on ischemia and related multiomics research on the topic. It contains 212 references, 2 tables, and 2 figures. The data visualization in relation to the amount of text is a bit too low; adding more figures and table summaries can improve article readability. The English is understandable; however, it needs correction for grammar issues. Not every aspect regards omics, paper is about other biomarkers too, consider removing the Multi-Omic from the title or changing content.

The abstract is a bit too long, please consider shortening

Line 76: As previously described, suggests that information is in the manuscript or the reference. One of it is missing.

Line 90: Is the insult correct? Maybe an injury?

Line 94: I believe the text in brackets are referring to produced examples of molecules, please correct the sentence to be clearer.

Line 107: Reference is missing

Line 285: the term hyperacute was used before, here we see hyper-acute (HAP). Please maintain one way of writing it.

Line 295: I strongly suggest to keep relating to original research in the review, not to other reviews. And this [44] does not relate to the content of the paragraph.

Line 317: I am sorry, but [48] does not refer to the stroke, this is suspicious.

I am not fully convinced what the authors refer to AI. This is now a little bit catchall and it would be perfect to explain what exactly is included within the definition.

Line 356: The caption is odd, please rewrite it properly. Same thing for caption of Table 2.

Line 363: Concluding perspective can and should be shortened

Line 554: The mentioned paper relates to pancreatitis, with a different pathophysiology than stroke, so the extrapolation is limited. Also the group was small, which was stated by the authors and I would avoid strong conclusions based on this work.

Line 595: I have a feeling that many references are very loosely connected with the content. For example: “Panels of biomarkers and imaging are being evaluated for patient selection for reperfusion trials; complement/adhesion crossing profiles are being investigated as a means of determining when immunomodulatory therapies should be initiated; and microRNA signatures are being examined as predictors of responses to neuroprotective therapies. Although many of these applications are still in early development, they illustrate how biomarkers may transform stroke care from disciplines focused on reactive measures to a predictive science [103]”

The cited paper ONLY refers to predicting the size of infarction, all of this is exaggerated. I am really sorry, but this relates to most of the papers I screened, that the content and reference does not match.

With this I feel obliged to reject your paper, as it does not relate to basic principles of scientific work despite that there is useful information, but not everything can be trusted. Please be more careful and write only the proper information to support your thoughts.

Line 1109: Figure 2 has low quality, its readability for colorblind people makes it difficult to benefit from.

Line 1147: I don’t understand the purpose of this paragraph. There is no useful information on those technologies.

Comments on the Quality of English Language

There are grammatic and editorial errors that need to be corrected. 

Author Response

Dear Esteemed Academic Reviewer,

We thank you for the time, rigor, and care you devoted to evaluating our manuscript. We are especially grateful for the clarity of your critiques and for your emphasis on scientific precision, accurate citation content alignment, and transparent interpretation. Your comments highlighted several issues that required substantive correction, and we have treated them as an opportunity to substantially strengthen the manuscript in both scientific reliability and readability.

Below, we provide a detailed point-by-point response and a concise summary of the major revisions implemented.

General Comments

Reviewer Comment: “The manuscript is extensive… data visualization is too low; adding more figures and table summaries can improve readability.”
Response: We appreciate this important observation. In the revised version Figure 2 has been redesigned for improved resolution and accessibility.

Reviewer Comment: “The English is understandable; however, it needs correction for grammar issues.”
Response: Thank you for noting this. We performed a full professional-level language revision across the manuscript to correct grammar, improve syntax, reduce redundancy, and enhance academic tone and clarity.

Reviewer Comment: “Not every aspect regards omics; paper is about other biomarkers too; consider removing Multi-Omic from the title or changing content.”
Response: We fully agree with this point and appreciate the conceptual clarity it provides. In the revised version, we adjusted the title to better reflect the manuscript’s scope, emphasizing dynamic, multi-compartment biomarker biology and the integration of omics as one component rather than the sole focus. We also revised several sections to ensure the narrative remains consistent with the updated framing.

Abstract

Reviewer Comment: “The abstract is a bit too long, please consider shortening.”
Response: We agree and have substantially shortened the abstract while preserving its essential content, novelty, and structural clarity. Redundant elements were removed and key mechanistic concepts were condensed to meet high-impact review standards.

Specific Line-by-Line Comments

Reviewer Comment (Line 76): “As previously described suggests that information is in the manuscript or the reference. One of it is missing.”
Response: Thank you for catching this imprecision. We removed ambiguous phrasing and replaced it with a direct statement. Where appropriate, we added the missing citation and ensured that the sentence is fully interpretable without relying on implied prior content.

Reviewer Comment (Line 90): “Is the insult correct? Maybe an injury?”
Response: We agree. We replaced “insult” with “injury” throughout the manuscript when referring to ischemic damage, to improve terminological precision and readability.

Reviewer Comment (Line 94): “Text in brackets refers to produced examples of molecules; please correct the sentence to be clearer.”
Response: We revised the sentence structure, improving syntactic clarity and avoiding ambiguity.

 

Reviewer Comment (Line 107): “Reference is missing.”
Response: The missing reference has been added and the paragraph was re-checked for citation completeness.

Reviewer Comment (Line 285): “Hyperacute used before, here hyper-acute (HAP). Please maintain one way of writing it.”
Response: We thank you for identifying this inconsistency. 

Reviewer Comment (Line 295): “Keep relating to original research… [44] does not relate to the content.”
Response: We fully agree and are grateful for this correction. We replaced review-based citations with primary research references wherever possible and removed [44] from that paragraph. We carefully revised the surrounding statements to ensure that all claims are supported by appropriate primary sources.

Reviewer Comment (Line 317): “[48] does not refer to stroke; suspicious.”
Response: We appreciate this important observation and agree that the mismatch is unacceptable. We removed the reference and restructured the paragraph to rely only on stroke-specific sources. We also conducted a comprehensive audit of the entire manuscript to ensure that all references match the specific claim they support.

Reviewer Comment: “Not convinced what the authors refer to AI… catchall… explain what exactly is included within the definition.”
Response: We agree completely and thank you for highlighting this conceptual gap.

Reviewer Comment (Line 356): “Caption is odd, please rewrite it properly. Same thing for Table 2.”
Response: Thank you. Both Table 1 and Table 2 captions have been rewritten in a compact, academically standard format, clearly stating scope, time scale, and biological relevance, without unnecessary narrative framing.

Reviewer Comment (Line 363): “Concluding perspective can and should be shortened.”
Response: We agree and substantially shortened the concluding perspective, removing redundant phrasing and maintaining only the essential mechanistic and translational message.

Reviewer Comment (Line 554): “Paper relates to pancreatitis… extrapolation limited… group small… avoid strong conclusions.”
Response: We appreciate this critical point. We revised the paragraph to explicitly acknowledge the limitations of extrapolating from non-stroke inflammatory conditions, removed any strong interpretive statements, and rephrased the discussion conservatively. We emphasized the need for stroke-specific validation cohorts and avoided drawing generalizable conclusions from small, disease-mismatched studies.

Reviewer Comment (Line 595): “Many references loosely connected… content and reference does not match… exaggerated.”
Response: We are sincerely grateful for this rigorous critique and fully acknowledge its seriousness.

Reviewer Comment (Line 1109): “Figure 2 has low quality… readability for colorblind people difficult.”
Response: Thank you for this important usability point. Figure 2 has been redesigned at higher resolution and adjusted to a colorblind-friendly palette, with improved contrast, clearer labeling, and enhanced readability.

Reviewer Comment (Line 1147): “Purpose of paragraph unclear; no useful information on those technologies.”
Response: We agree. We revised the section by removing non-informative or overly generic sentences and restructuring the paragraph to focus only on technologies with explicit mechanistic and translational relevance to stroke biomarker discovery. The revised version now clearly articulates why each approach is included and what unique biomarker-level contribution it enables.

 

We again thank you for your exceptionally careful review. Your comments directly improved the manuscript’s scientific integrity by prompting us to correct citation–content mismatches, refine conceptual boundaries, and strengthen the manuscript’s clarity and evidentiary discipline. We hope the revised version addresses all concerns and now reflects the level of rigor and reliability you appropriately expect.

With profound respect and appreciation!!!

Reviewer 2 Report

Comments and Suggestions for Authors

This manuscript presents a highly comprehensive and innovative review of ischemic stroke biology. The topic is timely, relevant, and of high potential impact, particularly given the increasing interest in precision medicine, liquid biopsies, multi-omics integration, and AI-guided clinical decision-making in cerebrovascular disease. However, the manuscript would benefit from structural refinement, improved clarity, reduction of redundancy, and stronger critical synthesis to enhance readability and translational relevance.

1- The manuscript is exceptionally long and dense, particularly in Sections 2 and 3. Please consider summarizing.

2- There is substantial redundancy, especially in the repetition of inflammatory pathways (e.g., DAMPs, inflammasomes, microglial activation) and the reiteration of EVs, miRNAs, and AI integration across multiple sections.

3- The authors should add a schematic figure early in the manuscript illustrating the temporal phases, the key molecular transitions, the compartments (brain–CSF–blood–periphery), and the clinical decision points.

4- The AI and machine learning section is repetitive. Please consider adding a concise critical paragraph addressing data harmonization challenges, model interpretability, and regulatory and validation hurdles

5- Briefly mention some specific AI model types from ischemic stroke research.

6- The author should correct the grammatical and punctuation errors, as well as abbreviations.

Author Response

Dear Esteemed Academic Reviewer,

We extend our gratitude for the thoughtful evaluation of our manuscript and for the exceptionally constructive and detailed recommendations. We are deeply appreciative of the time, rigor, and expertise you dedicated to this review. We agree that, despite the broad scope and conceptual ambition of the manuscript, its impact depends on structural refinement, reduction of redundancy, and stronger critical synthesis to enhance readability and translational clarity. In response, we undertook a comprehensive revision, aiming to preserve mechanistic depth while achieving a more coherent, streamlined, and clinically oriented narrative.

Below, we address each point in turn.

1. The manuscript is exceptionally long and dense, particularly in Sections 2 and 3. Please consider summarizing.

We fully agree with this concern. We have substantially condensed Sections 2 and 3 by removing repeated explanatory passages, merging overlapping mechanistic descriptions, and rewriting dense sections into more compact, information-rich syntheses. Our intention was to preserve all key mechanistic details and translational insights while improving readability and narrative flow. The revised structure now communicates the same depth with greater clarity and reduced textual burden.

 

2. There is substantial redundancy, including repeated inflammatory pathways and reiteration of EVs, miRNAs, and AI integration.

We are grateful for this observation and agree that redundancy weakened the manuscript’s readability. We therefore performed systematic de-duplication across Sections 2 and 3, removing repeated discussions of DAMP signaling, inflammasome biology, microglial activation, leukocyte recruitment, and BBB dysfunction. 

3. Add a schematic figure early in the manuscript illustrating phases, transitions, compartments, and clinical decision points.

We sincerely thank you for this highly valuable recommendation. We have now added a schematic figure early in the manuscript (Figure 1: Temporal Biomarker Atlas of Ischemic Stroke: Phases, Compartments, and Clinical Decisions). This figure provides a structured visual overview of: (i) the temporal phases of ischemic stroke (hyperacute to chronic), (ii) key molecular transitions across time, (iii) biomarker compartments (brain–CSF–blood–periphery), and (iv) clinically relevant decision points aligned to phase-specific biomarker trajectories. We placed this figure at the end of the Introduction to serve as a conceptual roadmap for the remainder of the review and to improve navigability.

4. The AI and machine learning section is repetitive; add a concise critical paragraph addressing harmonization, interpretability, and regulatory/validation hurdles.

We fully agree. We revised the AI/ML section to reduce repetition and added a concise, explicitly critical paragraph addressing the major translational barriers that currently limit clinical deployment.

5. Briefly mention specific AI model types from ischemic stroke research.

We appreciate this important suggestion and have incorporated concise examples of AI model classes commonly used in ischemic stroke research, including supervised machine learning classifiers (e.g., random forests, gradient-boosted models), deep learning approaches (e.g., convolutional neural networks for neuroimaging), multimodal fusion models integrating imaging and molecular data, temporal models for longitudinal trajectories (e.g., recurrent and transformer-based architectures), and graph-based learning for network-level inference. These additions increase specificity while maintaining the intended conceptual focus of the manuscript.

6. Correct grammatical and punctuation errors, as well as abbreviations.

We performed a comprehensive language and formatting revision across the manuscript, correcting grammar and punctuation, standardizing abbreviations and first-definition conventions, harmonizing terminology (including consistent phase naming), and improving stylistic clarity throughout. These edits were applied globally to strengthen readability and professionalism in line with journal standards.

 

Your comments substantially improved the manuscript’s structure, clarity, and translational relevance. We hope the revised version now reflects a more coherent and rigorous synthesis, with reduced redundancy, clearer organization, and a stronger critical perspective, while preserving the mechanistic depth and integrative ambition of the original work.

Reviewer 3 Report

Comments and Suggestions for Authors

In this review article, the authors review the evolving understanding of stroke biomarkers through dynamic multi-omics approaches and artificial intelligence to enhance personalized stroke care and treatment outcomes.

The review is well written and very well organized, it results interesting. The proposal for applying and combining emerging technologies and AI-driven biomarker discovering is worthy of note.

Major Comments

1. For the four phases of stroke, two include a table (hyperacute and chronic), with its characteristics biomarkers, other (subacute) include a figure with biological programs and representative biomarkers, but acute phase had none. Immune activation, neuroinflammatory cascade and BBB dynamics deserve at least one figure. That graphically synthesizes the information of this stage.
2. In addition, an integrative figure (probably located just before subsection 6) that somehow illustrates the four stages should be useful for the reader to have a panoramic view of the problem.

 

Author Response

Dear Esteemed Academic Reviewer,

We thank you for your careful reading of the manuscript and for your constructive recommendation to strengthen visual synthesis across the temporal phases of ischemic stroke. We fully agree with your underlying point: the acute phase contains dense mechanistic content (innate immune activation, neuroinflammatory cascades, BBB dynamics, and systemic crosstalk), and schematic visualization can substantially improve readability and conceptual integration.

At the same time, we also wished to avoid an unintended risk that additional complex figures in the acute phase could overstate the maturity or clinical readiness of certain mechanistic linkages and biomarker trajectories, particularly in areas where human validation remains heterogeneous, where the timing of biomarkers varies across cohorts, and where causality remains incompletely established. Because one of the strongest concerns raised in the review process was the need to ensure strict alignment between mechanistic statements and the supporting evidence, we prioritized revisions that reduced interpretive overreach and strengthened internal consistency rather than increasing figure density in sections where the literature remains rapidly evolving and not yet harmonized.

In response to your comment, we therefore implemented the following improvements that preserve scientific caution while still enhancing the manuscript’s visual and structural clarity:

Addition of a unified integrative overview (Figure 1).
We added a new Figure 1, placed early in the manuscript, that provides a panoramic and structured roadmap of the ischemic continuum across phases. Importantly, this figure was designed to summarize the framework of the review without implying a level of mechanistic certainty beyond what current validation supports. We believe it provides the panoramic view you recommended while remaining appropriately conservative and evidence-aligned.

Targeted revision and consolidation of the acute phase narrative (Section 3).
Rather than introducing an additional acute-phase figure that might appear overly definitive, we strengthened the readability and synthesis of the acute phase through substantial restructuring. Specifically, we removed repetition, merged overlapping mechanistic passages, and reorganized the acute phase into a more compact, clearly staged sequence. This revision retains the full mechanistic content while allowing the reader to follow the logic more efficiently, with less redundancy and greater translational clarity.

 

 

We hope you will find that this approach achieves the core goal of your recommendation; improved clarity, navigability, and phase-level synthesis; while also respecting an important principle of cautious scientific communication in a field where biomarker validation and mechanistic generalizability are still developing. We are profound grateful for your valuable feedback, which meaningfully improved both the structure and the readability of the revised manuscript.

With great respect and appreciation!!!

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Thank you for addressing my comments, I am happy that the manuscript was improved and better in quality