On 2025-12-30 09:40:06, user Sangeeta Nath wrote:

Please add the original link of the paper DOI: 10.1016/j.isci.2024.110565

On 2025-12-30 06:26:06, user THT wrote:

Three structures of HSV-1 HP and HPI have already been published several months ago, with coordinates released, and an additional manuscript is available on bioRxiv. The authors of the current submission have chosen not to reference these studies or to compare their data with the existing structural information.

On 2025-12-30 04:25:55, user Mojtaba Madadi Asl wrote:

This article has been certified by peer review, and published in the following journal:

PLoS Computational Biology 19(2): e1010853 (2023)<br /> DOI: https://doi.org/10.1371/journal.pcbi.1010853

On 2025-12-30 04:23:15, user Mojtaba Madadi Asl wrote:

This article has been certified by peer review, and published in the following journal:

Physical Review Research 7, 023128 (2025)<br /> DOI: https://doi.org/10.1103/PhysRevResearch.7.023128

On 2025-12-29 21:14:03, user Cornett, Evan M. wrote:

published 10.1021/acs.jproteome.4c00685

On 2025-12-29 21:12:51, user Hector Franco Loponte wrote:

This article has been published on Nature Communications ( https://www.nature.com/articles/s41467-025-65265-2 ).

On 2025-12-29 19:42:33, user Scott Zawieja wrote:

In the discussion the paragraph including the following "It also reasons that telocytes are involved in cLV contractions, as LMCs are akin to smooth muscle cells that lack the ionic mechanisms required for action potential regeneration and electrical signals that efficiently propagate between muscle cells (64). Thus, LMCs likely rely on a telocyte network for signal conduction. Consistently, telocytes mediate rhythmic electrical activity in other tissues (65), which is believed to depend on ion channels for generating pacemaking currents (66, 67). Interestingly, electrically coupled cells are typically connected by gap junctions (63), and evidence demonstrating this physical link between telocytes and LMCs does not exist (6). " should be corrected.

LMCs have been shown to express the calcium activated chloride current Ano1/TMEM16a in multiple publications and this channel is responsible for pacemaker activity in ICCs (PMID: 30862712, 37851027, 38704841, 40932335, 41279936. Furthermore, LMCs have gap junctions, specifically Cx45 (Gjc1) and its role in LMC-LMC electrical communication is well established (PMID: 30355030, 33050046, 40932335).

On 2025-12-29 19:21:43, user Renzo Huber wrote:

Nice exciting studies. <br /> To include this manuscript into the table of all human layer-fMRI papers , could you confirm few details that i could not find in the manuscript:

I assume the GRE BOLD sequence was a 2D-sequence, (not 3D that is used for most of other studie)?

I assume you used a SIEMENS 7T Magntom scanners (e.g. a 7T plus), not a clinical Terra or Terra.X scanner?

unrelated, are you sure that you had 32 transmit channels and 4 receive? I suspect it to be the other way around?

On 2025-12-27 21:28:41, user Suleman khan Zadran wrote:

This is indeed a nice work using a bispecific antibody targeting both CD276 and GD2. I would really appreciate including the amino acid sequences of anti-GD2 and anti-CD276 moieties in the method and material section.

On 2025-12-25 21:13:22, user Meinhard Simon wrote:

This manuscript is now published in Microbiome<br /> ( https://link.springer.com/article/10.1186/s40168-025-02259-8 )

On 2025-12-25 15:51:18, user Noam Guetta wrote:

This paper is very interesting. I just couldn't find the Asgard ESCRT-IIIA protein's N' terminal sequence from the accession number, can you refer me to it? Thank you!

On 2025-12-25 14:30:25, user Wenxing Yang wrote:

Hi all, this is Wenxing. This paper has been published in a Chinese Journal, which is indexed by Pubmed ( https://pmc.ncbi.nlm.nih.gov/articles/PMC12709095/ ). Please cite as: Feng L, Zhao R, Zhang K, Yang W. From the 2^-ΔΔCT Method to the 2^-CT Method: A More Rigorous Approach to Real-time Quantitative Polymerase Chain Reaction Data Analysis. Journal of Sichuan University (Medical Sciences). 2025. 56(5):1405–1411. DOI: 10.12182/20250960402.

On 2025-12-24 14:30:56, user Fabio wrote:

Are there plans for a similar study on Ethiopian Jews lineages?

On 2025-12-23 19:31:04, user Olivier de Jong wrote:

Final manuscript has been published: https://doi.org/10.1038/s41467-025-65995-3

On 2025-12-23 15:46:04, user SanACVE wrote:

This article is now published at https://doi.org/10.1016/j.isci.2025.113831

On 2025-12-23 11:02:16, user Kana M Sureshan wrote:

Metabolism has long been mischaracterized as a static, background process. This study challenges that view, demonstrating that core metabolic pathways and nutrient uptake fluctuate in sync with the cell cycle. By actively driving proliferation and cell fate, metabolism emerges as a dynamic regulator rather than a passive observer—a significant shift in our understanding of cellular biology. I wonder if the same sync can be seen in eukaryots ! Anyways, its a great study. Congratulations to the authors

On 2025-12-22 17:19:15, user Soumitra Pal wrote:

For EvoGeneX, could you please cite this paper? https://www.liebertpub.com/doi/10.1089/cmb.2022.0121 . Thank you.

On 2025-12-21 21:44:12, user Zhang Cheng wrote:

The article was published in Environ. Sci. Technol. 2025, 59, 42, 22624–22637.<br /> DOI: https://doi.org/10.1021/acs.est.5c05925

On 2025-12-21 08:01:33, user Bart De Spiegeleer wrote:

This is an interesting study. An attention point is the data-set used: it is recommended to include also recent studies with particular peptides (eg Biomolecules 2023, 13(2), 296; https://doi.org/10.3390/biom13020296 ), next to the mentioned databases.

On 2025-12-20 17:34:48, user Philipp Niethammer wrote:

A substantially revised version of Zaza's outstanding PhD work is accepted (in principle) at Nature Communications. Many thanks to the reviewers and editor for their constructive comments and guidance!

On 2025-12-20 16:11:26, user Ibrahim Hasan wrote:

Now published in IEEE IEEE Transactions on Neural Systems and Rehabilitation Engineering (TNSRE) doi: 10.1109/TNSRE.2025.3635012

On 2025-12-20 03:42:54, user Misha Koksharov wrote:

Is there a way to easily do something similar to Protein Blast on the public server (preferably, with taxonomy filtering)?

On 2025-12-19 20:20:10, user Michael Ailion wrote:

This manuscript documents careful genetic analysis to better understand where and how Rho signaling acts in the C. elegans egg laying circuit. The authors demonstrate that Rho functions in mature neurons to promote egg laying, as well as in vulval muscle. By using calcium imaging, the authors were able to demonstrate how Rho signaling (specifically in the HSN neurons) regulates cell excitability presynaptically (HSN) and postsynaptically (vulval muscles). We found the experiments to be well designed and the data to be robust, with the major conclusions to be supported by the data.

Minor comments:

1) The introduction included a detailed analysis of the Gq signaling pathway and the candidate targets that regulate neuronal activity (i.e. DAG-regulated effectors and ion channels), but the scope of the paper does not include testing or identifying the targets downstream of TrioRhoGEF/Rho. On the other hand, the focus of this manuscript is neurotransmission in the egg laying circuit, and little detail is provided about how and what neurotransmitters are released by HSN. Only in the results section is NLP-3 mentioned, but it is known that both serotonin and NLP-3 released from HSN each contribute significantly to egg laying. <br /> 2) The authors conclude that Rho promotes synaptic transmission, and this is on the whole correct, but the authors could be more careful/precise with their wording and interpretations. As noted in comment 1, both serotonin and NLP-3 contribute to synaptic transmission in the egg laying circuit, but it is not known how directly these two components act in synaptic transmission. For example, NLP-3 is a neuropeptide that is released from dense core vesicles (DCVs), and it is possible that serotonin is also incorporated into DCVs as well as synaptic vesicles. In addition, serotonin and NLP-3 are known to act extrasynaptically as well as synaptically, and it is possible that Rho contributes to extrasynaptic release of serotonin and NLP-3. <br /> 3) When analyzing their data, the authors bin calcium imaging measurements in the active vs inactive state. The active and inactive egg laying states are characteristic for wildtype worms, but as the authors show, altering the activity of the HSN affects egg laying. Another interpretation of their data is that when Rho is activated (HSN::Rho-1(G14V)) the worm is always in the active egg laying state, and when Rho is inhibited (HSN C3 Transferase) the worm never enters the active egg laying state. While we don’t think they need to change how they analyze the data, the authors could just add this interpretation to the discussion. <br /> 4) We feel like the authors should include a more detailed discussion of why they see a difference in the effect of expressing dominant negative Rho (T19N) vs the C3 transferase in HSN. Why did Rho-1(T19N) expressed in HSN not show such a clear inhibition of calcium activity and egg laying as the C3 transferase expressed in HSN?<br /> 5) In general, gain-of-function experiments are hard to interpret. Activated Rho could increase cell excitability, but that does not necessarily mean that is the function of Rho normally. The loss-of-function experiments are more convincing, aside from the discrepancy we noted in comment 4. This could be noted in the discussion. <br /> 6) Lines 148 & 179: provide more detail or a reference for how extrachromosomal arrays were integrated.<br /> 7) Lines 195 & 214: it is unclear how GCaMP arrays were confirmed by mCherry fluorescence (nlp-3p::mCherry) given that these strains also have arrays carrying tph-1p::mCherry and both nlp-3p::mCherry and tph-1p::mCherry should express in the HSNs.<br /> 8) Line 339: the authors conclude that Rho acts “downstream of Trio RhoGEF.” However, the data show that a Trio mutant is only partially bypassed by expression of activated Rho – i.e. # of eggs is intermediate between the Trio mutant alone and activated Rho alone. These data are consistent with Rho acting downstream of Trio, but with RhoGEF activity still contributing to full activation of the “activated” Rho(G14V). The data would also be consistent with Trio and Rho acting at least partially in parallel, which could occur within the same cell or in different cells. A further complication to the interpretation of these data is that different activated Rho arrays are used in the WT and Trio mutant backgrounds. These different arrays could have different expression levels, which is a big caveat to making these comparisons. Ideally, one would use the same array in the WT and Trio mutant backgrounds.<br /> 9) p. 16, lines 348-459: many of the Fig 2 callouts on this page refer to the wrong panel.<br /> 10) Line 347: says 70%, but the data in the figure show >80%.<br /> 11) Line 348: says 3 +/- 1 eggs, but Fig 2B says 3 +/- 0.2 eggs for same strain.<br /> 12) Line 363: we were confused by this. Are the authors suggesting that you can’t quantitatively compare the effects of the HSN vs. muscle specific expression of activated Rho(G14V) because the arrays are mosaic? While it is true that the arrays may be mosaic, they also carry an mCherry marker expressed in the same cells, so they should know whether the array is expressing activated Rho as intended in the worms assayed, and it is unclear why mosaicism is an issue. A bigger issue to quantitatively comparing these strains is that they probably have different expression levels of activated Rho.<br /> 13) Line 396: “outside of egg-laying active states (Figure 3A).” However, the data in Fig 3A shows HSN activity “during an egg-laying active state” according to the figure legend. Data showing activity outside egg-laying active states are not shown, but should be presented.<br /> 14) Line 423: it is unclear how “instantaneous” transient frequency is defined. This should be added to the methods or figure legend.<br /> 15) Line 428: says “more than 5 transients per minute” but the data in Fig 3C show it to be just under 4 transients per minute.<br /> 16) Line 561-562. “This difference largely resulted from a lack of twitch transients around egg-laying events in C3T-expressing animals.” This argument doesn’t make sense to us. How could a lack of twitch transients affect the amplitude of the transients that are seen?<br /> 17) Line 648: “we do not see dramatic effects on HSN morphology and presynaptic structure upon Rho inactivation.” Presynaptic structure was not assayed, so this should be cut.

Reviewed (and signed) by Amy Clippinger and Michael Ailion

On 2025-12-19 16:32:52, user Fernando Govantes (Fernan) wrote:

This is now published in Microbiological Research. doi: 10.1016/j.micres.2024.128033

On 2025-12-19 15:34:37, user Prof. T. K. Wood wrote:

1. Authors confuse the stress response with persister formation as persister cells are dormant and stressed cells become persisters by literally down-regulating ALL genes.

2. Line 103 is patently false: "However, these studies neither comprehensively characterize persister motility nor explore the potential interplay between swimming motility and persistence" since we discovered persister cells resuscitate using chemotaxis machinery (CheA, CheY) to sense nutrients and discovered the mechanism is via cAMP and (p)ppGpp (ref 39, 2020, iScience).

3. line 106 is false (see item 2) as we discovered how motility affects persister resuscitation.

4. Line 55 is incorrect: persister cells do NOT form stochastically and claims of stochasticity are bad science with carryover due to the inoculum.

5. Line 60: the seminal paper which discovered acid and oxidative stress induce persistence is Microbial Biotechnology (2012) 5(4), 509–522 doi:10.1111/j.1751-7915.2011.00327.x

6. line 73: "a definitive mechanism or universal determinant that fully explains the persister lifecycle remains elusive" is patently false. The ppGpp ribosome dimerization persister (PRDP) model should be cites as, unlike the PASH model that is cited and provides no mechanism, the PRDP model is universal and provides the current best mechanism (Biochemical and Biophysical Research Communications 523 (2020) 281e286).

7. line 716/723: we discovered chemotaxis machinery impacts persister resuscitation (your ref 39) and so it should be cited here.

8. If these matters are not addressed, I will ask the that the final publication be corrected.

On 2025-12-19 13:36:26, user William Cawthorn wrote:

Very interesting paper! One minor request: please abbreviate bone marrow adipocytes as BMAds and not as BMAs, as outlined in the standard nomenclature for the field:<br /> https://www.frontiersin.org/journals/endocrinology/articles/10.3389/fendo.2019.00923/full

(this is because 'BMA' is the officially recognised abbreviation for 'bone marrow adiposity')

On 2025-12-18 18:35:07, user Pat Johnston wrote:

...ok, so if I understand this correctly, there is little to no size difference in adults? what of the possibility that boys develop their bnst to maturity sooner than girls, for it to play a more active/involved role in their early male hormonal development? is their comparative size differences at pre-pubescent age ranges, and does that correlate to consequent emergence of any missized dysmorphic basis for gender dysphoria?

On 2025-12-18 17:04:15, user Lucia Jajcay wrote:

The fMRI and personality data are publicly available on the Open Science Framework (OSF) and have now been assigned a DOI: https://doi.org/10.17605/OSF.IO/795HB .

When using the dataset, please cite the published article: https://doi.org/10.1111/psyp.70203 .

On 2025-12-18 07:59:33, user Cryptex Technologies wrote:

Interesting preprint and a promising approach using real-time volatilomics for non-invasive analysis of microbiota–pathogen interactions. Looking forward to seeing how this method performs in larger and clinical studies. Thanks for sharing this work.

On 2025-12-18 02:37:38, user M Timothy Rabanus-Wallace wrote:

Hi Eds -- this work has been published (after a lot of revision) here: https://link.springer.com/article/10.1186/s12870-025-07328-6

On 2025-12-18 00:14:57, user Casey Nichols wrote:

Hello! I wanted to leave some constructive feedback on the way the common garden assays were described. On my initial read, I found that the generational framework was a bit hard to understand. When the paper introduces the “F1” flies used for the phenotypic assays, it wasn’t immediately clear as to what “F1” was referring to. I had initially interpreted this as an “F1” relative to the start of the experiment. This left me confused since it wouldn’t make sense to perform the phenotypic assays on the F1 experimental populations. It wasn’t until I read through the supplementary materials that it became clear how “F1” was being defined in this context. There, you explained that the assays were conducted on the F1 generations of the experimentally evolved populations. I think this clarification is extremely important for interpreting the rest of the paper correctly. Perhaps making this more explicit in the main text would likely prevent similar confusion for other readers. The experimental design made a lot more sense to me once to me once this confusion was cleared up. Overall, a great read!

Cheers,<br /> Casey

On 2025-12-17 07:52:26, user Emma Piraino wrote:

I found this paper to be very cohesive and organized in a very understandable way, including the order in which information was presented as well as the utilization of figures that were crucial to the findings of the paper, nothing less and nothing more. Throughout the paper I thought of several questions that I had regarding rationale behind parts of the study, interesting expansions that could be made to the study, and topics that were answered later on in the paper, such as what is a common-garden assay. Before I get to my questions/suggestions, I also wanted to note that I appreciated how consistent the paper was and that the authors mentioned important themes and contributing factors to the experiment throughout the paper, such as defining why phenotypic plasticity was such an important factor to study and analyze in this experiment.

A few of the main questions I had are regarding the impact of bleach on fly eggs and how that can impact the experiment. I understand that F1 flies were used in their assays, according to their supplementary information, but I wanted to know more about how the bleach could impact the flies, even the F1 offspring. Another question, or even interest, I had was regarding why the comparisons of the experiment were between populations with microbes vs. without, instead of possibly comparing the effects of microbes that originated from different fly line populations. I understand why they only transferred fecal microbes from one fly line to keep all variables consistent, but I think further experiments on this could be interesting. The transfer of the fecal microbes leads to my next question, why were the MB flies created involving bleaching as well, with a reintroduction of microbes from one of the fly populations. From my understanding, if the microbes were transferred from a different fly line than the one chosen, this could have completely altered the outcome of the experiment, due to the variation of microbiomes between populations.

Some other overall comments I had regarding the paper would be include more examples that were specific to drosophila, (the existing examples of things such as the stinkbugs were also important to the paper, though). Also, I believe there is a typo under the desiccation resistance portion of the methods section, (till al -> until all).

Overall, I found this paper to be very interesting and left me with several questions regarding microbiomes and how this experiment could be further expanded upon, as well as how important these findings are.

On 2025-12-17 19:16:43, user Misha Koksharov wrote:

Very interesting. <br /> 1) Though, as someone currently interested in evolution of several enzymes throughout the Tree of Life, I would note that the proper term for an existing protein of this kind is "archaic", not "ancient". "Ancient" is more appropriate for those proteins which are no longer around. E.g. there are works where people try to resurrect ancient proteins from phylogenetic trees of the existing ones.

For example, lungfishes are "archaic" while "ancient alpha-proteobacteria" or even "ancient proteobacteria" are remarkably different from those we can study today, by the benefit of being able to infer some of their complexity from proteins of mitochondrial origin in eukaryotes.

Originally I've seen this point made by one of the linguists about languages: Latin is an ancient language while some Baltic and Slavic languages may be considered archaic relative to the Proto-Indo-European.

2) Figure 2. <br /> Why no melanopsins as a natural outgroup in the phylogenetic tree? As I understand, it is the closest clade to arthropod's r-opsins.

On 2025-12-17 15:16:52, user Jacob Podesta wrote:

The data supporting this research is openly available from the research data repository of the University of York at https://doi.org/10.15124/6c307f02-b229-4d5a-8dda-760e088abd26

On 2025-12-16 19:56:10, user Michael Pusch wrote:

The authors should consider the following paper:<br /> https://pubmed.ncbi.nlm.nih.gov/26033718/

On 2025-12-16 10:56:23, user Evolutionary Health Group wrote:

We at the Evolutionary Health Group ( https://evoheal.github.io/) really enjoyed this paper! Here are our highlights:

The authors demonstrate that extremely small RNA-guided nucleases can be deliberately redesigned to yield dozens of active variants, by extracting evolutionary signals that indicate which residues are safe to modify and which must remain untouched. The result is a set of compact, efficient DNA-cleavage "tools" that nature never explored but that nevertheless prove to be functional.<br /> A simple and elegant scheme for expanding the sequence space was used: an evolution-informed mask, derived from large paired datasets = protein + its native nucleic-acid-partner, locks functionally essential positions while leaving peripheral regions free to vary. The generative model is allowed to modify only these safe-to-vary positions, effectively unlocking large new areas of sequence space that expand natural evolutionary solutions.<br /> This approach can serve as a prospective strategy for “filling in the gaps” within sequence space regions where no experimentally annotated variants exist. Given large sets of evolutionarily linked pairs (protein-protein or protein-DNA/RNA), co-evolutionary signals identify functional anchor points, while generative models safely and systematically explore the vast surrounding regions. This enables the design of new sequences in those areas that natural evolution never sampled, thereby expanding the functional repertoire of biomolecules beyond the observable space.

On 2025-12-16 06:46:28, user Giorgio Cattoretti wrote:

The complex and advanced type of analysis described, SpaCEy, unveils spatially-contiguous expression of proteins associated with low survival in breast cancer and MYC is reported to be one of those.<br /> The antibody used to identify MYC in the cohorts is an IgG1 mouse clone, 9E10, which is not recommended for that purpose in FFPE sections by a knowledge-based Ab resource ( https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/reagent_resources.html) and does not recognized MYC in flow cytometry, immunohistochemistry and IF (doi: 10.1074/jbc.L119.011910. PMID: 31924671) and performs poorly for the only assay where it may be used, immunoprecipitation (10.1126/scisignal.aax9730). Assuming that it recognizes in tissues the linear epitope used for the Ab generation, it may detect three different proteins bearing such epitope. To include MYC among proteins associated with survival in breast cancer is premature at best.

On 2025-12-15 22:38:23, user Simon Delagrave wrote:

This manuscript is now published: https://www.nature.com/articles/s41467-024-51064-8

On 2025-12-15 17:08:43, user Prof. T. K. Wood wrote:

Authors appear to ignore previously-published work about the most-prevalent anti-phage system, toxin/antitoxins, where the transcriptional regulation is well-studied during stress. Their methods are also skewed by using DefenseFinder, which ignores most TA systems. Odd to think the environmental/physiological factors can be discerned if the most-prevalent systems are ignored.

On 2025-12-15 15:12:34, user Jonathan Michaels wrote:

Please link to published article: https://journals.physiology.org/doi/full/10.1152/jn.00407.2025

On 2025-12-15 15:11:10, user Jonathan Michaels wrote:

Please link to published article: https://www.nature.com/articles/s41586-025-09690-9

On 2025-12-15 11:13:45, user Emmanuelle Munger wrote:

Now published in nature communications https://doi.org/10.1038/s41467-025-63122-w

On 2025-12-15 03:24:33, user Misha Koksharov wrote:

This is a very interesting and useful paper which was apparently published 3 years later in 2025 in the International Journal of Molecular Sciences: https://www.mdpi.com/1422-0067/26/12/5569

On 2025-12-12 23:57:22, user Noriko Osumi wrote:

This preprint has now been accepted in Lab Animal after all the review process.

On 2025-12-11 08:47:39, user Sultan Tarlacı wrote:

The preprint "Somatic mutations impose an entropic upper bound on human lifespan" presents a significant methodological advance in gerontology by developing a structured, incremental modeling framework to dissect the complex process of aging (Efimov et al., 2025). A key contribution of this work is its demonstration of a fundamental asymmetry in how somatic mutations affect different tissue types. The finding that post-mitotic cells (neurons and cardiomyocytes) act as critical longevity bottlenecks, while highly regenerative tissues like the liver can maintain functionality for millennia through cellular turnover, provides crucial guidance for future therapeutic prioritization (Kirkwood, 1977; López-Otín et al., 2013). Furthermore, the application of reliability theory, modeling the human body as a system of serially and parallelly connected components, successfully translates engineering principles to a biological context, offering a robust quantitative foundation.

However, the model notably overlooks critical evolutionary and biophysical determinants of human lifespan, particularly the deeply entrenched allometric relationship between brain size, metabolic rate, and maximum longevity. Anthropological and comparative biological studies have long established a robust scaling law, often expressed as Maximum Lifespan ≈ k * (Brain Mass)^α, where α approximates 0.56 (Sacher, 1959; Hofman, 1993). This relationship is not merely correlative but is underpinned by the immense metabolic cost of neural tissue. The human brain, representing only ~2% of body weight, consumes ~20-25% of the body's basal metabolic rate (BMR) (Aiello & Wheeler, 1995). This "expensive tissue" imposes a fundamental constraint: extending cognitive function and neural integrity over the model's predicted 134–170 year median lifespan would require not just resisting mutational entropy, but also sustaining this disproportionate energy allocation for over a century beyond current norms.

This biophysical reality directly engages with the model's parameters. The study's calculated theoretical non-aging baseline of 430 years (at age-30 mortality) and its subsequent reduction by somatic mutations, while mathematically sound, exist in an evolutionary vacuum. As noted in ancillary paleoanthropological analyses, a projected increase in maximum lifespan (AÖ) to 200 years is evolutionarily coupled with a required expansion of brain capacity to nearly 5,700 cm³ and a significant rise in total caloric consumption (Bozcuk, 1982). The current model, by treating organ capacity (K) as a static, log-normally distributed variable, fails to incorporate the dynamic, co-evolutionary feedback between longevity, encephalization, and the body's energy budget. Sustaining a ~1.4 kg brain for 150 years is metabolically challenging; sustaining the larger brain implied by such longevity evolution would dramatically alter the energy landscape, potentially intensifying oxidative stress and influencing mutation rates themselves—a variable currently held constant.

Thus, by isolating somatic mutation accumulation from the broader context of human encephalization and its requisite metabolic investment, the study risks presenting an upper bound that is neurobiologically and evolutionarily untenable. The "entropic upper bound" imposed by somatic mutations might be preempted by an earlier "energetic upper bound" imposed by the escalating cost of maintaining the very organ most critical to survival—the brain. A comprehensive model must integrate these scaling laws, recognizing that lifespan extension is not a singular process of damage repair but a systemic renegotiation of energy allocation and neural architecture (Robson & Wood, 2008; Fonseca-Azevedo & Herculano-Houzel, 2012).

A further significant limitation is the model's disconnection from life history evolution and fertility dynamics. A core tenet of evolutionary biology is the trade-off between longevity and reproduction (Stearns, 1992). Historical and paleoanthropological data suggest that increases in lifespan are accompanied by delayed sexual maturation and extended reproductive periods (Bogin & Smith, 1996; Gurven & Kaplan, 2007). For instance, a lifespan extending to 150 or 200 years would logically shift the onset of reproduction to later ages (e.g., 22-27 or 30-37 years, respectively). The study's "somatic-mutations-only" scenario does not account for how such a dramatic shift in the reproductive window would impact population dynamics, intergenerational intervals, and genetic diversity. Ignoring these demographic and evolutionary feedback mechanisms limits the realism of the proposed lifespan extension, as reproductive strategy is a fundamental pillar of a species' survival and adaptation.

Additionally, the model gives limited consideration to energy metabolism and other primary aging processes. Longevity is intricately linked not only to the accumulation of cellular damage but also to the economics of energy production, allocation, and consumption—concepts central to the Disposable Soma Theory (Kirkwood, 1977). The human brain is a metabolically expensive organ, consuming a disproportionate share of the body's energy budget (Aiello & Wheeler, 1995). Supporting its function over 150-200 years would impose immense metabolic costs, potentially exacerbating other aging hallmarks like mitochondrial dysfunction. By focusing predominantly on somatic mutations, the model sidelines the potential compounding effects and interactions with other critical aging processes such as loss of proteostasis, altered intercellular communication, and stem cell exhaustion (López-Otín et al., 2013). A comprehensive upper-bound estimate must integrate these interconnected mechanisms.

In conclusion, Efimov et al. provide a valuable and sophisticated starting point for quantifying the theoretical limit imposed by one fundamental aging process. Yet, a truly holistic model of human longevity must integrate constraints from evolutionary biology, life history theory, and systems metabolism. Future research should aim to create integrative frameworks that simulate not only the accumulation of somatic mutations but also the co-evolution of brain and body, shifts in reproductive strategies, and metabolic adaptations required for extreme longevity. Such a multidisciplinary approach, bridging gerontology, evolutionary anthropology, and systems biology, will deepen our understanding of human lifespan limits and provide a more robust foundation for evaluating potential intervention strategies.

References

Aiello, L. C., & Wheeler, P. (1995). The expensive-tissue hypothesis: the brain and the digestive system in human and primate evolution. Current Anthropology, 36(2), 199-221.

Bogin, B., & Smith, B. H. (1996). Evolution of the human life cycle. American Journal of Human Biology, 8(6), 703-716.

Efimov, E., Fedotov, V., Malaev, L., Khrameeva, E. E., & Kriukov, D. (2025). Somatic mutations impose an entropic upper bound on human lifespan. bioRxiv. https://doi.org/10.1101/2025.11.23.689982

Gurven, M., & Kaplan, H. (2007). Longevity among hunter-gatherers: a cross-cultural examination. Population and Development Review, 33(2), 321-365.

Hofman, M. A. (1993). Encephalization and the evolution of longevity in mammals. Journal of Evolutionary Biology, 6(2), 209-227.

Kirkwood, T. B. (1977). Evolution of ageing. Nature, 270(5635), 301-304.

López-Otín, C., Blasco, M. A., Partridge, L., Serrano, M., & Kroemer, G. (2013). The hallmarks of aging. Cell, 153(6), 1194-1217.

Robson, S. L., & Wood, B. (2008). Hominin life history: reconstruction and evolution. Journal of Anatomy, 212(4), 394-425.

Sacher, G. A. (1959). Relation of lifespan to brain weight and body weight in mammals. *Ciba Foundation Symposium - The Lifespan of Animals, 5*, 115-133.

Stearns, S. C. (1992). The evolution of life histories. Oxford University Press.

On 2025-12-10 22:00:45, user Thomas O'Dell wrote:

This article was published in the November 2025 issue of the journal Hippocampus: https://doi.org/10.1002/hipo.70043

On 2025-12-10 15:33:46, user Sungwhan Oh wrote:

This preprint is now published in a peer-reviewed journal.<br /> doi: 10.1038/s41564-025-02141-1

On 2025-12-10 12:42:53, user Rui Wang wrote:

This preprint has not undergone peer review. The final version of record of this article is published in the journal Biology of Sex Differences, and is available online at https://rdcu.be/eTRja and https://link.springer.com/article/10.1186/s13293-025-00801-9

On 2025-12-09 23:05:23, user Harrison Lee wrote:

Is Figure 2C mislabeled? Based on the lysis assay described in the methods section, it does not make sense that there should be such strong lysis (as evidenced by the dark plaques / clearing zone on the bacterial lawn) for the empty vector control.

Also, the word induction is misspelled as "inductuion" in this figure.

On 2025-12-09 21:06:51, user Etter wrote:

This paper has been accepted as scientific paper in Ticks and tick-borne diseases,16, 102569. https://doi.org/10.1016/j.ttbdis.2025.102569

On 2025-12-09 20:57:00, user Prof. T. K. Wood wrote:

Should cite the seminal work that discovered the most-prevalent defense system, toxin/antitoxins by showing Hok/Sok is related to T4 phage defense and by determining the mechanism, transcription shutoff: doi: 10.1128/jb.178.7.2044-2050.1996

On 2025-12-09 19:07:03, user Gabriel Rocklin wrote:

I think these experimental results are consistent with a model where all the domains do fold in the full length construct, but have somewhat different individual melting temperatures, so the DSC and CD results do not show a high level of cooperativity. Each domain is cooperatively folded within itself (even in the full length construct), but there is low or no cooperativity across domains. I would expect the domains are actually stably folded in the full length construct.<br /> Gabriel Rocklin

On 2025-12-09 09:57:47, user Evolutionary Health Group wrote:

We at the Evolutionary Health Group ( https://evoheal.github.io/) really enjoyed this paper.

Here are our highlights:

The authors test the popular idea that humans prefer partners with dissimilar HLA genotypes in order to increase the immunological diversity of their offspring. Instead of urban populations - where it is extremely difficult to disentangle social and biological drivers of mate choice - they analyze a small, endogamous community of Himba pastoralists in Namibia. This community includes both “purely romantic” unions and marriages arranged by families (and the anthropological record on Himba marital categories is considered a well-validated and reliable source of information).<br /> This elegant design gives the authors a rare opportunity to directly compare HLA similarity between “chosen” and “arranged” partnerships within a single culture while carefully controlling for genome-wide relatedness, using a relatively large dataset (about 250 partnerships).<br /> The results show NO significant differences in HLA diversity between arranged and chosen pairs. Likewise, the authors find no advantage of chosen unions in the predicted breadth of pathogen-peptide binding repertoires. Instead, they observe very frequent sharing of long HLA haplotypes - a pattern clearly consistent with recent episodes of fluctuating positive selection, which appears to be the main driver of HLA representational patterns in the population.<br /> In a global sense, there is good reason to believe that Himba genotype data can yield rich insights into selection in human populations, helping to separate biological evolution from cultural processes.

On 2025-12-08 23:51:39, user Anna wrote:

This work has been updated, peer reviewed and published.<br /> See: https://pubmed.ncbi.nlm.nih.gov/41188644/

On 2025-12-08 15:37:15, user Damien F. Meyer wrote:

Please take into account this paper https://doi.org/10.3389/fcimb.2017.00535 showing that tr1 is coregulated with the T4SS by ErxR in Ehrlichia ruminantium

On 2025-12-08 14:56:28, user Erica Newman wrote:

I enjoyed this article. You might be interested in a related article we wrote a few years ago, which is a study about a forest under succession: https://onlinelibrary.wiley.com/doi/abs/10.1111/geb.13711

On 2025-12-08 10:21:44, user mossab1hax wrote:

wonderful and helpful

On 2025-12-07 22:47:33, user Sam Aroney wrote:

Now published: Aroney, S.T.N., Newell, R.J.P., Tyson, G.W. et al. Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes. Nat Methods (2025). https://doi.org/10.1038/s41592-025-02901-1

On 2025-12-07 17:32:03, user José Meléndez wrote:

This paper has been published at https://ami.info.umfcluj.ro/index.php/AMI/article/view/1191

MELÉNDEZ-GALLARDO, J., & PLADA-DELGADO, D. (2025). Serotonergic Modulation of Motoneuronal Excitability and Its Impact on Muscle Force Generation: A Computational Study. Applied Medical Informatics, 47(3). Retrieved from https://ami.info.umfcluj.ro/index.php/AMI/article/view/1191

On 2025-12-07 06:13:20, user Zeyuan (Johnson) Chen wrote:

Dear Biorxiv,

Please link this preprint to the final publication: <br /> https://link.springer.com/article/10.1186/s13059-025-03776-3

Thanks

On 2025-12-06 18:02:31, user zhengt wrote:

doi: https://doi.org/10.1101/2024.01.27.577582 had been published by mBio https://journals.asm.org/doi/10.1128/mbio.03172-24

On 2025-12-06 17:59:22, user zhengt wrote:

https://doi.org/10.1101/2024.02.01.578320 had been published by eLife https://elifesciences.org/articles/102681

On 2025-12-06 11:00:44, user GC wrote:

great work, thaks for sharing! Have you tried to use gapTrick for scoring your predictions? It would be very interesting to see if removing pairing and training set bias would improve the tpr.

On 2025-12-06 05:54:26, user trankos_89 wrote:

Thank you for this excellent study.

I wanted to bring to your attention what I believe is an important missing citation: PMID: 32513799. This reference appears highly relevant to your findings and closely aligns with the data presented in your work.

I hope this feedback is helpful for strengthening your study.

On 2025-12-05 14:49:26, user LaDarrius wrote:

This was a great read!

On 2025-12-05 14:17:55, user Inna Volynkina wrote:

Now, this work is published under DOI: https://doi.org/10.1134/S0006297925603740

On 2025-12-05 04:37:32, user Alan Cotter wrote:

Please download the supplementary material to obtain the ECOLPS software and the Trials.txt files for parameters of the trial simulations. You'll need R and, I recommend, Tinn-R to run the trials. Instructions for running ECOLPS are in Annex 3 and, more extensively, in the ECOLPS text file itself.

On 2025-12-04 20:04:45, user Sean Johnson wrote:

You should compare to:<br /> https://elifesciences.org/articles/91415 (ESM2 3B directly to 3Di)<br /> https://academic.oup.com/nargab/article/6/4/lqae150/7901286 (ProtT5 directly to 3Di)<br /> and<br /> https://academic.oup.com/bioinformatics/article/40/11/btae687/7901215 <br /> (longer structure embeddings claimed to be more sensitive than 3Di)

Can you combine with one of the first two approaches to produce TEA and 3Di embeddings in a single pass through a ESM2 or ProtT5?

In the first work above, I tried making hmms from 3Di, but it didn't give better results, and the search was really slow. I wonder if 3Di/TEA/Reseek embeddings are already approaching some kind of limit it terms homology search sensitivity.

I'm very interested to hear how your efforts to make TEA-hmms will turn out.

On 2025-12-04 15:57:07, user Jill Zeilstra wrote:

Do the authors have any information regarding the tRNA used in translating the arginine codons? Since the mito genome does not encode an arginine tRNA for AGR codons, wouldn't translation involve an imported tRNA?

On 2025-12-04 14:19:00, user Zhi-Ming Zheng wrote:

doi: https://doi.org/10.1101/2020.06.25.171959 had been published officially by mBio 2024 https://journals.asm.org/doi/full/10.1128/mbio.00729-24 . Thank you for your attention! Zhi-Ming Zheng

On 2025-12-04 09:03:46, user Joris de Wit wrote:

This preprint is now published in Science Advances: 10.1126/sciadv.adx5140

On 2025-12-03 09:37:45, user FS wrote:

Very Cool!

On 2025-12-03 04:29:43, user Susan wrote:

This study introduces a NanoLuc-based Sec-signal reporter to assess whether the Type IVa pilus system (T4aPS) contributes to non-pilin protein secretion in Synechocystis. The reporter itself is a valuable methodological advance, offering markedly improved sensitivity over traditional secretion assays. However, several experimental and presentation issues limit the strength and generalizability of the authors’ biological conclusions.<br /> The central claim that T4aPS components are dispensable for secretion is based entirely on a single engineered substrate, the TfAA10A–NanoLuc fusion. Because endogenous secreted proteins may use distinct Sec signal or rely on alternative export mechanisms. Many of the T4aPS mutants display regulatory and envelope abnormalities, yet the study does not quantify NanoLuc expression across strains. Consequently, differences in luminescence may reflect altered expression rather than true differences in export efficiency. Normalization of secretion output to OD750 complicates interpretation. The authors note that aggregation affects OD measurements, and aggregation varies considerably among the mutants. <br /> Despite RbcL being present in supernatants, this cannot rule out subtle lysis, selective leakage, or extracellular degradation of NanoLuc, leaving open the possibility that luminescence does not strictly represent secreted protein. The subcellular fractionation experiments are promising but lack purity markers, loading controls, and quantitative analysis, making mechanistic conclusions uncertain. The statement that the PilQ secretin is unnecessary for secretion is weakened by the absence of functional validation demonstrating loss of PilQ activity in the ΔpilQ strain. Similarly, the proposed mechanism for enhanced secretion in ΔpilA1 remains speculative without supporting measurements of Sec-pathway components or alternative Sec substrates.<br /> Presentation issues also reduce clarity. Several figures lack color and contrast, limiting interpretability, and some figure descriptions have methodological information. Typographical inconsistencies and minimal statistical reporting, combined with reliance on a single 24-hour endpoint, further detract from the manuscript’s rigor. Overall, the NanoLuc reporter represents a promising tool for cyanobacterial secretion studies, but the biological interpretations require additional controls, expanded substrate testing, more robust normalization, and clearer data presentation. The study supports only the conclusion that this Sec-signal NanoLuc reporter does not depend on the T4aPS under the tested conditions, it does not justify broader claims about cyanobacterial non-pilin secretion pathways.

On 2025-12-03 03:45:39, user Sandro Santillan wrote:

Your study is important because it explores a classic question in evolutionary biology: whether humans share certain acoustic preferences with other animals. You also use a new comparative approach by testing sounds from many species, which makes the work original and valuable.<br /> An introduction should be added to generally speak about the topic of bioacoustics, and the reasoning behind the similarities in acoustic preference.<br /> Regarding the methodology, the design is appropriate to establish the correlation , however a main limitation is that the sounds used for the study don't reflect the natural context of the source. Digitally editing them and isolating them from their natural environment, could make the subject’s preferences biased. Also, because they came from different sources, it is difficult to ensure the uniformity of the quality and volume, which could also add a bias towards the preferences. Finally, the study doesn't control for a possible familiarity with the sounds in the participants, which could also add to the bias of the results. This should be added in your discussion.<br /> Concerning the results and their interpretation, there is a risk of overestimating the conclusion about the shared acoustic preferences between humans and non-human animals. This is because the percentage of agreement between the two was 56.4%. Even though this was statistically significant, it's still a very limited effect size. Moreover, the mechanisms of decision between humans and non-human animals when choosing a more “beautiful” sound should be supported by the fact that both groups prefer a certain acoustic feature. However, the results show the contrary, proving that specific acoustic features have no effect in sharing the same auditory taste. Finally, the group of sounds from species used in the study is small and not very diverse), which could undermine the generalization that humans share acoustic preferences with animals. <br /> The overall idea of the study is very interesting and it's not that well researched, showing great potential. Also, the main points made were communicated effectively in a way that is understandable. As a final suggestion, a short summary of the methodology employed could be added to the abstract.

On 2025-12-03 01:12:35, user Marcelo Salas wrote:

The manuscript addresses relevant protein targets associated with Parkinson’s disease and explores a set of phytocannabinoids with potential therapeutic implications. This integrative approach, combining docking, ADMET prediction, and molecular dynamics, is conceptually valuable and could provide meaningful preliminary insights. However, several methodological aspects require clarification or refinement to ensure that the conclusions presented are scientifically robust and reproducible.

From a methodological perspective, the docking section would benefit from substantial improvement. The study does not report a redocking of the co-crystallized ligand nor provide RMSD values, making it impossible to determine whether the docking protocol can accurately reproduce known binding poses. Furthermore, several essential parameters—such as exhaustiveness, number of runs or modes, pose-selection criteria, and software version are not specified, limiting reproducibility. Although the grid box dimensions are reported, their rationale is not explained, particularly for α-synuclein, an intrinsically disordered protein that lacks a stable binding pocket. Using a rigid docking protocol for such a target requires additional justification or alternative strategies.

The ADMET analysis also presents inconsistencies. Several LD₅₀ values appear implausible, suggesting potential issues with molecular input files or prediction settings. Moreover, some interpretations, such as characterizing compounds as “non-toxic if ingested", are too strong for in silico predictions, which should be framed as preliminary and subject to experimental validation.

The molecular dynamics section exhibits additional methodological ambiguities. The simulation box is reported with units incompatible with atomistic MD, and essential parameters such as ionic concentration, thermostat and barostat conditions, NVT/NPT equilibration steps, and time-step are not described. Only a single trajectory is presented without replicates, and the structural analyses are limited to basic RMSD and RMSF plots, without energetic evaluations such as MM-GBSA. These omissions hinder assessment of the stability and reliability of the proposed protein–ligand complexes.

Finally, several presentation issues affect clarity. Some tables lack units or clear column descriptions, and the selection criteria for the four compounds included in the interaction tables are not explained, despite docking fifteen molecules.

In summary, the manuscript addresses an interesting question and uses relevant targets, but significant methodological clarification and refinement are necessary before the results can support the conclusions drawn.

On 2025-12-02 23:22:28, user Jimena Patricia Giraldo Flores wrote:

We are undergraduate students from the Biology program at the Universidad Peruana de Ciencias Aplicadas (UPC). As part of our academic training, we are analyzing recent preprints and publications to strengthen our critical understanding of genomics. In this context, we would like to share our observations.

We recognize the important advances achieved in your zebrafish genome study, particularly the closure of gaps and the integration of third-generation sequencing technologies. Nevertheless, we believe certain methodological aspects require further consideration.

First, the figures presented in the preprint aren’t of the highest quality, making it difficult to see the graphics and plot names. Since figures are a central element in communicating scientific results, the image resolution is crucial to fully appreciate the data and conclusions.

Second, the exclusive reliance on Verkko as the assembler reduces reproducibility and methodological robustness. While Verkko is powerful, particularly for Telomere-to-Telomere projects, benchmarking against widely adopted assemblers such as Flye or Canu, or even Wengan is essential. Without such comparisons, it is difficult to determine whether the reported improvements in contiguity and gap closure are genuine biological advances or artifacts of the chosen software. We suggest doing further analysis and comparison of assemblers in order to have a more robust pipeline.

Third, we note the absence of detailed controls and verifications that would strengthen confidence in the assembly. These include: (1) confirmation of the absence of paternal contribution through comparative genotyping of TU mothers, AB sperm, and doubled-haploid adults; (2) verification of ploidy and mosaicism by karyotyping (3) cell culture controls such as reporting passage number, mycoplasma testing, and fibroblast karyotyping to ensure genomic stability.

The pangenome analysis, while mentioned, is not fully aligned with the study’s main objective of generating a gap-free reference. Broader and more systematic characterization of genetic diversity would be required before extending conclusions to the whole pangenome.

In conclusion, we recognize the importance of your work and its contribution to zebrafish genomics. Incorporating benchmarking, and systematic controls would further enhance the reproducibility, credibility, and long-term impact of this valuable resource.

On 2025-12-02 20:25:03, user MB wrote:

Fascinating findings and lovely work- congratulations to all the authors! One point of concern- as of 02 December none of the data/material sharing links provided (e.g. NCBI or Github) are available or return any information.

On 2025-12-02 14:42:29, user Deepak Modi wrote:

The manuscript is published and available at https://www.nature.com/articles/s41420-025-02799-w

On 2025-12-02 10:54:18, user Babür Erdem wrote:

This article was published in a peer-reviewed journal. Citation:<br /> Babur Erdem, Ayben Ince, Sedat Sevin, Okan Can Arslan, Ayse Gul Gozen, Tugrul Giray, Hande Alemdar,<br /> Api-TRACE: A system for honey bee tracking in a constrained environment to study bee learning process and the effect of lithium on learning,<br /> Computers and Electronics in Agriculture,<br /> Volume 241,<br /> 2026,<br /> 111236,<br /> ISSN 0168-1699,<br /> https://doi.org/10.1016/j.compag.2025.111236. <br /> ( https://www.sciencedirect.com/science/article/pii/S0168169925013420)

On 2025-12-02 02:52:36, user Anthony Gerber wrote:

This well done new work was in part anticipated by work from the Stallcup lab published in 2017 in 2017, which should be cited in the final publication.

On 2025-12-01 15:42:06, user Sherif wrote:

Great job

On 2025-12-01 13:50:34, user Abdelrahman Osman wrote:

congratulations Omar on publishing your impressive paper, you truly did a great work.

On 2025-12-01 02:54:02, user hibiscustea wrote:

Hi, thank you for sharing this preprint, it’s really bold work, and I enjoyed reading it. A couple of things you might consider for the next version: the Introduction would really benefit from explicit hypotheses, just so readers know what the expected contrasts were between phenology and morphology. Some of the modeling assumptions (equal evolutionary variances, missing environmental forcing) could use a clearer justification too. And the transition to the empirical motifs comes a bit abruptly, the Doñana system is very seasonal, so V+ motifs might appear for several reasons besides coevolution.<br /> But overall, really interesting work. Looking forward to seeing where it goes next. I'm a PhD student and we are reviewing a preprint paper for a class, I chose yours, thank you for your work.

On 2025-11-30 12:31:56, user David Greening wrote:

Please note this article has now been published in full: https://www.nature.com/articles/s41556-025-01795-7

Rai, A., Huynh, K., Cross, J. et al. Multi-omics identify hallmark protein and lipid features of small extracellular vesicles circulating in human plasma. Nat Cell Biol (2025). https://doi.org/10.1038/s41556-025-01795-7

On 2025-11-30 07:11:24, user Misha Koksharov wrote:

I presume the final version of this paper was published in 2024: <br /> Vedalankar, P., Tripathy, B.C. Light dependent protochlorophyllide oxidoreductase: a succinct look. Physiol Mol Biol Plants 30, 719–731 (2024). https://doi.org/10.1007/s12298-024-01454-5

On 2025-11-29 18:12:35, user Agata Leszczuk wrote:

The paper is currently published in Plant Science: https://doi.org/10.1016/j.plantsci.2025.112906

On 2025-11-28 21:08:51, user Andre Rendeiro wrote:

The manuscript from Pyne et al. develop a computational framework<br /> to predict potential trajectories of bone mineral density for<br /> particular individuals using generative adversarial networks (GANs).<br /> The manuscript is well written (despite being quite technical for<br /> an aging-specific audience) and the method is interesting, but the<br /> need for the application of GANs to this problem is not fully justified.<br /> In addition, the evaluation of the model's performance is as rigorous<br /> as it could be,<br /> and it is not clear whether the model is truly capable of generalizing<br /> to unseen timepoints of specific individuals or is simply learning to<br /> interpolate/extrapolate at the population level.

Major comments

1. It is known that several aging phenotypes are shared across a population<br /> with fairly moderate reproducibility/variability - which is what enables<br /> the establishment of population-level aging clocks which are mostly linear<br /> models. Therefore a baseline to compare to could be a linear regression model<br /> which accounts for individual-specific differences such as a linear mixed model that<br /> is trained on the same covariates as input, but seeing only a fraction of the timepoints<br /> and simply inter- or extrapolates to a held out timepoint. Another benchmark to beat<br /> could be a gaussian process regression model, which is well suited to modeling temporal<br /> data and supports irregular timelines and missing data. These models would be important<br /> baselines to assess the generative model's ability to capture individual-level trends<br /> rather than simply population-level trends.

2. The evaluation of the generated timepoints for various individuals is not rigorous<br /> enough. The simple quantification of a score with an arbitrary threshold is too<br /> lenient as it does not capture individual-specific trends,<br /> but can report inflate performance simply by capturing population-level trends.<br /> A more quantitative assessment of the model's ability to capture individual-level<br /> trends is needed.<br /> This could be done by evaluating the mean square error, mean absolute error,<br /> Pearson correlation and R^2 between predicted and true<br /> values at the held-out timepoint, as well as evaluating<br /> the ability of the model to rank individuals according to their predicted<br /> phenotype values at the held-out timepoint. Another approach could be to<br /> perform a clustering analysis of the predicted vs true values to see if<br /> the model can capture subgroups of individuals with similar aging trajectories.

3. I am not sure the model is truly capable of generalizing across time because it<br /> always sees timepoints 2 and 4 as inputs and predicts timepoints 5 and 8 as targets.<br /> So it may not necessarily ever learn to generalize to an unseen time index as it<br /> could simply learns the mapping of 2,4 to 5,8. What is being evaluated is therefore<br /> only a test of whether the model can inter- and extra-polate across individuals for<br /> these fixed visit times. In addition, the conditioning timepoints are assymetric<br /> (2 and 4 are both early). Related to my previous point, if the cohort shows<br /> predictable average decline between t4 to t5 and t5 to t8, then a simple<br /> baseline (like a linear mixed model or gaussian process) should capture this well.<br /> It would be interesting to see how the model performs when trained and evaluated<br /> on different timepoints. The hold out timepoint (7) does provide some evidence<br /> but is not sufficient to demonstrate generalization across time as the performance<br /> of predicting that one timepoint could be easily interpolated from the others<br /> at the population level and not at the individual level.

Minor comments

1. Some abbreviations need to be defined at first use (e.g. SIR).

2. The methods section could more explicitly describe that the timepoint 7 is<br /> held-out during training and only used for evaluation.

3. The specification of the various 'strata' is really not clear.

On 2025-11-28 12:37:29, user Jörg Klug wrote:

This preprint was published in 2023 already.<br /> DOI: 10.15252/embr.202357064<br /> Is this information not updated automatically?

On 2025-11-27 20:45:13, user Mucahit wrote:

Preprint Review of the Article Titled

‘’Immune Profiling of the Axilla with Fine Needle Aspiration is Feasible to Risk-Stratify Breast Cancer’’

doi: https://doi.org/10.1101/2025.10.22.683956

The research conducted by Naidoo et al shows that immune profiling of axillary lymph nodes (ALN) samples taken by fine needle aspiration (FNA) would be an efficient method to predict breast cancer (BC) prognosis. As FNA is a less invasive method for obtaining samples from patients, the article's findings would provide new insights for researchers and clinicians. Another important result of the article is that the immune cell profile of a single reactive ALN appears to reflect the patient's entire immune status in the axilla.

The article has explained that FNA itself has sufficient leukocytes for comprehensive cell immunophenotyping of reactive ALN.

The research question was well explained, and the results were presented clearly. The results of the study have given significant and novel information about the concept.

All conclusions are well-supported by the results. Results obtained from different directions have backed each other up. Results might be supported more effectively by using control groups more in experiments. Yields of the animal study might be stronger if it were applied to animals with breast cancer.

The quality of writing is fine. It seems to be accessible to both experts and semi-experts. Figures in the text were well presented, and legends provided enough information.

The publication appears to attract a lot of interest from clinicians and researchers in different areas.

The authors’ contributions were fairly explained. It was a remarkable point to know that samples were de-identified in the study before being released to researchers to ensure blinded data analysis.<br /> Increasing the number of patients participating in the study would lead to an improvement in the statistical significance of the results.

Using only the results of the article is not sufficient to make a generalized conclusion about BC diagnosis. Results need to be confirmed by further studies to change the current approach to BC diagnosis.

On 2025-11-27 20:34:42, user Paola Murgas PhD wrote:

This is an interesting manuscript showing the non-inflammatory function of STING, confirming our previously published data ( https://doi.org/10.1186/s40659-025-00624-3) .

We found that STING deficiency results in increased body weight, independent of alterations in locomotor activity or food consumption.

Moreover, STING-null mice exhibited markedly elevated circulating triglyceride and total cholesterol levels. Furthermore, histological and morphological analysis demonstrated augmented fat accumulation in adipose and hepatic tissues, despite the lack of nutritional or genetic metabolic stress.

These findings indicated a crucial function for STING in the control of lipid homeostasis across the lifespan ( https://doi.org/10.1186/s40659-025-00624-3) .

Although we did not test in other species, it is important to note that STING is an evolutionarily conserved regulator of lipid metabolism beyond its well-known inflammatory role.

On 2025-11-27 15:35:01, user Manuel Mendoza wrote:

Peer-reviewed version available in JCB https://doi.org/10.1083/jcb.202502014

On 2025-11-27 06:01:48, user Merlyn wrote:

Romiumeter: An Open-Source Inertial Measurement Unit-Based Goniometer for Range of Motion Measurements<br /> Basinepalli Kothireddy Gari Diwakarreddy, S Abishek, Amal Andrews, Lenny Vasanthan, View ORCID ProfileSivakumar Balasubramanian<br /> doi: https://doi.org/10.1101/2024.05.29.596353

Brilliant article !is it published or still under peer review.

On 2025-11-26 05:26:36, user Prof. T. K. Wood wrote:

Please cite the seminal paper that initiated research on the impact of bacteria-derived indole on human physiology: http://www.pnas.org/cgi/doi/10.1073/pnas.0906112107 <br /> This manuscript was the first to find indole tightens epithelial cell junctions.

On 2025-11-26 05:03:47, user Oded Beja wrote:

Our preprint is now published in Nature https://www.nature.com/articles/s41586-025-09656-x

On 2025-11-26 02:46:52, user Tania Perroux wrote:

This article is now published in Journal of Zoology<br /> https://doi.org/10.1111/jzo.13017

On 2025-11-26 02:44:40, user Tania Perroux wrote:

Now published in Royal Society Open Science https://doi.org/10.1098/rsos.250379

On 2025-11-25 23:52:27, user Huigang Shi wrote:

Please note: The author name “Wuchun Ling” appears incorrectly in the preprint metadata and PDF.<br /> The correct name is “Chunling Wu,” as shown in the published journal version.

On 2025-11-25 21:14:55, user Evolutionary Health Group wrote:

We at the Evolutionary Health Group ( https://evoheal.github.io/ ) really enjoyed this paper.

Here are our highlights:

Including nutrient availability shifts the focus of antibiotic control from "more drug vs less drug" to how the population's vulnerability state can be altered as a mechanism driving extinction.

The reinforcement learning (RL) agent discovers strategies that humans would be unlikely to design, such as giving nutrients before antibiotics and pausing drug application until cells return to a susceptible state, illustrating how machine learning-guided therapy can find hidden leverage points.

It's unlikely that clinicians will have access to "full-state" information like subpopulation composition or proteome sector fractions. By restricting the agent's observations to the population growth rate, the authors demonstrate that RL-based population control is feasible even with severely limited observability.

Rigorously testing the generalizability of the RL method shows that it can discover principles of susceptibility that are broadly applicable. Uncovering such principles enables RL to propose treatment strategies that leverage fundamental cellular physiology, rather than simply fitting a training scenario.

On 2025-11-25 15:00:15, user Evolutionary Health Group wrote:

We at the Evolutionary Health Group ( https://evoheal.github.io/) really enjoyed this paper.

Here are our highlights:

This work evaluates the potential for oral microbiome sequencing to predict esophageal squamous cell carcinoma. The authors transparently evaluate the potential for their model to generalize to external, held-out datasets.

We like how the formulation of the method is clearly articulated, beginning with simpler descriptive statistics and culminating in the final model.

The authors compute and visualize SHAP values, revealing that some of the top predictive features are microbes already putatively associated with disease incidence. While the biological properties of these features are described in detail, the authors are also careful to emphasize that causality has not been robustly assessed (in this work, or more broadly).

We like how the authors emphasize that the oral microbiome is relatively stable over time compared to other body sites. We are excited by the possibility that, in principle, this stability could support individual longitudinal surveillance efforts that could lead to the discovery of predictive signatures with greater generalizability (accounting for individual baseline variability).

On 2025-11-25 11:41:10, user Evolutionary Health Group wrote:

We at the Evolutionary Health Group ( https://evoheal.github.io/) really enjoyed this paper. Here are our highlights:

This study provides a clear and thoughtful evaluation of whether modern deep generative models can meaningfully improve ancestral sequence reconstruction (ASR). The authors explore a compelling idea: that variational autoencoders (VAE), trained on homologous protein families, might capture epistatic interactions that classical site-independent evolutionary models omit.<br /> A key highlight is the demonstration that VAE latent spaces do recover meaningful phylogenetic structure. The authors show that relationships among sequences are encoded coherently in the latent representation, suggesting that deep models can learn informative global organization from sequence data - an encouraging insight for future machine-learning approaches to molecular evolution.Another important contribution is the comparison across simulated evolutionary scenarios, with and without epistasis. Across all cases, classical maximum-likelihood ASR methods outperform the VAE-based approach.<br /> Finally, the study identifies the decoder as a key bottleneck, offering a constructive direction forward for the field. Even when the latent space contains strong phylogenetic signal, reconstructing accurate ancestral sequences remains challenging. The authors highlight a concrete opportunity for model development and for integrating phylogenetic constraints more explicitly into deep generative architectures.

On 2025-11-25 09:07:03, user Layue wrote:

Unbelievable，do immune cells also display “associative learning” like brain?

On 2025-11-25 08:53:39, user Kris wrote:

The topic of the manuscript is conceptually intriguing.....

On 2025-11-24 17:41:36, user Andrew Castonguay wrote:

This is very nice work! Looks like the image files were maybe compressed prior to submission; would the authors kindly re-upload with high DPI?

On 2025-11-24 13:12:26, user Stefano Busti wrote:

Nice follow-up of the 2019 paper. One thing it's unclear to me: for NIRFPs, how did you provide biliverdin ? Were the proteins expressed in a bioengineered strain to slef-produce chromophore?

On 2025-11-24 08:18:05, user Mikhail Kutuzov wrote:

Dear authors,

it was a great interest to read the article «Nucleosome unwrapping and PARP1 allostery drive affinities for chromatin and DNA breaks» devoted to study of PARP1 interaction with DNA and nucleosome providing at a single molecule level. It’s really exciting to see “the molecular face”. You made a very intriguing experiment with the partially NCP unwrapping and received a hopeful result on it. One more interesting feature is relative to PARP1 trapping mode in the presence of different inhibitors that is a direct demonstration of protein holds-on on DNA.<br /> However, after discussion your paper on a lab seminar I have got several questions that probably arise due to I am not a specialist in optical tweezer and confocal microscopy fields. I hope that you could clarify it for me.<br /> 1. I couldn’t find in the text how the dwell and gap times were converted to k(off) and k(on app). Is it just the reciprocal value of the projection of the inflection point of the sigmoid approximation onto the time axis? Additionally, is it correct the kon app = k(on)/C(PARP1)? How did you estimate the DNA concentration under single molecule conditions? I also could not find the PARP1 concentration used in the experiments. Is that 0.1 nM?<br /> 2. The time resolution of microscope used in the work is 1/10s. One of the basic assumptions for result interpretation was the absence of association/dissociation acts of the DNA-protein complexes during this time period. As far as spontaneous collisions are limited by diffusion and can happen 10^9 times/s, how do you estimate the probability of reassociation of dissociated complexes during the dwell periods? To exclude the reassociation did you try to transfer the trapped DNA with bounded PARP1 molecules to the channel without PARP1 (with buffer) with keeping the flow? In my opinion it could allow to avoid PARP1 reassociation events from the calculation.<br /> 3. In the text you do not discuss potential dimerization of PARP1 and PARP2 under DNA/nucleosome bounding. Although, it seems to me that it is important for Kd calculations.<br /> 4. According to your data, the binding manner of PARP1 with nick-sites is different in frames of one DNA molecule. Part of tracks demonstrate a long dwell and gap periods; another part is characterized short dwell and gap periods. Did you take it into account in any way at the constant calculations or results interpretation?<br /> Moreover, on the kymograph of PARP2 binding there are only two nick sites from seven were found in association, and due to long dwell periods, it led to low Kd calculated value. Could you somehow comment your interpretation of the obtained result and the feasibility of using calculation method?<br /> 5. I didn't find in the text and references what kind of plasmids did you use for the transient overexpression of the fluorescent-tagged proteins.<br /> I will be very grateful for clarification these questions for me.

Thanks in advance,<br /> Mikhail

On 2025-11-23 04:39:09, user Ainsley wrote:

In Figure 3, the inconsistency between the usage of triangles to represent pulses or constancy between A/B and C/D is harmful to the efficacy of the figure’s data presentation. Picking one shape for pulses and one for constancy would be better. Additionally, the colors chosen for pulse 2 and pulse 3 in C/D are too close together in color and make the figure more confusing to read. Otherwise, the figures are very well made and effectively present the dense information from this complex research.

On 2025-11-22 23:05:01, user SF wrote:

Overall, I thought that this manuscript provided an interesting look into the diet of the Reunion Island free-tailed bat and its implications. However, compared to the rest of the text, I thought that the Discussion section could benefit from more integration with the overarching ideas addressed towards the beginning of the Introduction. Tying the conclusion back to the big picture (i.e. potential applications of understanding bat diets on pest management, agriculture, and disease vector control in modified landscapes) could help re-establish the importance of this study beyond Reunion Island and create cross-disciplinary connections with other fields such as agricultural science, economics, and public health. It may also be helpful to reiterate a few points from the first paragraph of the Introduction (lines 44-56) to emphasize the importance of understanding ecological dynamics in highly-modified landscapes that are often major sites of human settlement/ interest.

On 2025-11-22 18:00:08, user Michael wrote:

Extremely cool work, well done!

On 2025-11-22 11:27:20, user Néstor de la Visitación wrote:

This preprint has been published in Circulation research. DOI: https://doi.org/10.1161/CIRCRESAHA.124.324068

On 2025-11-22 02:22:59, user Sandy Emery wrote:

The blanket descriptor of rhizobacterial inoculated plants gets used in earlier sections while in later situations you specify the specific rhizobacteria. This got confusing because at one point it seemed like all three were in one group because of the generalized statement; however, it is just grouping the three treatments together. I think you should think about changing your phrasing from the general statement to “the three rhizobacterial inoculated plants” for ease of understanding. As I read further, it was easily understood, but in the beginning when its not as clear of all the aspects of the experiment specifying its for all three groups would have be nice.

On 2025-11-22 01:36:22, user Birdie wrote:

L77-81: “As forests grow in age and complexity, they are able to sustain stable microclimates that are on average cooler than in deforested areas during the day and in the summer, and warmer at night and in winter, as a result of changes in the vertical and horizontal structure of forest canopies and understories. These cooler microclimates buffer many species from extreme temperatures and can facilitate local persistence” [italics added]). This is one of many instances in the manuscript where I am left unsure whether it is the coolness per se of the plots for which microclimates are valuable habitats or whether it is because of their bufferedness/stability. In the first sentence bufferedness seems to be the important quality, but in the latter sentence coolness seems to be. This lack of clarity regarding bufferedness versus coolness recurs throughout the manuscript. Early in the introduction, the manuscript should clearly outline the relationship among microclimates, coolness, and bufferedness and their relative uses in the text.

On 2025-11-21 20:26:09, user Anita Salamon wrote:

Thank you for sharing this exciting work. In addition to empagliflozin, have you tested any other SGLT2 inhibitors for binding to PANK1? I’m particularly interested in bexagliflozin.

On 2025-11-21 18:49:01, user Max Seldes wrote:

To the authors, I very much enjoyed reading this manuscript! I found the introduction and discussion sections to be particularly well structured and were very logical in their progression. I wanted to know if you have any way of retrieving or calculating the specific locations of calls or relative density of calls along your transects? I think this project could really grow from investigating the correlation of call frequency/density with canopy cover as an explanatory variable in something like a GLMM or ANOVA. If you were able to do this, I think it would be really cool to create some additional layers like percent road coverage within a 1km buffer or percent surface water to test some of the suggested explanations for the shift in overall abundances. You could even quantify stuff like distance to forest patch or something like that to really hone in on patch effects. I think this project has a really great direction and could really easily be expanded upon! Best of luck to the authors on your future endeavors and I hope to see more from you!

On 2025-11-21 18:43:34, user AzC919 wrote:

A key issue that substantially limits the strength of this manuscript is the decision to pool three bee guts into a single microbiome sample for each microcolony. While pooling can reduce sequencing costs and simplify workflow, it also eliminates all variation at the individual level. This variation is essential for understanding how thermal stres and pathogen infection can impact hosts differently. Individual bees vary in microbiome composiiton, immune status, body size, and infection intensity, and these variations are biologically meaningful. When you average individuals inot a singular pooled sample, it blurs whether observed microbial shifts reflect consistent responses across bees or the cominance of a single/few outlier(s). This loss of clarity can affect nearly every analysis presented in the manuscript, including alpha and beta diversity estimates, infection quantification, and the interpretation of taxa associated with particular treatments. <br /> Even though the manuscript briefly acknowledges this limitation, they frame it mainly as a reduction in sequencing resolution rather than a core biological constraint. The manuscript would benefit from a clearer justification for pooling, whether it was due to logistics, cost, survivorship, or colony level focus. Also a more explicit discussion of how pooling influences the interpretation of microbiome patterns would greatly clarify this inconsistency. Overall, addressing this issue directly in the manuscript would improve the transparency in the study’s results, and strengthen the conclusions.

On 2025-11-21 17:10:10, user Liz Cramer wrote:

Hi authors! I really enjoyed this paper! The topic is very relevant and important to be researching. I also thought you did and excellent job of setting up the novelty of the study and justification of why you chose to study these factors. However, when I was reading your methods I may have found something you might want to look into. I will say I am not an expert in statistical analyses, but based on my knowledge, these are my suggestions. First, you assigned distance to forest patch as a fixed effect, but I think this effect would be more accurately described as random. Since there is a range of possibilities for distance to forest patch I believe this should be a random effect because there are not a fixed number of possibilities for this variable. Unless you predetermined and intentionally chose certain distances to forest patches. Additionally, I think orchard ID should be a fixed effect, not random. Since orchard ID was predetermined and there is a fixed number of possibilities for this variable, I think it should be treated as a fixed effect rather than random.

On 2025-11-21 16:57:05, user Troy Kervin wrote:

Hi all, overall an excellent manuscript. There are a few things I would like to mention.

We have already resolved the question you pose: "But we are unsure which came first: is it the proteins that bring these ordered lipids with them, or do the lipids form domains into which the proteins partition?" Indeed, we built a theoretical framework where one of the central theories is that lipids do not form stable subregions that subsequently recruit proteins ( https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-024-01849-6 ). The answer lies with lipid fingerprints ( https://pubs.acs.org/doi/10.1021/acscentsci.8b00143) .

Suppose lipid-lipid interactions were strong enough to form platforms large enough to accommodate proteins (the evidence for this is very poor, by the way). It wouldn't matter. The idea that the proteins and lipids are collectively present in the final structure suggests that the proteins have preferential interactions with the lipids, so there would have to be a very good reason why the lipids would "ignore" the proteins such that they cluster and then recruit the proteins in a sequential manner. If this is insufficient to cover all cases (for example, if the proteins are not initially present in the membrane when the lipids supposedly cluster), there are many other reasons why this cannot occur. For example, if the lipid platforms are ordered, one would expect there to be a free energy barrier for protein entry. I could go on and on, but there is really no need. It is a thermodynamically absurd notion.

This sequential mechanism was popularized by the original lipid raft theory. Since it was false, lipid rafts underwent many ad hoc modifications and should now be regarded as pseudoscience ( https://www.researchgate.net/publication/397646378_Lessons_from_pseudoscience_in_biology ). I should also mention that the phase separation narrative (which I debunk here: https://doi.org/10.5281/zenodo.17201253 ), and Kusumi et al.'s picket fence/tiered mesoscale domain model are also wrong. I think you will understand why after reading lipid fingerprints ( https://pubs.acs.org/doi/10.1021/acscentsci.8b00143) and the proteolipid code ( https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-024-01849-6 ).

Since I am challenging so many of their beloved theories, the lipid raft people, who still run the place, do not want you to know that the proteolipid code exists. I hope that this excuses my somewhat aggressive promotion ( https://proteolipid.org ).

Best of luck with this.<br /> Troy

On 2025-11-21 14:42:48, user ARB wrote:

I am writing this comment as an assignment for a graduate-level class.

I thoroughly enjoyed the overall conceptualization of this manuscript, and I believe it effectively addresses the current gap in eco-evolutionary studies. I also appreciated the manuscript's approach to connecting empirical studies with the theoretical model to evaluate eco-evolutionary dynamics in real communities. However, I think the manuscript can benefit from a writing review. For instance:<br /> Line 243: The whole paragraph from Line 243 to Line 247 is an exact copy of the previous paragraph.<br /> Line 261: The usage of linear regression analysis to examine the relationship between warming rate and different stabilities is mentioned several times in different paragraphs. It is also the case for the next paragraph from Line 268 to Line 274.

On 2025-11-21 08:40:17, user Catherine Etchebest wrote:

This paper is now published in J. Chem. Inf. Model. 2025, 65, 20, 11454–11472

On 2025-11-21 01:22:49, user Aline Machado wrote:

This study explores how Pheidole bergi colonies are distributed across habitats and spatial scales in the Monte desert, and how natural and anthropogenic environmental variation affects colony density and spatial structure. Long-term data reveal strong preference for protected algarrobal habitat; major density declines through drought years; density-dependent shifts from aggregation to more dispersed patterns; consistent microhabitat selection toward inter-patch borders and open patches.<br /> This is a promising and well-executed spatial ecology study, but several issues must be addressed for clarity and robustness. The largest concerns involve justification of biological assumptions, narrative organization, overinterpretation of environmental drivers, and insufficient integration of the anthropogenic component.

MAJOR ISSUES<br /> 1. The assumption that each nest corresponds to a separate colony must be justified<br /> This is the main flaw of this study. The analyses assume that each nest entrance represents an independent colony, but this assumption is never justified. Many Pheidole species are polydomous, meaning that multiple nests may belong to the same colony. If P. bergi is polydomous, nest counts may not correspond to colony counts, spatial clustering may reflect intra-colony nest structure rather than interactions among colonies, observed “repulsion” could represent spacing among satellite nests, and density declines may reflect contraction of colony structure rather than colony mortality. This has direct implications for all spatial analyses. Given that the authors note that little is known about the natural history of P. bergi, this issue needs to be addressed explicitly. The manuscript should clarify whether P. bergi is known to be monodomous or polydomous, how this was assessed in the field, and what implications this uncertainty may have for interpreting spatial patterns.

1. The manuscript does not explicitly link its predictions to its results and discussion<br /> The Introduction presents several detailed, scale-specific predictions regarding habitat-level differences in aggregation, drought-induced density-dependent thinning, mosaic-driven microhabitat selection, predicted shifts in inter-colony interactions, and responses to anthropogenic disturbance. However, these predictions are not revisited consistently in the Results or Discussion. In several sections it is unclear which prediction a given result addresses, or whether a result supports or contradicts the authors' expectations. Reorganizing the Results and Discussion using a clear prediction–finding–interpretation structure would substantially improve narrative clarity and help readers understand how each analysis addresses the study’s questions.

2. Anthropogenic variation is stated as a major objective but receives insufficient analysis <br /> The Introduction frames the study as examining abundance, habitat associations, and spatial arrangement across both natural and anthropogenic sources of environmental variation. Yet the anthropogenic component receives very limited treatment. The “grazed algarrobal” appears only in a single 2021 sampling, with no information provided about the intensity or history of grazing, and anthropogenic predictions are not explicitly stated. In the Discussion, the potential effects of grazing and dirt-road disturbance are mentioned only briefly, without deeper engagement or clear linkage back to the stated objectives. Clarifying the expected ecological effects of grazing and dirt roads, showing how those expectations were tested, and revisiting these comparisons explicitly in the discussion would bring the manuscript into better alignment with its claims.

3. A spatial overview map is essential but missing<br /> An important limitation is the absence of a spatial overview map. Because spatial scale and spatial context are central to the study, a map showing the locations of all dirt-road transects, he positions of dirt-road transects (D, F, D1, D2, F1, T, L, P1, P2, M), and the two permanent grids (J, V), habitat boundaries such as algarrobal, sand dunes, and grazed lands, and approximate distances among sites is essential for interpreting habitat comparisons and understanding how environmental heterogeneity relates to the observed patterns. Without such a map, it is difficult for readers to evaluate the spatial independence of sampling areas or the relevance of local heterogeneity. Including a map would greatly improve the clarity of the manuscript.

4. Environmental drivers underlying heterogeneous intensity patterns are inferred but not measured<br /> Along the dirt-road transects, for example, environmental attributes such as soil texture, moisture, or vegetation structure are invoked to explain variation in colony distribution, but these variables were not measured. Thus the interpretations rely on assumptions rather than data. The manuscript would benefit from acknowledging more explicitly that interpretations of road-scale heterogeneity are speculative unless environmental covariates are incorporated into the analyses.

5. Gibbs point-process model interpretation requires additional clarification<br /> These models are a strength of the manuscript, but their biological meaning is not always clear. The significance of positive versus negative interaction parameters may not be obvious to readers unfamiliar with point-process modeling. In addition, the first-order and second-order terms operate at similar spatial scales, leading to partial confounding that complicates interpretation. Although this confounding is acknowledged late in the Discussion, it would be more helpful to flag it earlier, so that readers can interpret the model results with appropriate caution. Providing more biological explanation of what the model components represent would enhance accessibility.

6. The long-term population decline is compelling but causality is overstated <br /> The manuscript describes a greater than fifty percent decline in colony density between 2001 and 2019, and an additional approximately forty percent decline between 2019 and 2025. These changes are attributed largely to drought. While this is plausible, causal claims are currently too strong given the absence of direct soil moisture data, prey availability measurements, reproductive output data, or queen survival data. Phrasing should be adjusted to reflect that the observed pattern is consistent with drought effects rather than demonstrating causality, and alternative explanations such as detectability changes, nest dormancy, or colony relocation should be acknowledged.

MINOR ISSUES<br /> 1. The introduction overextends and lacks a clear conceptual framework<br /> The introduction reviews many ecological processes (competition, habitat heterogeneity, disturbance, droughts) but does not clearly articulate which mechanisms the authors expected to dominate at each scale (macro vs micro), or how these mechanisms generate distinct predictions.<br /> Explicitly state what processes are expected to drive spatial patterns at macro scale (abiotic heterogeneity vs density-dependent thinning) vs micro scale (territoriality, vegetation mosaic), and indicate which predictions are tied to drought, habitat type, or population density.

1. The macro-scale interpretation equates heterogeneous intensity with ecological responses, but the ecological drivers remain untested<br /> Along dirt roads, the intensity of colonies is strongly heterogeneous in algarrobal but not in grazed or dune habitats. However, the manuscript interprets these heterogeneities as linked to soil or vegetation structure, but these environmental variables were not quantified. The interpretation of “inverse density-dependent thinning” from 2019–2025 is plausible but speculative without a formal test.<br /> Acknowledge explicitly that without measured habitat covariates along the roads, the environmental interpretation is inferential. Clarify limitations of attributing density changes to specific drivers.

2. Visual presentation of spatial results needs improvement<br /> Several figures (especially 2, 3, and 4) are extremely dense. Overlapping confidence envelopes make interpretation difficult. Lack of legends for symbols or shading in some subpanels. Figure 5 has too many components on a single page.<br /> Simplify or divide composite figures. Ensure that interpretation of Ripley’s L and pair-correlation graphs is clearly explained in captions. Highlight key distances at which patterns deviate from CSR.

WRITING QUALITY<br /> The manuscript is written in generally clear and grammatically correct English, and the overall academic tone is appropriate. However, the prose is often excessively dense, with very long paragraphs and sentences that embed multiple ideas at once. The abstract is longer than necessary and would benefit from reduction. Parts of the Introduction are dense and could be streamlined. Important predictions, results, and conceptual transitions are sometimes buried within complex constructions, which makes the narrative harder to follow. Key terms and modeling approaches would benefit from brief explanatory context. In addition, the Discussion section is unusually long and occasionally repetitive, with several arguments stated multiple times across different paragraphs, while others are presented with more certainty than the data justify. This dilutes the impact of the key findings and makes it harder for readers to follow the logical flow of the authors’ interpretations. Overall, the manuscript would benefit from substantial stylistic polishing aimed at improving clarity, structure, and readability for organization and flow. Reference formatting should be checked for consistency.

CONCLUSION<br /> In conclusion, the manuscript is based on a strong dataset with considerable potential. Addressing the issues outlined above, especially the need for clear hypothesis integration, fuller treatment of anthropogenic variation, inclusion of a spatial map, justification of assumptions about colony structure, and more cautious interpretation of environmental drivers, will substantially strengthen the scientific clarity and impact of the work.

On 2025-11-20 22:10:54, user ML wrote:

Hi Finand & Kotze,

I really enjoyed reading this paper! I liked how this manuscript was framed. However, I have a few comments/criticisms:

I think there is an opportunity to discuss the metapopulation model here. Dispersal is highlighted heavily in this manuscript, but the metapopulation model isn't mentioned at all.

Perhaps more a personal preference, but I would like you to define want a "specialist" is. This term is NOT adequately defined in the introduction. "Specialist” refers to a lot of things. Are we studying diet specialists, habitat specialists, or something else? I assume we are studying habitat specialists, but that’s based in context clues.

The use of PCA and PERMANOVA is appropriate, however, the "vegan" package in R makes certain assumptions that you may NOT want. I would highly recommend using the PRIMER-E software to double check your analyses.

The axes aren't grounded, also! They should start at zero. that being said, I enjoyed the color selection here.

Overall, I thought this was a great manuscript, with a really robust dataset.

ML

On 2025-11-20 20:55:07, user SB wrote:

Peer reviewed and published October 24, 2025 in Vaccine<br /> https://www.sciencedirect.com/science/article/pii/S0264410X25010813 <br /> https://doi.org/10.1016/j.vaccine.2025.127784

On 2025-11-20 19:31:12, user Rodrigo Santibanez wrote:

Please find the accepted paper here https://www.cell.com/cell-systems/fulltext/S2405-4712(25)00284-4

On 2025-11-20 18:54:11, user Vanja Klepac-Ceraj wrote:

This work was published in January 2025: https://www.nature.com/articles/s41467-025-56072-w

On 2025-11-20 15:34:33, user Evolutionary Health Group wrote:

We at the Evolutionary Health Group ( https://evoheal.github.io/) really enjoyed this paper. Here are our highlights:

This work demonstrates that metagenomes contains a vast layer of “not yet genome-resolved” biodiversity. According to the results, up to ~80% of putative species-level clusters are not represented by genomes of cultivated organisms or by MAGs.

The study quantitatively shows that species discovery is far from saturation and strongly habitat-dependent. Human gut samples and anthropogenic environments are already densely sampled and contribute few new lineages per additional metagenome, whereas soils, aquatic ecosystems, the rhizosphere, and non-mammalian hosts remain true hotspots of unexplored diversity.

A separate and fundamentally important result - confirmed numerically- is the observation that the structure of prokaryotic diversity follows the same universal statistical laws (the power-law Willis-Yule / Yule-Simon distributions) as that of eukaryotes. In other words, the authors demonstrate that the same simple macroevolutionary regularities operate across the entire Tree of Life.

On 2025-11-20 03:10:28, user osedaxMucofloris wrote:

This is a really interesting study, and I'm happy to see Darlingtonia featured so prominently as it gets less attention than many other carnivorous plant taxa. that being said, I believe that the framing of this paper around mutualism is not accurate to the biology of the system involved. A true mutualistic interaction is one in which both partners benefit from the interaction. While there may be some cheating involved, the basis of the relationship must be mutually beneficial to both organisms involved. In the case of pitcher plants and insects, there can only be a single benefactor to any interaction. If the plant benefits from consuming an insect, the insect does not benefit. If the insect benefits from consuming pitcher extrafloral nectar, then that insect must not fall into the plant's trap and thus the plant does not benefit. There cannot be a true mutualism here. For the same reason, the sentiment of a "reciprocal nutrient exchange between carnivorous plants and local insect populations" (line 235) is misleading, as the insects which obtain nutrients from the carnivorous plants in question are, by necessity, not the same insects which provide nutrients to the carnivorous plants.

The most appropriate framing device for this paper in my opinion would be to simply focus on whether any insects are able to obtain a significant portion of their nutritional requirements from carnivorous plants, which would make Darlingtonia not a strict predator; instead, it would occupy a less straightforward place in the trophic web of the serpentine fen. The manuscript does mention this concept several times, but never as the driving concept or overall thrust of the paper. I think reframing the paper, including the title, around questioning whether carnivorous plants are always strict predators of insects would improve the manuscript. To further the potential novelty of this paper, reframing could focus on the fact that it is already known that specialist insects benefit from interactions with pitcher plants (often in an actually mutually beneficial manner, sensu detritivorous pitcher plant inquilines) but far less is known about whether any generalist insects may benefit from interactions with the plants.

Darlingtonia's focal status in this study is more or less self-explanatory, but the use of Vespula specifically is far less so. At no point in the introduction are yellowjackets set up to be a good candidate for the study at hand, nor do the methods explain why Vespula was chosen. It is my belief that the use of Vespula wasps is a strength of this study's design, and the manuscript should make that clear. There are several reasons why Vespula is an ideal choice here. For example, it is stated that wasps rarely fall prey to pitchers despite visiting them regularly, thus they are good candidate insects for an investigation of nitrogen isotopes which originate from pitcher nectar. Studies which investigate compounds that are found in higher concentrations at higher trophic levels (i.e., are biomagnified) might benefit from first looking at the highest trophic levels; if no signature is detected at the greatest point of biomagnification, then it is likely that lower trophic levels will likewise show no difference in bioaccumulated material. Vespula wasps occupy a high trophic level in this ecosystem, making them a good candidate for this study in this aspect as well. Yellowjackets are also easy to selectively capture in great numbers due to the availability of specialized traps, meaning there are cheap, effective, passive methods for sampling a large number of them. This paper does address that these wasps forage in localized patches, and thus can be more reliably assigned to either "fen" or "forest" patches, but this is brought up in passing. Any number of these points can and should be addressed, as it stands there is no explicit justification given for using these wasps as opposed to any other group of insects.

On 2025-11-19 21:19:50, user Daniel Vásquez-Restrepo wrote:

This preprint already received a “major revision” decision. Unfortunately, the original reviewers were not available to evaluate it again, and the process stalled. Despite sending 15 additional peer-review invitations, no one agreed to take it on. Although the manuscript has now entered a new review process, I am attaching the previous reviewers’ comments.

Reviewer 1

This isn’t a finding as not only is it already available information, the use of the available IUCN maps and statuses was part of the methodology.

R/ We rephrased the sentence to clarify that it refers to the underlying data itself and not to our results.

I like the approach they’ve taken, but none of this is novel information or unexpected.

R/ Although it is well known that mountains promote diversity and endemism at a global macroevolutionary scale, this information has not been explicitly tested in Colombian squamates in conjunction with threat categories. We consider that clearly stating the result of hotspots of diversity and endemism in Colombian squamates can help local environmental policies. Therefore, while our results are consistent with theoretical expectations, this alignment does not diminish the novelty of our findings, as we provide the first quantitative analysis supporting these patterns in the local context.

This is the main novel finding of the work and I’d recommend reorganising the text to stress this.

R/ We modified several sections of the text to emphasize the finding highlighted by the reviewer, also in accordance with comments made by the other reviewer.

Unclear what this means in the context of this paper.<br /> R/ We rephrased the section for clarity.

This is just the existing EDGE list, so I’m not sure it warrants mentioning as an output here.

R/ In accordance with a comment from Reviewer 2, we acknowledge that this is a local rather than a global list, and that species rankings may differ between the two. Therefore, we believe it is an output worth highlighting. Nevertheless, we have clarified in the text the differences between the local and global scores and their implications.

This entire paragraph seems superfluous, and this work has nothing to do with the latitudinal gradient so it’s a strange thing to focus discussion on.

R/ While we briefly mention the latitudinal gradient, the main purpose of this introductory paragraph is to provide general context on biodiversity, leading into the key argument of the subsequent sections: the need to understand biodiversity and extinction risk as multidimensional phenomena. We have made minor adjustments to better integrate the role of the latitudinal gradient in promoting tropical diversity, thereby reinforcing the importance of prioritizing conservation efforts in regions of exceptionally high biodiversity.

Suggested added context as this was unclear as worded.

R/ We accepted the reviewer’s suggestion and revised the text accordingly.

I’m not sure this follows - more that, as the paragraph goes onto say, it results in a lack of understanding of the impacts and vulnerability of the species.

R/ We rephrased the idea to make it clearer.

This seems to be an inappropriate reference, as Paez et al. 2006 focused on turtles rather than squamates. Please check and reword as needed.

R/ We double-checked the reference and confirmed that it is correct, as it covers not only turtles but all Colombian reptiles (including squamates, crocodiles, and turtles).

This seems inconsistent with the earlier statement that “a local assessment is lacking” - should this rather say a recent local assessment? Though as the paper goes on to reference a 2015 ‘local assessment’, it’s unclear what this section means.

R/ We agree with the reviewer and revised the text to clarify that we refer to a recent assessment that also considers different facets of biodiversity, not just species richness (i.e., taxonomic diversity).

The figure given later is 597, and that was used as the basis for the analysis. This may be a discrepancy due to a later update, but the same Reptile Database update should be cited throughout the paper for consistency.<br /> R/ In the Introduction, we refer to the most recent estimate of 620 reptile species for Colombia, based on the latest update of the Reptile Database (2024). However, the analyses in this study were based on the 2023 version of the database, which listed 597 species at that time. Given that the analyses were conducted using the 2023 data, and a complete reanalysis would be required to incorporate the updated figures, we chose to retain the original dataset to ensure consistency and reproducibility. We have clarified this point in the text to avoid confusion.

Better to use the term ‘squamates’ rather than ‘reptiles’ if crocs and turtles are to be excluded.

R/ Done, we have consistently replaced "reptiles" with "squamates" throughout the text where appropriate.

Once again, this could benefit from clarity. The data in the Reptile Database should be reviewed with reference to available material and literature to be used as a formal checklist, but it should be ‘complete’ - it’s more likely to erroneously list species from a country than to miss ones that actually occur there.

R/ We agree with the reviewer and rephrased the sentence to make the idea clearer.

Are the authors able to explain the discrepancy between this figure and the maps (which represented 81% of the dataset)? Most IUCN assessments will have maps, but no IUCN maps will be associated with species that don’t have assessments.

R/ The figures were validated against the information provided in Table S1. As the reviewer correctly points out, there are more assessments than polygons, consistent with the supplementary material. The figure of 77% corresponds to 461 species (excluding DD and NE categories) out of 597 species in our dataset (461/597 = 0.77). Meanwhile, the figure of 81% refers to 481 species with available geographic information, including species categorized as DD (481/597 = 0.81). The discrepancy arises because DD species were included when considering geographic data but excluded from threat category analyses. We have revised the Methods and Results sections to clarify this distinction explicitly. Also, we updated the previous 77% figure to include DD species too, increasing it to 92%.

This is not a sufficient way to evaluate whether the assessments are likely to need updating - the Criteria take account of the distribution and extent of threats to each species, not simply its distribution. The ‘needs update’ tag is applied by the Red List only to assessments more than 10 years old, which is all that should be mentioned here.

R/ We understand the reviewer’s concern and acknowledge that a mismatch between EOO and threat classification is not sufficient by itself to determine if an update is needed. We have separated these ideas in the text: first, we highlight species whose assessments are formally tagged as “needs update” after 10 years; second, we discuss species whose EOO does not align with their current threat classification. We moved the second point to the 3.2 Geographic patterns section, and expanded the Discussion to better explain these observations.

See above. The authors didn’t ‘show’ this, they interpreted the Criteria incorrectly.

R/ See previous answer. We further expanded the Discussion section to better frame this point.

I would consider it suitable for the manuscript to be more fully revised as a shorter paper, as the region-scale analysis within Colombia and the phylogenetic results are of more interest than the well-trodden path of identifying the Andes as an area of greater endemism than Amazonia and the additional analyses included in the paper render its main findings somewhat opaque in places.

R/ We consider that highlighting the Andes as an area of high endemism is necessary to provide context for interpreting the patterns of phylogenetic diversity. While it may be a well-known topic, not all readers will have the same background. Although the manuscript is extensive because it covers taxonomic, geographic, and phylogenetic patterns, its current length (ca. 6,300 words, excluding references) is well within the 9,000-word limit for Original Research articles in Biodiversity and Conservation and only slightly above the typical 5,000-word range. Nevertheless, we made an effort to shorten unnecessary sections to improve focus and clarity. For example, we removed some analysis related to diversification rates and extinction risk, since as the Reviewer 2 pointed out, some metrics depending on branch lengths may be biased.<br /> <br /> Reviewer 2

L393-405: it is important to acknowledge the phylogenetic incompleteness of a national-level analysis, and how that might be affecting these results – divergence times are influenced by phylogenetic coverage and structure, removing >90% of squamate species from the phylogeny will give you divergence times between Colombian species, not true lineage age/divergence time information. This could be addressed with sensitivity analyses to explore how lineage age varies between pruned and complete trees, or with stronger discussion of the pitfalls of this approach in the methods and discussion, with clearer wording in the results.

R/ We appreciate the reviewer’s insightful comment and fully agree. We performed additional calculations to assess sensitivity, and indeed, the age of some lineages can be severely affected, while others remain largely unchanged. Following the reviewer’s recommendation, we revised the Methods and Discussion sections to place greater emphasis on the limitations of using evolutionary metrics derived from pruned trees and on the considerations needed when interpreting these results. As the reviewer also notes, these results are not necessarily incorrect, since global conservation priorities do not always align with local ones. Additionally, we introduced local and global subscripts to our metrics to explicitly distinguish between them.

407-418: Distinction is needed between EDGE scores and national EDGE scores (literally just saying ‘national EDGE scores’ would suffice). It may also be useful to identify national-specific priorities – i.e. high ranking national EDGE species that are not highly ranked in global context. There are EDGE scores available for all vertebrates at the global level here ( https://www.nature.com/articles/s41467-024-45119-z) . There are endemic Colombian squamates that are high EDGE in this study and also high EDGE at the global scale (e.g. Lepidoblepharis miyatai) but also species that are high EDGE nationally because of the phylogenetic diversity they are solely responsible for in Colombia, but the responsibility for which is shared beyond Colombia’s borders. These key cases can be instrumental in ensuring species that are globally ‘safe’ but locally important do not fall through the cracks.

R/ Please refer to the previous response. We now explicitly distinguish between national EDGE scores and global EDGE scores throughout the text and highlight cases where species are locally important but not necessarily globally prioritized.

L41 and throughout: “threatenedness” = “extinction risk” or “level of threat”.

R/ Done.

Throughout: It’s the IUCN Red List, not IUCN, particularly when referring to versions of the Red List database.

R/ Done.

L145: make it clear you’re referring to national endemics.

R/ The Resolución 0126/2024 from Colombia’s Ministry of Environment (MADS) covers not only national endemics but all species occurring within the country’s administrative boundaries.

L167: ensure it’s clear that its imputation based on taxonomy alone.

R/ Done.

L182: check references.

R/ We reviewed the references cited at this point and confirm they are correct.

L222-224 and throughout: phylogenetic diversity == Faith’s PD – the other measures are indices of phylogenetic distance/relatedness that are calculated in same units as PD, but are not phylogenetic diversity – that should be clarified.

R/ Done. We clarified that Faith’s PD refers specifically to phylogenetic diversity, while the other metrics represent measures of phylogenetic relatedness or distance.

L393: extinction risk should not be though of as a trait evolving but as the manifestation of extrinsic and intrinsic factors.

R/ Agreed. We rewrote the sentence.<br /> L393-397: unclear what the relationships discussed are, and what they infer.

R/ We have removed this section from both the Methods and Results. Given that the correlations discussed involved metrics dependent on branch length — and, as the reviewer previously pointed out, branch lengths can be affected by pruning the phylogenetic trees — we decided to eliminate this section. Overall, it did not substantially contribute to the text or to the discussion.

L428-429: This is higher than, or at least comparable to, the global % of DD/NE squamates I think, so might not be considered relatively low for squamates.

R/ We rewrote the sentence to clarify that it is comparable to or higher than the global percentage, as the reviewer correctly pointed out.

L429-432: it might be worth highlighting how taxonomists and others can contribute to rapid reassessment of species with basic information in ecological publications see: https://doi.org/10.1016/j.biocon.2018.01.022