Screenager: screening times at bioRxiv

Abstract: When a preprint is uploaded to bioRxiv, it undergoes screening before it appears online. How long does it take for Affiliates to screen preprints at bioRxiv? tl;dr I used R to look at bioRxiv screening times.


Files removed following a technical error

Abstract: This manuscript was removed because it posted owing to a technical error


ShoRtcut from bioRxiv to GigaScience

Abstract: <em> <strong> Authors can now submit their bioRxiv preprints directly to GigaScience via the biorXiv platform, at the push of a button. This handy technical integration is another hallmark of biology preprints becoming a normal, accepted, and speedy way of communicating research results. </strong> </em> Pre-prints, versions of a scholarly paper that precede formal publication in a peer-reviewed journal are&nbsp; becoming increasingly mainstream.


ShoRtcut from bioRxiv to GigaScience


Screenager: screening times at bioRxiv


White label: the growth of bioRxiv

Abstract: bioRxiv, the preprint server for biology,&nbsp;recently turned 2 years old. This seems a good point to take a look at how bioRxiv has&nbsp;developed over this time and to discuss any concerns sceptical people may have about using the service.


Over and Over: Preprint revisions on bioRxiv

Abstract: The aim of this post is to look at revisions of bioRxiv preprints. I'm interested how long preprint versions exist on bioRxiv. In other words: how long do revisions to preprints take? The data from bioRxiv is a complex dataset with many caveats as I'll explain further down, but some interesting details do emerge.


White label: the growth of bioRxiv


Searching medRxiv and bioRxiv Preprint Data

Abstract: Background &amp; motivation medRxiv, as the preprint repository for papers in the medical, clinical, and related health sciences, <sup> 1 </sup> has become a central source of new studies related to the COVID-19 pandemic.


Ozymandias: A biodiversity knowledge graph available as a preprint on Biorxiv

Abstract: I've written up my entry for the 2018 GBIF Challenge ("Ozymandias") and posted a preprint on Biorxiv (https://www.biorxiv.org/content/early/2018/12/04/485854). The DOI is https://doi.org/10.1101/485854 which, last time I checked, still needs to be registered. The abstract appears below. I'll let the preprint sit there for a little while before I summon the enthusiasm to revisit it, tidy it up, and submit it for publication.


The Rise and Fall: impact of the COVID-19 pandemic on bioRxiv preprints

Abstract: As the COVID-19 pandemic continues, different countries are experiencing various restrictions including lockdowns. Some of these restrictions alter our ability to do science: by hindering lab access or taking time away from researchers for homeschooling. So, what impact has the pandemic had on scientific output?


Exploring the bioRxiv API with R, httr2, rvest, tidytext, and Datawrapper

Abstract: Collect metadata and publication details for &gt;200k preprints over a 10 year period, investigate trends, and scrape full text for sentiment analysis


Exploding, Impacting: looking at bioRxiv preprint view dynamics with R

Abstract: One of the joys of posting a preprint is seeing that people are viewing, downloading and (hopefully) reading your paper. On bioRxiv you can check out the statistics for your paper in the metrics tab.


PREreview of bioRxiv article “Subfamily-specific functionalization of diversified immune receptors in wild barley”

Abstract: This is a review of Maekawa et al. bioRxiv 293050; doi: https://doi.org/10.1101/352278 posted on June 20, 2018. In this paper, the authors mined the transcriptomes of 50 different accession of wild barley, generating a rich library of natural variants of the MLA immune receptor—a classical nucleotide-binding domain and leucine-rich repeat-containing (NLR) protein. They grouped the MLA variants in two subfamilies with all receptors known to be effective against the powdery mildew fungus grouping in one subfamily.


Analyzing Preprints: The challenges of working with metadata from bioRxiv

Abstract: <strong> By Mario Malički, Maria Janina Sarol, and Juan Pablo Alperin </strong> <em> This blog post is the third in a four part series documenting the methodological challenges we faced during our </em> <em> project </em> <em> investigating preprint growth and uptake. </em>


bioRxiv: the preprint server for biology


Tracking the popularity and outcomes of all bioRxiv preprints


Llama 3.2 summaries of bioRxiv and medRxiv preprints with biorecap

Abstract: The biorecap package can now summarize bioRxiv and medRxiv preprints, and uses the llama-3.2-3b model by default.


PREreview of bioRxiv article "A generalist pathogen view of diverse host evolutionary histories through polygenic virulence"

Abstract: This is a review of Caseys et al. bioRxiv doi: https://doi.org/10.1101/507491 posted on June 25, 2019. This study aims at addressing whether coevolutionary models of host-pathogen interactions apply to a generalist pathogen that exhibits quantitative virulence across a broad range of plants. They generated an exhaustive virulence matrix for the nectrophic fungus Botrytis cinerea on 90 genotypes of 8 plant species. They conclude that this pathosystem doesn’t fit traditional arms-race coevolution models with quantitative variation in susceptibility distinct from the phylogenetic relationships between the examined plants.


Abstract: (Presented by Richard Abdill.) Researchers in the life sciences are posting work to preprint servers at an unprecedented and increasing rate, sharing papers online before (or instead of) publication in peer-reviewed journals. Though the increasing acceptance of preprints is driving policy changes for journals and funders, there is little information about their usage. Here, we collected and analyzed data on all 37,648 preprints uploaded to bioRxiv.org, the largest biology-focused preprint server, in its first five years. We find preprints are being read more than ever before (1.1 million downloads in October 2018 alone) and that the rate of preprints being posted has increased to a recent high of 2,100 per month, driven primarily by exponential growth in the number of papers in neuroscience and bioinformatics. We also find that two-thirds of preprints posted before 2017 were later published in peer-reviewed journals, and that preprints with more downloads tend to appear in journals with a higher impact factor. The age of preprints appearing in journals also differs by publication, with journals such as G3 publishing most preprints within four months of their appearance on bioRxiv. Lastly, we developed Rxivist.org, a web application providing multiple ways of interacting with preprint metadata, including an API and website that allows users to sort preprints related to their interests based on Twitter activity or bioRxiv download metrics.


biorecap: an R package for summarizing bioRxiv preprints with a local LLM

Abstract: This is re-posted from my newsletter, where I'll be posting from now on: https://blog.stephenturner.us/p/biorecap-r-package-for-summarizing-biorxiv-preprints-local-llm ---TL;DR I wrote an R package that summarizes recent bioRxiv preprints using a locally running LLM via Ollama+ollamar, and produces a summary HTML report from a parameterized RMarkdown template.


Abstract: The biorecap package summarizes bioRxiv preprints using a local LLM. I used two LLMs to help me write the package, and two other LLMs to help me write a paper about the package, published on arXiv.


PREreview of bioRxiv article “Convergent evolution of effector protease recognition by Arabidopsis and barley”

Abstract: This is a review of Carter, Helm et al. bioRxiv 374264; doi: https://doi.org/10.1101/374264 posted on July 23, 2018. In this paper, the authors showed that diverse barley cultivars are able to respond to the Pseudomonas syringae effector AvrPphB and they characterized both the effector target (PBS1) and the receptor (PBR1) responsible for this recognition. Furthermore, their phylogenetic analyses revealed that the immune receptor involved in this response is not orthologous to a previously characterized receptor (RPS5) from Arabidopsis thaliana that has a functionally analogous AvrPphB recognition mechanism. This leads the authors to conclude that recognition of the AvrPphB protease has evolved independently in Arabidopsis and barley.


The effect of bioRxiv preprints on citations and altmetrics


PREreview of bioRxiv article “Structure-function analysis of ZAR1 immune receptor reveals key molecular interactions for activity”

Abstract: This is a review of Baudin, Schreiber, Martin et al. bioRxiv doi: https://doi.org/10.1101/592824 posted on March 29, 2019. The authors used structural modelling to identify elements required for self-association of the NLR immune receptor ZAR1, specifically its N-terminal CC-domain ZAR1CC. They discovered that the N-terminal α1 helix and EDVID motif in ZAR1CC are important for oligomerization and function of ZAR1. This complements recent findings by Wang et al. (2019) based on cryo-EM structures, highlighting the importance of the α1 helix for the activity of ZAR1 although some differences were noted that could reflect the different experimental set ups (CC domain vs full-length protein) as discussed in the paper.


PREreview of bioRxiv article “The vesicular trafficking system component MIN7 is required for minimizing Fusarium graminearum infection”


Pre-print journal club review of BioRxiv article: Uncovering the hidden antibiotic potential of Cannabis


PREreview of bioRxiv article “Roq1 confers resistance to Xanthomonas, Pseudomonas syringae and Ralstonia solanacearum in tomato”


Nicholas Fraser, Fakhri Momeni, Philipp Mayr, Isabella Peters

Abstract: 1. Abstract A potential motivation for scientists to deposit their scientific work as preprints is to enhance its citation or social impact, an effect which has been empirically observed for preprints in physics, astronomy and mathematics deposited to arXiv. In this study we assessed the citation and altmetric advantage of bioRxiv, a preprint server for the biological sciences. We retrieved metadata of all bioRxiv preprints deposited between November 2013 and December 2017, and matched them to articles that were subsequently published in peer-reviewed journals. Citation data from Scopus and altmetric data from Altmetric.com were used to compare citation and online sharing behaviour of bioRxiv preprints, their related journal articles, and non-deposited articles published in the same journals. We found that bioRxiv-deposited journal articles received a sizeable citation and altmetric advantage over non-deposited articles. Regression analysis reveals that this advantage is not explained by multiple explanatory variables related to the article and its authorship. bioRxiv preprints themselves are being directly cited in journal articles, regardless of whether the preprint has been subsequently published in a journal. bioRxiv preprints are also shared widely on Twitter and in blogs, but remain relatively scarce in mainstream media and Wikipedia articles, in comparison to peer-reviewed journal articles.


Abstract: Abstract Researchers in the life sciences are posting work to preprint servers at an unprecedented and increasing rate, sharing papers online before (or instead of) publication in peer-reviewed journals. Though the increasing acceptance of preprints is driving policy changes for journals and funders, there is little information about their usage. Here, we collected and analyzed data on all 37,648 preprints uploaded to bioRxiv.org, the largest biology-focused preprint server, in its first five years. We find preprints are being downloaded more than ever before (1.1 million tallied in October 2018 alone) and that the rate of preprints being posted has increased to a recent high of 2,100 per month. We also find that two-thirds of preprints posted before 2017 were later published in peer-reviewed journals, and find a relationship between journal impact factor and preprint downloads. Lastly, we developed Rxivist.org, a web application providing multiple ways of interacting with preprint metadata.


Linguistic Analysis of the bioRxiv Preprint Landscape

David N. Nicholson, Vincent Rubinetti, Dongbo Hu, Marvin Thielk, Lawrence E. Hunter, Casey S. Greene

Abstract: Abstract Preprints allow researchers to make their findings available to the scientific community before they have undergone peer review. Studies on preprints within bioRxiv have been largely focused on article metadata and how often these preprints are downloaded, cited, published, and discussed online. A missing element that has yet to be examined is the language contained within the bioRxiv preprint repository. We sought to compare and contrast linguistic features within bioRxiv preprints to published biomedical text as a whole as this is an excellent opportunity to examine how peer review changes these documents. The most prevalent features that changed appear to be associated with typesetting and mentions of supplementary sections or additional files. In addition to text comparison, we created document embeddings derived from a preprint-trained word2vec model. We found that these embeddings are able to parse out different scientific approaches and concepts, link unannotated preprint-peer reviewed article pairs, and identify journals that publish linguistically similar papers to a given preprint. We also used these embeddings to examine factors associated with the time elapsed between the posting of a first preprint and the appearance of a peer reviewed publication. We found that preprints with more versions posted and more textual changes took longer to publish. Lastly, we constructed a web application ( https://greenelab.github.io/preprint-similarity-search/ ) that allows users to identify which journals and articles that are most linguistically similar to a bioRxiv or medRxiv preprint as well as observe where the preprint would be positioned within a published article landscape.


Quantifying and contextualizing the impact of bioRxiv preprints through automated social media audience segmentation

Abstract: Abstract Engagement with scientific manuscripts is frequently facilitated by Twitter and other social media platforms. As such, the demographics of a paper’s social media audience provide a wealth of information about how scholarly research is transmitted, consumed, and interpreted by online communities. By paying attention to public perceptions of their publications, scientists can learn whether their research is stimulating positive scholarly and public thought. They can also become aware of potentially negative patterns of interest from groups that misinterpret their work in harmful ways, either willfully or unintentionally, and devise strategies for altering their messaging to mitigate these impacts. In this study, we collected 331,696 Twitter posts referencing 1,800 highly tweeted bioRxiv preprints and leveraged topic modeling to infer the characteristics of various communities engaging with each preprint on Twitter. We agnostically learned the characteristics of these audience sectors from keywords each user’s followers provide in their Twitter biographies. We estimate that 96% of the preprints analyzed are dominated by academic audiences on Twitter, suggesting that social media attention does not always correspond to greater public exposure. We further demonstrate how our audience segmentation method can quantify the level of interest from non-specialist audience sectors such as mental health advocates, dog lovers, video game developers, vegans, bitcoin investors, conspiracy theorists, journalists, religious groups, and political constituencies. Surprisingly, we also found that 10% of the highly tweeted preprints analyzed have sizable (>5%) audience sectors that are associated with right-wing white nationalist communities. Although none of these preprints intentionally espouse any right-wing extremist messages, cases exist where extremist appropriation comprises more than 50% of the tweets referencing a given preprint. These results present unique opportunities for improving and contextualizing research evaluation as well as shedding light on the unavoidable challenges of scientific discourse afforded by social media.


International authorship and collaboration across bioRxiv preprints

Richard J. Abdill, Elizabeth M. Adamowicz, Ran Blekhman

Abstract: Abstract As preprints become integrated into conventional avenues of scientific communication, it’s critical to understand who is included and who is not. However, little is known about which countries are participating or how they collaborate with each other. Here, we present an analysis of all 67,885 preprints posted on bioRxiv (through 2019) using the first comprehensive dataset of country-level preprint author affiliations. We find the plurality of preprints (39%) come from the United States, and that countries such as the U.S. and U.K. are overrepresented on bioRxiv relative to their overall scientific output, while countries including China, Russia, and Turkey show lower bioRxiv adoption. We describe a set of “contributor countries” including Uganda, Croatia and Thailand that appear almost exclusively as non-senior authors on international collaborations. Lastly, we find multiple journals that publish a disproportionate number of preprints from some countries, a dynamic that almost always benefits manuscripts from the U.S.


Indian COVID-19 Preprints Submissions in bioRxiv and medRxiv Preprint Servers

Narayanaswamy Vasantha Raju, Murtala Ismail Adakawa, N.S. Harinarayana, Chandrappa

Abstract: ABSTRACT This research aimed at determining the growth of deposition of preprints on servers by Indian researchers during COVID-19 pandemic. In the pre-pandemic period, the dominant server was arXiv upon which research from physics and other related domains have been the most predominant depositors. When the pandemic erupted and the need to share research findings became imperative, many previously dormant preprint servers received vibrant activations from several scientists across the globe. This is with the intention of bridging the gap between delays inherent in reviewing process and the dire need to share information for finding everlasting solutions to the raging pandemic. Many researchers, institutions, countries, etc. have contributed in this regard. The study used quantitative method and iSearch Portfolio expert-curated source for publications and preprints related to either COVID-19 or the novel coronavirus SARS-CoV-2 developed and maintained by National Institute of Health (NIH), US iSearch COVID-19 Portfolio. The study examined the Indian COVID-19 preprints deposited in bioRxiv and medRxiv preprint servers. The findings indicated that, Indian researchers have posted their papers in large numbers in bioRxiv and medRxiv servers with the medRxiv having the highest preprints (417, 40.44%) in 2020 against its counterpart bioRxiv (118, 10.96%) in the same year. Similarly, infectious diseases (except HIV/AIDS) (311) had the highest recurrence of the preprints submitted for deposition in servers. This is followed by epidemiology (263), public and global health (122), bioinformatics (59), among others. There is high collaboration among researchers who deposited their preprints in these servers where about 257 (24.93%) preprints were co-authored by 11+ authors followed by 3-authored and 4-authored with 124 preprints respectively (together accounts for 24.06%) and 2-authroed (114 (11.04%) preprints) respectively in a diminishing manner. The study concluded that, Indian researchers are actively participating in depositing preprints in servers notably bioRxiv and medRxiv.


PREreview of bioRxiv article "NRG1-mediated recognition of HopQ1 reveals a link between PAMP and Effector-triggered Immunity"

Abstract: This is a review of Brendolise et al. bioRxiv 293050; doi: https://doi.org/10.1101/293050 posted on April 1, 2018. This paper adds to a current body of research detailing the resistance mechanism triggered by the Pseudomonas syringe pv. tomato effector HopQ1 in the model plant Nicotiana benthamiana . This plant can be used as a source of novel disease resistance genes against plant pathogens.


Pre-print journal club review of BioRxiv article: Discovery of a prevalent picornavirus by visualizing zebrafish immune responses


Motivations, concerns and selection biases when posting preprints: a survey of bioRxiv authors

Nicholas Fraser, Philipp Mayr, Isabella Peters

Abstract: Abstract Since 2013, the usage of preprints as a means of sharing research in biology has rapidly grown, in particular via the preprint server bioRxiv. Recent studies have found that journal articles that were previously posted to bioRxiv received a higher number of citations or mentions/shares on other online platforms compared to articles in the same journals that were not posted. However, the exact causal mechanism for this effect has not been established, and may in part be related to authors’ biases in the selection of articles that are chosen to be posted as preprints. We aimed to investigate this mechanism by conducting a mixed-methods survey of 1,444 authors of bioRxiv preprints, to investigate the reasons that they post or do not post certain articles as preprints, and to make comparisons between articles they choose to post and not post as preprints. We find that authors are most strongly motivated to post preprints to increase awareness of their work and increase the speed of its dissemination; conversely, the strongest reasons for not posting preprints centre around a lack of awareness of preprints and reluctance to publicly post work that has not undergone a peer review process. We additionally find weak evidence that authors preferentially select their highest quality, most novel or most significant research to post as preprints, however, authors retain an expectation that articles they post as preprints will receive more citations or be shared more widely online than articles not posted.


Một bản thảo về virus corona trên bioRxiv bị rút: Khoảnh khắc quan trọng đối với xuất bản học thuật

Abstract: SSHPA (05-02-2020; Nguyễn Thị Linh) — Bài viết này tóm lược thảo luận quan trọng của hai tác giả Ivan Oransky và Adam Marcus về câu chuyện một bản thảo trên bioRxiv bị rút bỏ và ý nghĩa của nó với xuất bản học thuật hiện nay (nguồn ghi ở mục Tham khảo, dẫn chiếu Retraction Watch và STAT News).


PREreview of bioRxiv article “Ptr1 evolved convergently with RPS2 and Mr5 to mediate recognition of AvrRpt2 in diverse solanaceous species"


VLIB: Unveiling insights through Visual and Linguistic Integration of Biorxiv data relevant to cancer via Multimodal Large Language Model

Abstract: Abstract The field of cancer research has greatly benefited from the wealth of new knowledge provided by research articles and preprints on platforms like Biorxiv. This study investigates the role of scientific figures and their accompanying captions in enhancing our comprehension of cancer. Leveraging the capabilities of Multimodal Large Language Models (MLLMs), we conduct a comprehensive analysis of both visual and linguistic data in biomedical literature. Our work introduces VLIB, a substantial scientific figure-caption dataset generated from cancer biology papers on Biorxiv. After thorough preprocessing, which includes figure-caption pair extraction, sub-figure identification, and text normalization, VLIB comprises over 500,000 figures from more than 70,000 papers, each accompanied by relevant captions. We fine-tune baseline MLLMs using our VLIB dataset for downstream vision-language tasks, such as image captioning and visual question answering (VQA), to assess their performance. Our experimental results underscore the vital role played by scientific figures, including molecular structures, histological images, and data visualizations, in conjunction with their captions, in facilitating knowledge translation through MLLMs. Specifically, we achieved a ROUGE score of 0.66 for VQA and 0.68 for image captioning, as well as a BLEU score of 0.72 for VQA and 0.70 for image captioning. Furthermore, our investigation highlights the potential of MLLMs to bridge the gap between artificial intelligence and domain experts in the field of cancer biology.


MUSCLE: multiple sequence alignment with high accuracy and high throughput


DADA2: High-resolution sample inference from Illumina amplicon data

Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson, Susan P Holmes


QIIME allows analysis of high-throughput community sequencing data

J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Peña, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld, Rob Knight


Cutadapt removes adapter sequences from high-throughput sequencing reads


A low-cost, high-efficiency solar cell based on dye-sensitized colloidal TiO2 films


GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

Mark James Abraham, Teemu Murtola, Roland Schulz, Szilárd Páll, Jeremy C. Smith, Berk Hess, Erik Lindahl

European Research Council, Swedish Research Council, ScalaLife EU infrastructure


Executive Summary of the Third Report of the National Cholesterol Education Program (NCEP) Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults (Adult Treatment Panel III)

JAMA: The Journal of the American Medical Association


HTSeq—a Python framework to work with high-throughput sequencing data

Simon Anders, Paul Theodor Pyl, Wolfgang Huber

Genome Biology Unit, European Molecular Biology Laboratory, 69111 Heidelberg, Germany

Abstract: Abstract Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. Availability and implementation: HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq . Contact: sanders@fs.tum.de


THE USE OF LEAD CITRATE AT HIGH pH AS AN ELECTRON-OPAQUE STAIN IN ELECTRON MICROSCOPY

From the Department of Anatomy, Harvard Medical School, Boston


A unified formulation of the constant temperature molecular dynamics methods

Division of Chemistry, National Research Council of Canada, Ottawa, Ontario, Canada, K1A OR6

Abstract: Three recently proposed constant temperature molecular dynamics methods by: (i) Nosé (Mol. Phys., to be published); (ii) Hoover et al. [Phys. Rev. Lett. 48, 1818 (1982)], and Evans and Morriss [Chem. Phys. 77, 63 (1983)]; and (iii) Haile and Gupta [J. Chem. Phys. 79, 3067 (1983)] are examined analytically via calculating the equilibrium distribution functions and comparing them with that of the canonical ensemble. Except for effects due to momentum and angular momentum conservation, method (1) yields the rigorous canonical distribution in both momentum and coordinate space. Method (2) can be made rigorous in coordinate space, and can be derived from method (1) by imposing a specific constraint. Method (3) is not rigorous and gives a deviation of order N−1/2 from the canonical distribution (N the number of particles). The results for the constant temperature–constant pressure ensemble are similar to the canonical ensemble case.


Very high resolution interpolated climate surfaces for global land areas

Robert J. Hijmans, Susan E. Cameron, Juan L. Parra, Peter G. Jones, Andy Jarvis


Measurements of Ω and Λ from 42 High‐Redshift Supernovae

S. Perlmutter, G. Aldering, G. Goldhaber, R. A. Knop, P. Nugent, P. G. Castro, S. Deustua, S. Fabbro, A. Goobar, D. E. Groom, I. M. Hook, A. G. Kim, M. Y. Kim, J. C. Lee, N. J. Nunes, R. Pain, C. R. Pennypacker, R. Quimby, C. Lidman, R. S. Ellis, M. Irwin, R. G. McMahon, P. Ruiz‐Lapuente, N. Walton, B. Schaefer, B. J. Boyle, A. V. Filippenko, T. Matheson, A. S. Fruchter, N. Panagia, H. J. M. Newberg, W. J. Couch, The Supernova Cosmology Project


High-Resolution Image Synthesis with Latent Diffusion Models

2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)

Robin Rombach, Andreas Blattmann, Dominik Lorenz, Patrick Esser, Bjorn Ommer

Ludwig Maximilian University of Munich & IWR, Heidelberg University,Germany


The Seventh Report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure<SUBTITLE>The JNC 7 Report</SUBTITLE>


MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification


High resolution two-dimensional electrophoresis of proteins.


Nanostructured High‐Entropy Alloys with Multiple Principal Elements: Novel Alloy Design Concepts and Outcomes

J.‐W. Yeh, S.‐K. Chen, S.‐J. Lin, J.‐Y. Gan, T.‐S. Chin, T.‐T. Shun, C.‐H. Tsau, S.‐Y. Chang

Abstract: A new approach for the design of alloys is presented in this study. These “high‐entropy alloys” with multi‐principal elements were synthesized using well‐developed processing technologies. Preliminary results demonstrate examples of the alloys with simple crystal structures, nanostructures, and promising mechanical properties. This approach may be opening a new era in materials science and engineering.


Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D Thompson, Desmond G Higgins


A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity


Improved patch-clamp techniques for high-resolution current recording from cells and cell-free membrane patches

Pflügers Archiv - European Journal of Physiology

O. P. Hamill, A. Marty, E. Neher, B. Sakmann, F. J. Sigworth


ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data


Possible highT c superconductivity in the Ba?La?Cu?O system

Zeitschrift f�r Physik B Condensed Matter


Third Report of the National Cholesterol Education Program (NCEP) Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults (Adult Treatment Panel III) Final Report

Ovid Technologies (Wolters Kluwer Health)


Room-Temperature Ionic Liquids. Solvents for Synthesis and Catalysis

Department of Chemistry, Imperial College of Science Technology and Medicine, South Kensington, London SW7 2AY, U.K.


Theory of Superconductivity

J. Bardeen, L. N. Cooper, J. R. Schrieffer


Large-Area Synthesis of High-Quality and Uniform Graphene Films on Copper Foils

American Association for the Advancement of Science (AAAS)

Xuesong Li, Weiwei Cai, Jinho An, Seyoung Kim, Junghyo Nah, Dongxing Yang, Richard Piner, Aruna Velamakanni, Inhwa Jung, Emanuel Tutuc, Sanjay K. Banerjee, Luigi Colombo, Rodney S. Ruoff

Department of Mechanical Engineering and the Texas Materials Institute, 1 University Station C2200, The University of Texas at Austin, Austin, TX 78712–0292, USA.

Abstract: Growing Graphene The highest quality graphene samples, single-atom-thick layers of carbon, are suspended flakes exfoliated from graphite, but these samples are very small in size (square micrometers). For many electronics applications, larger areas are needed. Li et al. (p. 1312 , published online 7 May) show that graphene grows in a self-limiting way on copper films as large-area sheets (one square centimeter) from methane through a chemical vapor deposition process. The films, which are mainly one layer in thickness, can be transferred to other substrates and have electron mobilities as high as 4300 square centimeters per volt second.


Aram V. Chobanian, George L. Bakris, Henry R. Black, William C. Cushman, Lee A. Green, Joseph L. Izzo, Daniel W. Jones, Barry J. Materson, Suzanne Oparil, Jackson T. Wright, Edward J. Roccella, the National High Blood Pressure Education Program Coordinating Committee

From Boston University School of Medicine (A.V.C.), Boston, Mass; Rush University Medical Center (G.L.B., H.R.B.), Chicago, Ill; Veterans Affairs Medical Center (W.C.C.), Memphis, Tenn; University of Michigan (L.A.G.), Ann Arbor, Mich; State University of New York at Buffalo School of Medicine (J.L.I. Jr.), Buffalo, NY; University of Mississippi Medical Center (D.W.J.), Jackson, Miss; University of Miami (B.J.M.), Miami, Fla; University of Alabama at Birmingham (S.O.), Birmingham, Ala; Case Western...

Abstract: The National High Blood Pressure Education Program presents the complete Seventh Report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure. Like its predecessors, the purpose is to provide an evidence-based approach to the prevention and management of hypertension. The key messages of this report are these: in those older than age 50, systolic blood pressure (BP) of greater than 140 mm Hg is a more important cardiovascular disease (CVD) risk factor than diastolic BP; beginning at 115/75 mm Hg, CVD risk doubles for each increment of 20/10 mm Hg; those who are normotensive at 55 years of age will have a 90% lifetime risk of developing hypertension; prehypertensive individuals (systolic BP 120–139 mm Hg or diastolic BP 80–89 mm Hg) require health-promoting lifestyle modifications to prevent the progressive rise in blood pressure and CVD; for uncomplicated hypertension, thiazide diuretic should be used in drug treatment for most, either alone or combined with drugs from other classes; this report delineates specific high-risk conditions that are compelling indications for the use of other antihypertensive drug classes (angiotensin-converting enzyme inhibitors, angiotensin-receptor blockers, beta-blockers, calcium channel blockers); two or more antihypertensive medications will be required to achieve goal BP (<140/90 mm Hg, or <130/80 mm Hg) for patients with diabetes and chronic kidney disease; for patients whose BP is more than 20 mm Hg above the systolic BP goal or more than 10 mm Hg above the diastolic BP goal, initiation of therapy using two agents, one of which usually will be a thiazide diuretic, should be considered; regardless of therapy or care, hypertension will be controlled only if patients are motivated to stay on their treatment plan. Positive experiences, trust in the clinician, and empathy improve patient motivation and satisfaction. This report serves as a guide, and the committee continues to recognize that the responsible physician’s judgment remains paramount.


High-Resolution Global Maps of 21st-Century Forest Cover Change

M. C. Hansen, P. V. Potapov, R. Moore, M. Hancher, S. A. Turubanova, A. Tyukavina, D. Thau, S. V. Stehman, S. J. Goetz, T. R. Loveland, A. Kommareddy, A. Egorov, L. Chini, C. O. Justice, J. R. G. Townshend

Department of Geographical Sciences, University of Maryland, College Park, MD 20742, USA.

Abstract: Forests in Flux Forests worldwide are in a state of flux, with accelerating losses in some regions and gains in others. Hansen et al. (p. 850 ) examined global Landsat data at a 30-meter spatial resolution to characterize forest extent, loss, and gain from 2000 to 2012. Globally, 2.3 million square kilometers of forest were lost during the 12-year study period and 0.8 million square kilometers of new forest were gained. The tropics exhibited both the greatest losses and the greatest gains (through regrowth and plantation), with losses outstripping gains.


Rapid isolation of high molecular weight plant DNA


Sequential deposition as a route to high-performance perovskite-sensitized solar cells

Julian Burschka, Norman Pellet, Soo-Jin Moon, Robin Humphry-Baker, Peng Gao, Mohammad K. Nazeeruddin, Michael Grätzel


Li–O2 and Li–S batteries with high energy storage

Peter G. Bruce, Stefan A. Freunberger, Laurence J. Hardwick, Jean-Marie Tarascon


Global analyses of sea surface temperature, sea ice, and night marine air temperature since the late nineteenth century

Journal of Geophysical Research: Atmospheres

N. A. Rayner, D. E. Parker, E. B. Horton, C. K. Folland, L. V. Alexander, D. P. Rowell, E. C. Kent, A. Kaplan

Hadley Centre for Climate Prediction and Research Met Office  Bracknell UK

Abstract: We present the Met Office Hadley Centre's sea ice and sea surface temperature (SST) data set, HadISST1, and the nighttime marine air temperature (NMAT) data set, HadMAT1. HadISST1 replaces the global sea ice and sea surface temperature (GISST) data sets and is a unique combination of monthly globally complete fields of SST and sea ice concentration on a 1° latitude‐longitude grid from 1871. The companion HadMAT1 runs monthly from 1856 on a 5° latitude‐longitude grid and incorporates new corrections for the effect on NMAT of increasing deck (and hence measurement) heights. HadISST1 and HadMAT1 temperatures are reconstructed using a two‐stage reduced‐space optimal interpolation procedure, followed by superposition of quality‐improved gridded observations onto the reconstructions to restore local detail. The sea ice fields are made more homogeneous by compensating satellite microwave‐based sea ice concentrations for the impact of surface melt effects on retrievals in the Arctic and for algorithm deficiencies in the Antarctic and by making the historical in situ concentrations consistent with the satellite data. SSTs near sea ice are estimated using statistical relationships between SST and sea ice concentration. HadISST1 compares well with other published analyses, capturing trends in global, hemispheric, and regional SST well, containing SST fields with more uniform variance through time and better month‐to‐month persistence than those in GISST. HadMAT1 is more consistent with SST and with collocated land surface air temperatures than previous NMAT data sets.


Exploration, normalization, and summaries of high density oligonucleotide array probe level data


A critical review of high entropy alloys and related concepts


High-performance medicine: the convergence of human and artificial intelligence


Room-Temperature Ultraviolet Nanowire Nanolasers

Michael H. Huang, Samuel Mao, Henning Feick, Haoquan Yan, Yiying Wu, Hannes Kind, Eicke Weber, Richard Russo, Peidong Yang

Department of Chemistry, University of California,

Abstract: Room-temperature ultraviolet lasing in semiconductor nanowire arrays has been demonstrated. The self-organized, <0001> oriented zinc oxide nanowires grown on sapphire substrates were synthesized with a simple vapor transport and condensation process. These wide band-gap semiconductor nanowires form natural laser cavities with diameters varying from 20 to 150 nanometers and lengths up to 10 micrometers. Under optical excitation, surface-emitting lasing action was observed at 385 nanometers, with an emission linewidth less than 0.3 nanometer. The chemical flexibility and the one-dimensionality of the nanowires make them ideal miniaturized laser light sources. These short-wavelength nanolasers could have myriad applications, including optical computing, information storage, and microanalysis.


Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

H. Thorvaldsdottir, J. T. Robinson, J. P. Mesirov


Stop explaining black box machine learning models for high stakes decisions and use interpretable models instead


Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

J Gregory Caporaso, Christian L Lauber, William A Walters, Donna Berg-Lyons, James Huntley, Noah Fierer, Sarah M Owens, Jason Betley, Louise Fraser, Markus Bauer, Niall Gormley, Jack A Gilbert, Geoff Smith, Rob Knight

Department of Computer Science, Northern Arizona University , Flagstaff, AZ , USA

Abstract: Abstract DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.


Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I

Peter W.J. Rigby, Marianne Dieckmann, Carl Rhodes, Paul Berg

American Cancer Society, U.S. Public Health Service


AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Mihaly Varadi, Stephen Anyango, Mandar Deshpande, Sreenath Nair, Cindy Natassia, Galabina Yordanova, David Yuan, Oana Stroe, Gemma Wood, Agata Laydon, Augustin Žídek, Tim Green, Kathryn Tunyasuvunakool, Stig Petersen, John Jumper, Ellen Clancy, Richard Green, Ankur Vora, Mira Lutfi, Michael Figurnov, Andrew Cowie, Nicole Hobbs, Pushmeet Kohli, Gerard Kleywegt, Ewan Birney, Demis Hassabis, Sameer Velankar

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK

Abstract: Abstract The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions. Powered by AlphaFold v2.0 of DeepMind, it has enabled an unprecedented expansion of the structural coverage of the known protein-sequence space. AlphaFold DB provides programmatic access to and interactive visualization of predicted atomic coordinates, per-residue and pairwise model-confidence estimates and predicted aligned errors. The initial release of AlphaFold DB contains over 360,000 predicted structures across 21 model-organism proteomes, which will soon be expanded to cover most of the (over 100 million) representative sequences from the UniRef90 data set.


Marching cubes: A high resolution 3D surface construction algorithm

Association for Computing Machinery (ACM)

General Electric Company, Schenectady, NY

Abstract: We present a new algorithm, called marching cubes , that creates triangle models of constant density surfaces from 3D medical data. Using a divide-and-conquer approach to generate inter-slice connectivity, we create a case table that defines triangle topology. The algorithm processes the 3D medical data in scan-line order and calculates triangle vertices using linear interpolation. We find the gradient of the original data, normalize it, and use it as a basis for shading the models. The detail in images produced from the generated surface models is the result of maintaining the inter-slice connectivity, surface data, and gradient information present in the original 3D data. Results from computed tomography (CT), magnetic resonance (MR), and single-photon emission computed tomography (SPECT) illustrate the quality and functionality of marching cubes . We also discuss improvements that decrease processing time and add solid modeling capabilities.


Amazon's Mechanical Turk

Michael Buhrmester, Tracy Kwang, Samuel D. Gosling

Department of Psychology, University of Texas at Austin

Abstract: Amazon’s Mechanical Turk (MTurk) is a relatively new website that contains the major elements required to conduct research: an integrated participant compensation system; a large participant pool; and a streamlined process of study design, participant recruitment, and data collection. In this article, we describe and evaluate the potential contributions of MTurk to psychology and other social sciences. Findings indicate that (a) MTurk participants are slightly more demographically diverse than are standard Internet samples and are significantly more diverse than typical American college samples; (b) participation is affected by compensation rate and task length, but participants can still be recruited rapidly and inexpensively; (c) realistic compensation rates do not affect data quality; and (d) the data obtained are at least as reliable as those obtained via traditional methods. Overall, MTurk can be used to obtain high-quality data inexpensively and rapidly.


Unconventional superconductivity in magic-angle graphene superlattices

Yuan Cao, Valla Fatemi, Shiang Fang, Kenji Watanabe, Takashi Taniguchi, Efthimios Kaxiras, Pablo Jarillo-Herrero


High-precision sampling for Brillouin-zone integration in metals


Overview of the High Efficiency Video Coding (HEVC) Standard

Institute of Electrical and Electronics Engineers (IEEE)

IEEE Transactions on Circuits and Systems for Video Technology

Gary J. Sullivan, Jens-Rainer Ohm, Woo-Jin Han, Thomas Wiegand


VASPKIT: A user-friendly interface facilitating high-throughput computing and analysis using VASP code

Vei Wang, Nan Xu, Jin-Cheng Liu, Gang Tang, Wen-Tong Geng


The Resonating Valence Bond State in La 2 CuO 4 and Superconductivity

Department of Physics, Princeton University, Princeton, NJ 08544.

Abstract: The oxide superconductors, particularly those recently discovered that are based on La 2 CuO 4 , have a set of peculiarities that suggest a common, unique mechanism: they tend in every case to occur near a metal-insulator transition into an odd-electron insulator with peculiar magnetic properties. This insulating phase is proposed to be the long-sought "resonating-valence-bond" state or "quantum spin liquid" hypothesized in 1973. This insulating magnetic phase is favored by low spin, low dimensionality, and magnetic frustration. The preexisting magnetic singlet pairs of the insulating state become charged superconducting pairs when the insulator is doped sufficiently strongly. The mechanism for superconductivity is hence predominantly electronic and magnetic, although weak phonon interactions may favor the state. Many unusual properties are predicted, especially of the insulating state.


The Temperature Dependence of Relaxation Mechanisms in Amorphous Polymers and Other Glass-forming Liquids

Journal of the American Chemical Society

Malcolm L. Williams, Robert F. Landel, John D. Ferry


Room-temperature fabrication of transparent flexible thin-film transistors using amorphous oxide semiconductors

Kenji Nomura, Hiromichi Ohta, Akihiro Takagi, Toshio Kamiya, Masahiro Hirano, Hideo Hosono


Coupling measurements for the 125 GeV Higgs Boson in the fermion decay channels with the ATLAS detector5 GeV Higgs Boson in the fermion decay channels

Proceedings of XXV International Workshop on Deep-Inelastic Scattering and Related Subjects — PoS(DIS2017)


Measurements of Higgs boson properties using a combination of different Higgs decay channels

Proceedings of The 39th International Conference on High Energy Physics — PoS(ICHEP2018)


Search for invisible decay modes of the Higgs boson with the ATLAS detector.

Proceedings of 38th International Conference on High Energy Physics — PoS(ICHEP2016)


Search for the standard model Higgs boson through the H → ZZ decay channels with the ATLAS detector


Search for the decay of the Higgs boson into two nMSSM pseudo-scalar particles.


Higgs Boson measurements in the H$\rightarrow$WW$\rightarrow\ell\nu\ell\nu$ decay channel

Proceedings of 40th International Conference on High Energy physics — PoS(ICHEP2020)


Proceedings of The European Physical Society Conference on High Energy Physics — PoS(EPS-HEP2017)


Standard Model Higgs boson production in the decay mode H->bb in association with a W or Z boson for High Luminosity LHC Running

Proceedings of XXVII International Symposium on Lepton Photon Interactions at High Energies — PoS(LeptonPhoton2015)

Flavia De Almeida Dias, ATLAS Collaboration


Measurement of the Higgs boson coupling properties in the diphoton and $ZZ$ decay channels using the ATLAS detector


Higgs boson measurements in third generation decay channels (excluding ttH) with ATLAS and CMS

Proceedings of The Eighth Annual Conference on  Large Hadron Collider Physics — PoS(LHCP2020)

Stephen Jiggins, ATLAS and CMS Collaborations


Experimental results using the decay of the Higgs boson to tau leptons and muons

Proceedings of Sixth Annual Conference on Large Hadron Collider Physics — PoS(LHCP2018)

Mareike Meyer, ATLAS and CMS Collaborations


Cross section and coupling measurements with the ATLAS detector for the 125 GeV Higgs Boson in the diboson decay channels


EFT interpretation of off-shell Higgs boson to $ZZ \rightarrow 4\ell$ and $ZZ \rightarrow 2\ell2\nu$ decay channels at ATLAS

Proceedings of The Eleventh Annual Conference on Large Hadron Collider Physics — PoS(LHCP2023)


Exploiting the Higgs Boson for Discovery

Office of Scientific and Technical Information (OSTI)


Measurement of cross sections and couplings of the SM Higgs boson in the ZZ decay channel using the ATLAS detector

Ludovica Aperio Bella, ATLAS Collaboration


Search for the SM Higgs boson in the diboson decay modes with the ATLAS detector

German Carrillo-Montoya, the ATLAS Collaboration


Constraining the Higgs boson self-coupling in a combined measurement of single and double Higgs boson channels at the ATLAS experiment

Proceedings of 41st International Conference on High Energy physics — PoS(ICHEP2022)


Search for a Charged Higgs Boson via $H^+ \rightarrow \tau^+\nu$


Measurement of the SM Higgs boson mass in the diphoton and $4\ell$ decay channels using the ATLAS detector

Karolos Jozef Potamianos, ATLAS Collaboration


Constraining the Higgs boson self-coupling via single-Higgs production measurements

Proceedings of European Physical Society Conference on High Energy Physics — PoS(EPS-HEP2019)


Measurement of fermionic couplings of the Standard Model Higgs boson using the $b\bar b, τ^{+}τ^{−} and μ^{+} μ^{−}$ decay channels with the ATLAS detector


Constraints on the Higgs boson self-coupling from the combination of single-Higgs and double-Higgs production analyses performed with the ATLAS experiment


Non-resonant Higgs boson pair production and Higgs-self couplings measurements by ATLAS with Run 2

Proceedings of The Thirteenth Annual Large Hadron Collider Physics — PoS(LHCP2025)


Higgs boson production and properties at ATLAS: decays into boson pairs, and overall combination

Proceedings of The European Physical Society Conference on High Energy Physics — PoS(EPS-HEP2025)


Standard model Higgs boson searches in ATLAS


Search for rare Higgs boson decays and BSM Higgs bosons

Proceedings of 12th Large Hadron Collider Physics Conference — PoS(LHCP2024)

Shigeki Hirose, ATLAS and CMS Collaborations


Measurement of the properties of the Higgs boson at ATLAS


Search for the Standard Model Higgs boson in theH→bb̄andH→τ+τ−decay modes with the ATLAS detector


Higgs boson couplings at ATLAS


Search for a charged Higgs boson decaying to a top and a bottom quarks in ATLAS

Proceedings of Prospects for Charged Higgs Discovery at Colliders — PoS(CHARGED2016)


Searches for BSM and Higgs boson at LHC

O. Jinnouchi, ATLAS Collaboration, CMS Collaboration


The Higgs boson at the LHC: standard model Higgs properties and beyond standard model searches

Proceedings of An Alpine LHC Physics Summit — PoS(ALPS2018)

Anne-Marie Magnan, ATLAS and CMS Collaborations


Search for the standard model Higgs boson in the H → WW(

Magda A. Chelstowska, ATLAS Collaboration


Search for a low mass standard model Higgs Boson with the ATLAS detector at the LHC


Measurement of the Higgs boson mass

William Axel Leight, ATLAS Collaboration


Search for Rare Decays of the Observed Higgs Boson and Additional Higgs Bosons with the ATLAS Detector


Measurements of Higgs boson properties with the ATLAS detector

Proceedings of The 43rd International Symposium on Physics in Collision — PoS(PIC2024)


Search for Higgs boson pair production with the ATLAS detector


Final Technical Report: New Physics in Higgs or Higgsinos Using Vector Boson Fusion, Missing Energy, and ATLAS Trigger System Upgrades


Higgs boson coupling measurements in ATLAS

Antonio Jesus Gomez Delegido, ATLAS Collaboration


Higgs boson measurements

Roberto SALERNO, ATLAS and CMS Collaborations


Higgs Boson Searches at ATLAS


Combined Higgs boson measurements at the ATLAS experiment

Matthew Henry Klein, ATLAS Collaboration


Higgs boson mass, width and CP measurements with the ATLAS detector

Proceedings of XXXII International Workshop on Deep Inelastic Scattering and Related Subjects — PoS(DIS2025)


Measurements of the CP structure of Higgs-boson couplings with the ATLAS experiment

Proceedings of 31st International Workshop on Deep Inelastic Scattering — PoS(DIS2024)


Measurements of the Higgs boson decays to two bottom quarks

Proceedings of XXIX International Symposium on Lepton Photon Interactions at High Energies — PoS(LeptonPhoton2019)


Higgs boson couplings and properties

Proceedings of 7th Annual Conference on Large Hadron Collider Physics — PoS(LHCP2019)

Luca Cadamuro, ATLAS and CMS Collaborations


Publisher Correction: A detailed map of Higgs boson interactions by the ATLAS experiment ten years after the discovery


Measurements and searches of Higgs boson decays to two fermions

Proceedings of XXVI International Workshop on Deep-Inelastic Scattering and Related Subjects — PoS(DIS2018)


Probing the nature of electroweak symmetry breaking with Higgs boson pairs in ATLAS


Review for "Microglial Clearance of Alzheimer’s Amyloid-Beta Obstructed by Nanoplastics"


Decision letter for "Microglial Clearance of Alzheimer’s Amyloid-Beta Obstructed by Nanoplastics"


<i>μ</i> -Opioid Endomorphins and DDP-IV Inhibitor Sitagliptin Enhance Amyloid-Beta Clearance and Memory in an Alzheimer’s Cell Model

Abstract: Abstract Alzheimer’s Disease is a neurodegenerative disorder caused by A β 42 aggregation. Endomorphins 1 and 2 (EM1, EM2), two novel μ -opioid agonists, have been implicated in protecting against A β 42 toxicity, though it is unclear how the endomorphins achieve their effects. Phase one of the study found that EM1 and EM2 activation protected A β 42 -treated cells. This protection, mediated by μ -opioid receptor (MOR) activation, also reduced rotenone-induced oxidative stress, both in a dose-dependent manner. Pretreatment with naloxone, a μ -opioid antagonist, reversed these effects, confirming MOR involvement in EM1 and EM2’s actions. In phase two, molecular docking techniques suggested that sitagliptin can prevent intracellular EM1 degradation. In vitro assays demonstrated that sitagliptin enhanced intracellular EM1’s beneficial effects in promoting cell survival and reducing cell apoptotic activity, A β 42 aggregation, and hydrogen peroxide free radical concentrations. This suggests intracellular EM1 can mitigate the toxic effects of A β 42 aggregation. However, sitagliptin did not enhance EM1’s effects on BDNF expression or neurite outgrowth, suggesting that MOR activation, rather than intracellular EM1, primarily drives mechanisms associated with memory improvement. Collectively, our findings suggest that both intracellular EM1 and EM1-mediated MOR activation offer potential therapeutic avenues for mitigating memory impairment in Alzheimer’s and potentially COVID-19. Furthermore, this research underscores the critical role of the MOR in broader memory mechanisms.


Author response for "Microglial Clearance of Alzheimer’s Amyloid-Beta Obstructed by Nanoplastics"

Yue Wang, Gangtoh Huang, Xiufang Liang, Nicholas Andrikopoulos, Huayuan Tang, Feng Ding, Pu Chun Ke, Yuhuan Li


BPS2025 - Concentration-dependent role of apolipoprotein E in amyloid beta clearance by human astrocytes


Binding Characteristics of PRX012 Surrogate Demonstrate Potent Engagement of Toxic Amyloid Beta Protofibrils and Robust Clearance of Pyroglutamate-modified Amyloid Beta (P7-9.003)

Brian Campbell, Gang Zhang, Joshua Salmans, Abderrahman Elmaarouf, Stephen Tam, Amir Porat, Michael Skov, Philip Dolan, Gene Kinney, Wagner Zago


Polystyrene Nanoplastics Induce Alzheimer's Disease Through Itpkb-Mediated Neuroinflammation, Mitochondrial Dysfunction, and Compromised Amyloid-Beta Clearance

Junjie Shao, Amin Guo, Shuangshuang Tian, Fang Zhang, Junhu Li, Yanqin Liu, Xiu-zhao Fan, Xiaoshuang Zhou


525 REVERSING LIVER SINUSOIDAL ENDOTHELIAL AGING RESTORES CLEARANCE OF AMYLOID BETA AND LDL CHOLESTEROL

Sam de Leve, Xiangdong Wang, Helia Alavifard, Lily Dara, Laurie DeLeve


Dual Amyloid Beta/Tau Vaccine PRX123 Surrogate Results in Robust Clearance of Amyloid Plaques in Brains of Aggressive APP/PS1 Mouse Model (P7-9.015)

Robin Barbour, Clara Tourino, Alyssa Trumble, LeeAnn Louie, Gene Kinney, Wagner Zago, Brian Campbell

Current and former employees of Prothena Biosciences Inc


Repeat Opioid Use Modulates Microglia Activity and Amyloid Beta Clearance in a Mouse Model of Alzheimer’s Disease

Joseph V Gogola, Sung Won Stephanie Wee, Alfredo J Garcia

Abstract: Abstract In addition to driving dependency and overdose, illicit use of opioids, such as fentanyl, is linked to the risk for cognitive decline and dementia. Growing evidence also indicates that opioid use is associated with pathological features, paralleled early in Alzheimer’s disease (AD), which raises the possibility of the involvement of mechanistic interactions between opioid use and AD progression. Here, we investigate how chronic fentanyl use (i.e., 20 days) influences the neuroimmune state, microglial activity, and amyloid burden in wildtype and APPPS1-21 mice, a transgenic model of AD. In wild-type mice, fentanyl use promoted a pro-inflammatory state without increasing the incidence of disease-associated microglia. In APPPS1-21 mice, chronic fentanyl use led to a shift favoring an anti-inflammatory state, which was associated with increased microglia clustering and activation at Aβ plaques, increased Aβ internalization in plaque-associated activated microglia, decreased soluble Aβ, and decreased plaque burden. Our findings indicate that chronic fentanyl use fundamentally changes the trajectory of neuroimmune activity and features characteristic of early AD by enabling microglia to enhance Aβ clearance. The interactions demonstrate how substance use can reshape the neuroimmune landscape in neurodegenerative disease, emphasizing the importance of tailored treatment strategies.


Modelling Amyloid-beta clearance dynamics across sleep-wake cycles in healthy conditions

S. Sangeet, A. D'Rozario, C. Phillips, C. Hoyos, S. Postnova

Woolcock Institute of Medical Research, University of Sydney


Rapid Brain Hemorrhage in Mice Treated with Anti-Amyloid-Beta Immunotherapy in the Absence of Amyloid Plaque Clearance or Marked Astrocyte Dysfunction

Rebecca  L. Gillani, Maria V. Sanchez-Mico, Moustafa Algamal, Sarena Abdallah, Sara Whiteman, Rachel Paredes, Wadzanai  H. Ndambakuwa, Uma Sanker, Ashley  A. Scherlek, Steven  S. Hou, Thierry Bussière, Michael Levy, Brian  J. Bacskai


Investigating a Relation between Amyloid Beta Plaque Burden and Accumulated Neurotoxicity Caused by Amyloid Beta Oligomers

Department of Mechanical and Aerospace Engineering, North Carolina State University, Raleigh, NC 27695-7910, USA

Abstract: Abstract Alzheimer’s disease (AD) is characterized by the accumulation of amyloid-β (Aβ), yet the specific link between plaque burden and cognitive decline remains a subject of intense investigation. This paper presents a mathematical model that simulates the coupled dynamics of Aβ monomers, soluble oligomers, and fibrillar species in the brain tissue. By modifying existing moment equations to include a dedicated conservation equation for Aβ monomers, the model explores how various microscopic processes, such as primary nucleation, surface-catalyzed secondary nucleation, fibril elongation, and fragmentation, contribute to macroscopic disease progression. Central to this study is the concept of “accumulated neurotoxicity” as a surrogate marker of biological age, defined as the time-integrated concentration of soluble Aβ oligomers. Unlike plaque burden, accumulated neurotoxicity cannot be reversed, and the harm it causes depends critically on the sequence of events that produced it. Numerical results demonstrate that while plaque burden and neurotoxicity both increase over time, their relationship is non-linear and highly sensitive to the efficiency of protein degradation machinery. Specifically, impaired degradation leads to a rapid advancement of biological age relative to calendar age. The model further identifies oligomer dissociation and fibril fragmentation as potential protective mechanisms that can counterintuitively reduce neurotoxic burden by diverting monomers away from the soluble oligomer pool. These findings provide a quantitative framework for understanding why individuals with similar plaque burdens may experience vastly different cognitive outcomes, underscoring the importance of targeting soluble oligomers early in therapeutic interventions.


Long-Term High-Fat Diet Impairs AQP4-Mediated Glymphatic Clearance of Amyloid Beta

Wei Peng, Ye Yuan, Jingna Lei, Yi Zhao, Yan Li, Qiumin Qu, Jin Wang


Synchrotron Fourier Transform Infrared Microspectroscopy (Sftirm) Analysis of Beta Amyloid Aggregation/Clearance in Al-Induced Alzheimer’S’ Disease in Rat Brain Hippocampal Tissue

Safaa  K. H. Khalil, Waleed El hotaby, Gehan  Abdel-Raouf Ahmed, Gihan Kamel, Hadeer  H.A. Sherif, Lamyaa Abbas


Corrigendum to “Heparan sulfate from porcine mucosa promotes amyloid-beta clearance in APP/PS1 mice and alleviates Alzheimer's pathology” [Carbohydrate Polymers 285 (2022) 119205]

Lidan Wu, Wenjie Jiang, Na Zhao, Fengshan Wang


Amyloid beta related angiitis


Switch to phagocytic microglia by CSFR1 inhibition drives amyloid-beta clearance from glutamatergic terminals rescuing LTP in acute hippocampal slices

Gaia Piccioni, Nunzia Maisto, Asia d’Ettorre, Georgios Strimpakos, Robert Nisticò, Viviana Triaca, Dalila Mango


Identification of Inhibitors for Amyloid-beta in Alzheimer's Disease and Cerebral Amyloid Angiopathy

Wake Early College of Health and Sciences

Abstract: The neurodegenerative illness Alzheimer's disease causes 70% of cases of dementia, leading to the impairment of behavioral and cognitive functions such as language, attention, memory, judgment, and reasoning. The disease is caused by the buildup of amyloid fibrils in brain neurons. Recently, in 2023, a new type of amyloid fibril extracted from the leptomeninges of Alzheimer’s disease patients has been resolved. This structure has a different shape and size than the earlier 2019 structure. We hypothesize that since the two structures are different, the ligands binding and inhibiting the structure should also be different. Therefore, a rigorous research process was undertaken, including molecular docking simulations to identify inhibitors that can bind at the fibril interface and prevent fibril formation. A total of 8216 ligands were docked on the amyloid protein, and the best five ligands based on the binding interactions were selected for further evaluation. These results were further validated using a machine-learning technique called P2Rank. Finally, molecular docking and molecular dynamics simulations in the protein-fibril complex were performed to understand the interactions between amyloid peptide/fibril and the plasma membrane. The thoroughness of our research process instills confidence in the potential of developing inhibitors that can prevent fibril formation, potentially leading to new treatments for the disease.


Exogenous Amyloid Sequences: Their Role in Amyloid-Beta Heterotypic Aggregation


Amyloid Beta Revisited: A Versatile Immune Polypeptide

Abstract: Alzheimer's disease affects about fifty million people worldwide. Its main symptoms are the formation of amyloid deposits and of neurofibrillary tangles, and cognition loss. To date, no clear etiology for this disease could be identified. Metal ions have been shown to accumulate in amyloid deposits. Moreover, multiple infections have been shown to be risk factors for the development of Alzheimer's and other dementia, with vaccines playing protective roles. I will here elaborate on the likelihood that Amyloid b is not a toxic molecule, but a protective protein fragment, targeted both against infections and metals. A combination of chemical and biological exposures, with metals playing a key role, would thus be key factors in the triggering of Alzheimer's disease.


Abstract: Alzheimer's disease affects about fifty million people worldwide. Its main symptoms are the formation of amyloid deposits and of neurofibrillary tangles, and cognition loss. To date, no clear etiology for this disease could be identified. I will here elaborate on the likelihood that Amyloid b is not a toxic molecule but a protective protein fragment, and that a combination of chemical and biological exposures, with metals playing a key role, are the triggering factors for Alzheimer's type dementia.


Systematic review of amyloid-beta clearance proteins from the brain to the periphery: implications for Alzheimer’s disease diagnosis and therapeutic targets

Letian Huang, Mingyue Liu, Ze Li, Bing Li, Jiahe Wang, Ke Zhang

Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China

Abstract: Amyloid-beta clearance plays a key role in the pathogenesis of Alzheimer’s disease. However, the variation in functional proteins involved in amyloid-beta clearance and their correlation with amyloid-beta levels remain unclear. In this study, we conducted meta-analyses and a systematic review using studies from the PubMed, Embase, Web of Science, and Cochrane Library databases, including journal articles published from inception to June 30, 2023. The inclusion criteria included studies comparing the levels of functional proteins associated with amyloid-beta clearance in the blood, cerebrospinal fluid, and brain of healthy controls, patients with mild cognitive impairment, and patients with Alzheimer’s disease. Additionally, we analyzed the correlation between these functional proteins and amyloid-beta levels in patients with Alzheimer’s disease. The methodological quality of the studies was assessed via the Newcastle‒Ottawa Scale. Owing to heterogeneity, we utilized either a fixed-effect or random-effect model to assess the 95% confidence interval (CI) of the standard mean difference (SMD) among healthy controls, patients with mild cognitive impairment, and patients with Alzheimer’s disease. The findings revealed significant alterations in the levels of insulin-degrading enzymes, neprilysin, matrix metalloproteinase-9, cathepsin D, receptor for advanced glycation end products, and P-glycoprotein in the brains of patients with Alzheimer’s disease, patients with mild cognitive impairment, and healthy controls. In cerebrospinal fluid, the levels of triggering receptor expressed on myeloid cells 2 and ubiquitin C-terminal hydrolase L1 are altered, whereas the levels of TREM2, CD40, CD40L, CD14, CD22, cathepsin D, cystatin C, and α2 M in peripheral blood differ. Notably, TREM2 and cathepsin D showed changes in both brain (SMD = 0.31, 95% CI: 0.16–0.47, P < 0.001, I 2 = 78.4%; SMD = 1.24, 95% CI: 0.01–2.48, P = 0.048, I 2 = 90.1%) and peripheral blood (SMD = 1.01, 95% CI: 0.35–1.66, P = 0.003, I 2 = 96.5%; SMD = 7.55, 95% CI: 3.92–11.18, P < 0.001, I 2 = 98.2%) samples. Furthermore, correlations were observed between amyloid-beta levels and the levels of TREM2 ( r = 0.16, 95% CI: 0.04–0.28, P = 0.009, I 2 = 74.7%), neprilysin ( r = –0.47, 95% CI: –0.80–0.14, P = 0.005, I 2 = 76.1%), and P-glycoprotein ( r = –0.31, 95% CI: –0.51–0.11, P = 0.002, I 2 = 0.0%) in patients with Alzheimer’s disease. These findings suggest that triggering receptor expressed on myeloid cells 2 and cathepsin D could serve as potential diagnostic biomarkers for Alzheimer’s disease, whereas triggering receptor expressed on myeloid cells 2, neprilysin, and P-glycoprotein may represent potential therapeutic targets.


Liver as a new target organ in Alzheimer’s disease: insight from cholesterol metabolism and its role in amyloid-beta clearance

Beibei Wu, Yuqing Liu, Hongli Li, Lemei Zhu, Lingfeng Zeng, Zhen Zhang, Weijun Peng

Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China

Abstract: Alzheimer’s disease, the primary cause of dementia, is characterized by neuropathologies, such as amyloid plaques, synaptic and neuronal degeneration, and neurofibrillary tangles. Although amyloid plaques are the primary characteristic of Alzheimer’s disease in the central nervous system and peripheral organs, targeting amyloid-beta clearance in the central nervous system has shown limited clinical efficacy in Alzheimer’s disease treatment. Metabolic abnormalities are commonly observed in patients with Alzheimer’s disease. The liver is the primary peripheral organ involved in amyloid-beta metabolism, playing a crucial role in the pathophysiology of Alzheimer’s disease. Notably, impaired cholesterol metabolism in the liver may exacerbate the development of Alzheimer’s disease. In this review, we explore the underlying causes of Alzheimer’s disease and elucidate the role of the liver in amyloid-beta clearance and cholesterol metabolism. Furthermore, we propose that restoring normal cholesterol metabolism in the liver could represent a promising therapeutic strategy for addressing Alzheimer’s disease.


Anti-amyloid-β monoclonal antibodies induce brain atrophy through amyloid clearance cascade reaction

Yu-Hui Qiu, He-Jin Wang, Min-Hua Zheng, Shijie Zhang, See PDF


N-Terminal-Targeted Anti-Amyloid-β Monoclonal Antibodies Induce Brain Atrophy through Amyloid Clearance Cascade Reaction

Yu-Hui Qiu, He-Jin Wang, Shijie Zhang, See PDF

Abstract: Three anti-amyloid-β (Aβ) monoclonal antibodies (mAbs) have been approved by FDA for&nbsp;Alzheimer’s disease(AD) therapy. However, a reduction of brain volume was also been observed. In this analysis, we aimed to identify whether the brain volume reduction was induced by N-terminal-targeted mAbs via Aβ clearance. All the published RCTs of mAbs in AD were included, which reported detailed magnetic resonance imaging data. The literature search identified&nbsp;totally 22 RCTs. The&nbsp;N-terminal-targeted mAbs&nbsp;accelerated whole-brain atrophy and ventricular enlargement,&nbsp;with limited hippocampal&nbsp;atrophy. The N-terminal-targeted mAbs significantly reduced amyloid-PET. Additionally, amyloid-PET change was correlated with&nbsp;the whole-brain atrophy and the ventricular&nbsp;enlargements. The mediation analysis showed that the association between&nbsp;N-terminal-targeted mAbs&nbsp;and whole-brain and ventricular volumetric changes were mediated by amyloid-PET reduction. These findings constitute a “phenomenological theory”: The whole-brain atrophy and ventricular enlargement were mainly induced by N-terminal-targeted mAbs through amyloid clearance cascade reaction.


Aging modulates amyloid clearance kinetics during anti-amyloid therapy: evidence from real-world serial amyloid PET

Tomomichi Iizuka, Toshiaki Watanabe, Masashi Kameyama

Abstract: Background Anti-amyloid antibodies have been shown to reduce cerebral amyloid burden in early Alzheimer’s disease (AD), yet considerable interindividual variability in treatment-associated amyloid reduction has been observed. The biological factors underlying this variability remain unclear. In particular, the influence of aging on amyloid clearance dynamics during anti-amyloid therapy has not been well characterized in real-world clinical settings. Methods We conducted a prospective observational study of 23 patients with early-stage AD receiving lecanemab who underwent serial 18 F-flutemetamol amyloid PET at baseline and after 6 and 12 months. Amyloid burden was quantified in centiloid units. Cognitive outcomes were assessed using the Mini-Mental State Examination (MMSE) and Clinical Dementia Rating–Sum of Boxes (CDR-SB). Baseline cerebral perfusion was evaluated using 123 I-IMP SPECT with three-dimensional stereotactic surface projection (3D-SSP) analysis. Results All participants showed reductions in amyloid burden on serial PET; however, the magnitude of reduction varied substantially across individuals. Older patients tended to exhibit larger and more rapid reductions in amyloid burden, whereas younger patients demonstrated more modest decreases despite comparable baseline amyloid levels and standardized dosing. Amyloid reduction at 6 months strongly predicted the magnitude of reduction at 12 months, suggesting that early PET changes capture subsequent amyloid clearance trajectories. Cognitive decline occurred in a subset of patients despite substantial amyloid reduction and was associated with marked baseline temporo-parietal hypoperfusion on SPECT rather than insufficient amyloid removal. Conclusion In this real-world cohort, aging appeared to influence the observable kinetics of amyloid reduction during anti-amyloid therapy. Early serial amyloid PET may provide useful information regarding longer-term amyloid dynamics, while baseline perfusion imaging may help identify patients with substantial downstream neurodegenerative burden who remain at risk for cognitive decline despite amyloid clearance. These findings highlight biological heterogeneity in treatment response and underscore the value of multimodal imaging for monitoring disease-modifying therapies in AD.


Amyloid Beta


Review for "ArcheD, a residual neural network for prediction of cerebrospinal fluid amyloid-beta from amyloid PET images"


Reviewer #2 (Public review): Connections across regional glymphatic clearance, neural activity and amyloid-β deposition in cortex


eLife Assessment: Connections across regional glymphatic clearance, neural activity and amyloid-β deposition in cortex

National Institute of Neurological Disorders and Stroke, National Institute of Health


ApoE Mimic Peptide COG1410 Enhances Beta-Amyloid Clearance and Improves Cognitive Function by Inducing&nbsp;The Transformation of A1/ A2 Reactive Astrocytes And&nbsp;Increasing the BDNF Concentration in Brain of APP/PS1 Double Transgenic Mice

Ying Ma, Yue Qiao, Hang Liu, Chaoying He


Structural and Functional Analysis of TREM2 Interactions with Amyloid Beta Reveal Molecular Mechanisms That Mediate Phagocytosis of Oligomeric Amyloid Beta

Jessica Greven, Omar Osorio, Jay Nix, Jen Alexander-Brett, Thomas J. Brett


Research progress on vascular endothelial growth factor C in meningeal lymphatic vessel-mediated clearance of amyloid &beta;-protein

Journal of Zhejiang University (Medical Sciences)

Zhaoxie YU, Yao WANG, Yanan LI, Feng SHEN, Yanchun WANG


Reviewer #3 (Public review): Connections across regional glymphatic clearance, neural activity and amyloid-β deposition in cortex


Isobavachalcone ameliorates Alzheimer disease pathology by autophagy-mediated clearance of amyloid beta and inhibition of NLRP3 inflammasome in 5XFAD mice

Dilpreet Kour, Parul Khajuria, Kuhu Sharma, Alpa Sharma, Ankita Sharma, Syed Mudassir Ali, Priya Wazir, P Ramajayan, Sanghapal D. Sawant, Utpal Nandi, Zabeer Ahmed, Ajay Kumar

CSIR-Indian Institute of Integrative Medicine

Abstract: Abstract The complex pathology of Alzheimer disease (AD) has led to failure of multiple drugs in clinical trials. We hypothesized that targeting multiple aspects AD pathology may yield better results. Therefore, we identified isobavachalcone (IBC) as a natural compound with dual activity against AD pathology. IBC caused AMPK phosphorylation through CAMKK2 to induce autophagy and inhibit NLRP3 inflammasome in primary astrocytes. The inhibition of NLRP3 inflammasome by IBC was completely reversed when autophagy was inhibited by siAMPK or bafilomycin A1. Further, the primary astrocytes treated with IBC showed a significant intracellular clearance of amyloid beta, which was added externally to the culture. However, when autophagy was inhibited by siRNA-mediated downregulation of AMPK, the clearance of amyloid beta was significantly reduced. Moreover, the inflammatory phenotype of astrocytes also displayed a sharp decline, as indicated by the reduced levels of GFAP and IL-1β. We validated the anti-Alzheimer effect of IBC by treating transgenic 5XFAD mice for two months with IBC. The 5XFAD mice showed a significant improvement in brain health as indicated by improved memory behavior in the radial arm maze test, along with better performance in the open field and rotarod tests. The data revealed that IBC upregulated the autophagic proteins, which led to decreased levels of amyloid beta in the brain and plasma, which further led to reduced levels of neuroinflammation and improved brain health. This study highlights the importance of autophagy in the simultaneous clearance of amyloid beta and inhibition of NLRP3 inflammasome to ameliorate AD pathology.


Reviewer #1 (Public review): Connections across regional glymphatic clearance, neural activity and amyloid-β deposition in cortex


Decision letter for "ArcheD, a residual neural network for prediction of cerebrospinal fluid amyloid-beta from amyloid PET images"


The Neuroprotective Effects of Berberine in Alzheimer’s Disease Mouse Model via Improvement of Mitochondrial Dysfunction and Enhanced Amyloid-beta Peptide Clearance

The Korean Society for Biomedical Laboratory Sciences

Department of Biomedical Laboratory Science, College of Medical Science, Konyang University, Daejeon 35365, Korea


Structural and functional analysis of TREM2 interactions with amyloid beta reveal molecular mechanisms that mediate phagocytosis of oligomeric amyloid beta

Jessica A. Greven, Omar Osario, Jay C. Nix, Jennifer M. Alexander-Brett, Tom J. Brett

Abstract: Abstract The TREM2 receptor is expressed on microglia in the brain, where it plays critical roles regulating microglia function. TREM2 engages a number of ligands involved in Alzheimer’s disease, and consequent signaling triggers phagocytosis, activation, survival, and proliferation. TREM2 has emerged as a drug target for AD, however very little is known regarding the structural basis for TREM2 microglial functions. Here we investigated the engagement of oligomeric amyloid beta (oAβ42) with TREM2. Using familial variants of amyloid beta, we show that mutations in the N-terminal portion of Aβ, notably residues H6 and D7, disrupt binding to TREM2. We then co-crystallized TREM2 with Aβ(1-8) peptide and determined the high resolution crystal structure. The structure revealed the peptide binds to the hydrophobic site of TREM2, closest to CDR1. Mutational and binding studies using BLI confirmed that mutations to the hydrophobic site ablate binding to oAβ42. Finally, we show that these interactions are critical to triggering phagocytosis of oAβ42, as oAβ42 variants H6R and D7N are not phagocytosed. Altogether, these data indicate that TREM2 engages oAβ42 using the hydrophobic site on TREM2 and the N-terminal portion of Aβ, and that this interaction is critical to trigger signaling and phagocytosis.


Ergothioneine, a dietary antioxidant improves amyloid beta clearance in the neuroretina of a mouse model of Alzheimer’s disease

Printha Wijesinghe, Clayton A. Whitmore, Matthew Campbell, Charles Li, Miranda Tsuyuki, Eleanor To, Justin Haynes, Wellington Pham, Joanne A. Matsubara

Abstract: IntroductionErgothioneine (Ergo) is a naturally occurring dietary antioxidant. Ergo uptake is dependent on the transporter, organic cation transporter novel-type 1 (OCTN1) distribution. OCTN1 is highly expressed in blood cells (myeloid lineage cells), brain and ocular tissues that are likely predisposed to oxidative stress. Ergo may protect the brain and eye against oxidative damage and inflammation, however, the underlying mechanism remains unclear. Amyloid beta (Aβ) clearance is a complex process mediated by various systems and cell types including vascular transport across the blood–brain barrier, glymphatic drainage, and engulfment and degradation by resident microglia and infiltrating innate immune cells. Impaired Aβ clearance is a major cause for Alzheimer’s disease (AD). Here we investigated neuroretinas to explore the neuroprotective effect of Ergo in a transgenic AD mouse model.MethodsAge-matched groups of Ergo-treated 5XFAD, non-treated 5XFAD, and C57BL/6J wildtype (WT controls) were used to assess Ergo transporter OCTN1 expression and Aβ load along with microglia/macrophage (IBA1) and astrocyte (GFAP) markers in wholemount neuroretinas (n = 26) and eye cross-sections (n = 18). Immunoreactivity was quantified by fluorescence or by semi-quantitative assessments.Results and discussionOCTN1 immunoreactivity was significantly low in the eye cross-sections of Ergo-treated and non-treated 5XFAD vs. WT controls. Strong Aβ labeling, detected in the superficial layers in the wholemounts of Ergo-treated 5XFAD vs. non-treated 5XFAD reflects the existence of an effective Aβ clearance system. This was supported by imaging of cross-sections where Aβ immunoreactivity was significantly low in the neuroretina of Ergo-treated 5XFAD vs. non-treated 5XFAD. Moreover, semi-quantitative analysis in wholemounts identified a significantly reduced number of large Aβ deposits or plaques, and a significantly increased number of IBA1(+)ve blood-derived phagocytic macrophages in Ergo-treated 5XFAD vs. non-treated 5XFAD. In sum, enhanced Aβ clearance in Ergo-treated 5XFAD suggests that Ergo uptake may promote Aβ clearance possibly by blood-derived phagocytic macrophages and via perivascular drainage.


Chronic inhibition of receptor protein tyrosine phosphatase β/ζ reduces amyloid plaque load and modulates pleiotrophin-expressing glial cells, glial-plaque interactions and genes related to amyloid beta clearance

Teresa Fontán-Baselga, Héctor Cañeque-Rufo, Elisa Rivera-Illades, Esther Gramage, José María Zapico, Beatriz de Pascual-Teresa, María del Pilar Ramos-Álvarez, Marta Vicente-Rodríguez, Gonzalo Herradón

Department of Health and Pharmaceutical Sciences, Faculty of Pharmacy, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe

Abstract: Alzheimer’s disease (AD) is the most common cause of dementia. Pleiotrophin (PTN) is a neurotrophic factor relevant for central nervous system repair, neuron differentiation and survival. It is upregulated in different neuroinflammatory conditions. PTN is an endogenous inhibitor of Receptor Protein Tyrosine Phosphatase (RPTP) β/ζ. In a previous study, we showed that a short treatment with the RPTPβ/ζ inhibitor MY10 reduced amyloid beta (Aβ) plaque formation and glial activation in old APP/PS1 mice. Nevertheless, these preliminary data required new studies to prove the disease-modifying potential of RPTPβ/ζ inhibition by using younger animals and a longer treatment with MY10. Thus, we have now treated for 3 months five- to seven-month-old wild type (WT) and APP/PS1 mice with MY10. This treatment decreased Aβ plaque formation and increased the number of microglial cells in the dorsal subiculum of APP/PS1 mice. In addition, MY10 reduced the number of GFAP+, not Iba1+, cells surrounding Aβ plaques. As expected, PTN expression was upregulated in the brain of APP/PS1 compared to WT mice and it was mainly found in Iba1+ and GFAP+ cells. Interestingly, treatment with MY10 significantly decreased the expression of PTN and the number of PTN-expressing Iba1+ and GFAP+ cells. MY10 induced a significant decrease of Mmp9 expression in the hippocampus of APP/PS1 mice, a key enzyme in AD progression. In summary, chronic inhibition of RPTPβ/ζ in APP/PS1 mice reduces Aβ plaque deposition, modulating glial-plaque interactions and the expression of specific genes including Ptn and its receptor.


SAMHWANG-SASIM DECOCTION ATTENUATES COGNITIVE DECLINE AND NEURONAL CELL DEATH THROUGH AMYLOID-BETA CLEARANCE AND BDNF SIGNALING IN ALZHEIMER’S DISEASE MOUSE MODELS

Malk Eun Pak, Yeo Jin Park, Buyun Kim, Hye Jin Yang, Wei Li, Younghoon Go


Protein Extraction for Amyloid Beta Fractionation v1

Abstract: This protocol can be used to isolate protein from murine brain tissue (volumes listed are for hippocampal samples) by solubility. It creates three protein fractions: tris soluble, triton soluble, and formic acid soluble. This protocol can be helpful when evaluating amyloid beta pathology as different amyloid beta structures can be found within each fraction. For example, insoluble amyloid beta associated with amyloid plaques will be found within the formic acid soluble fraction, whereas more soluble non-plaque associated amyloid beta will be found within the other two fractions.


Review for "Amyloid‐Beta, Tau, and Microglial Activation in Aged Felid Brains"


Speech-to-Image Generation Using Audio Embeddings and Latent Diffusion Models

2025 Eighth International Conference on Image Information Processing (ICIIP)

Visvesvaraya Technological University,Department of CS&E RNS Institute of Technology,Bangalore,India


High-resolution efficient image generation from WiFi CSI using a pretrained latent diffusion model

2025 IEEE Globecom Workshops (GC Wkshps)

Institute of Science Tokyo,School of Engineering


Controllability and Structural Stability in Latent Diffusion Image Generation

2026 9th International Conference on Advanced Algorithms and Control Engineering (ICAACE)

Shenyang Jianzhu University,Department of Artistic Design,Shenyang,China


CT cardiac image and label generation by a 3D latent diffusion model

Ashok Vardhan Addala, Quanqi Hu, Masaki Ikuta, Ravi Soni, Gopal Avinash


Efficient Atlas Generation for Medical Imaging Via Groupwise Latent Diffusion Models

2025 IEEE International Conference on Image Processing (ICIP)

The Hong Kong University of Science and Technology,Department of Computer Science and Engineering


LSGDM: shadow generation for composite image with latent diffusion model

Fourth International Conference on Image Processing and Intelligent Control (IPIC 2024)


Text to Image Latent Diffusion Model with Dreambooth Fine Tuning for Automobile Image Generation

2022 5th International Seminar on Research of Information Technology and Intelligent Systems (ISRITI)

Muhammad Fariz Sutedy, Nunung Nurul Qomariyah

School of Computing and Creative Arts, Bina Nusantara University,Computer Science Department,Jakarta,Indonesia,11480


Hybrid Quantum-Classical Latent Diffusion Models for Medical Image Generation

2025 IEEE International Conference on Quantum Computing and Engineering (QCE)

Nora Bauer, Kübra Yeter-Aydeniz, Max Masnick

The MITRE Corporation,Quantum Information Sciences, Optics and Imaging Department,McLean,USA


Sketch-Guided 3D Tree Voxel Generation Using Latent Diffusion Model

2026 IIEEJ International Conference on Image Electronics and Visual Computing (IEVC)

Japan Advanced Institute of Science and Technology,Ishikawa,Japan


Orchid: Image Latent Diffusion for Joint Appearance and Geometry Generation

2025 IEEE/CVF International Conference on Computer Vision (ICCV)

Akshay Krishnan, Xinchen Yan, Vincent Casser, Abhijit Kundu


Advancing Image Generation: Integrating Transformer-Based Latent Diffusion With Semantic Clip Embeddings

2026 International Conference on Intelligent Computing, Networks, and Security (IC-ICNS)

Suthir Sriram, Karthikeyan, Nivethitha V

Amrita Vishwa Vidyapeetham,Amrita School of Computing,Dept. of Computer Science Engineering,Chennai,India


Latent Multi-Scale Diffusion Model for Neural Implicit 3D Shape Generation

2023 International Conference on Machine Vision, Image Processing and Imaging Technology (MVIPIT)

Hangzhou Dianzi University Hangzhou,School of Digital Media Technology,China


Arbitrary-Scale Image Generation and Upsampling Using Latent Diffusion Model and Implicit Neural Decoder

2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)


Medical Image Generation based on Latent Diffusion Models

2023 International Conference on Artificial Intelligence Innovation (ICAII)

Wenbo Song, Yan Jiang, Yin Fang, Xinyu Cao, Peiyan Wu, Hanshuo Xing, Xinglong Wu

School of Computer Science & Engineering, Wuhan Institute of Technology,Hubei Key Laboratory of Intelligent Robot,Wuhan,Hubei,China


ReLAD: Retrieval-Augmented LAtent Diffusion for Complex Aerial Image Generation

2025 IEEE International Conference on Big Data (BigData)

Douglas Townsell, Lingwei Chen, Mimi Xie, Chen Pan, Wen Zhang

Wright State University,Department of Computer Science and Engineering,Dayton,OH,USA,45431


Latent Space Super-Resolution for Higher-Resolution Image Generation with Diffusion Models

2025 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)

Jinho Jeong, Sangmin Han, Jinwoo Kim, Seon Joo Kim


StereoDiffusion: Training-Free Stereo Image Generation Using Latent Diffusion Models

2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)

Lezhong Wang, Jeppe Revall Frisvad, Mark Bo Jensen, Siavash Arjomand Bigdeli


Conditional Image-to-Video Generation with Latent Flow Diffusion Models

2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)

Haomiao Ni, Changhao Shi, Kai Li, Sharon X. Huang, Martin Renqiang Min

The Pennsylvania State University,University Park,PA,USA


ZoomLDM: Latent Diffusion Model for multi-scale image generation

Srikar Yellapragada, Alexandros Graikos, Kostas Triaridis, Prateek Prasanna, Rajarsi Gupta, Joel Saltz, Dimitris Samaras


Direct3D: Scalable Image-to-3D Generation via 3D Latent Diffusion Transformer

Neural Information Processing Systems Foundation, Inc. (NeurIPS)

Advances in Neural Information Processing Systems 37

Shuang Wu, Youtian Lin, Feihu Zhang, Yifei Zeng, Jingxi Xu, Philip Torr, Xun Cao, Yao Yao


Semi Synthetic Iris Image Generation with Identity Preservation Using Latent Diffusion Models

2026 IEEE 20th International Conference on Automatic Face and Gesture Recognition (FG)

Zhuotong Jin, Juan E. Tapia, Christoph Busch

Technical University of Denmark (DTU),Denmark


Enhancing Image Generation with Diffusion Transformer Architecture

SCITEPRESS - Science and Technology Publications

Proceedings of the 1st International Conference on Engineering Management, Information Technology and Intelligence

Software engineering, Nankai University, Tianjin, China, --- Select a Country ---


Transcending Image Generation Paradigms: Fusion of Transformer-Based Latent Diffusion and Semantic Clip Embeddings

2025 Second International Conference on Computing, Semiconductor, Mechatronics, Intelligent Systems and Communications (COSMIC)

Sasi Vardhan Reddy Mandapati, Venkata Mani Nikhil Reddy Mandapati

Indian Institute of Technology (BHU),Department of Electronics Engineering,Varanasi,India


Ultrasound image generation using latent diffusion models

Medical Imaging 2025: Ultrasonic Imaging and Tomography

Benoit Freiche, Anthony El-Khoury, Ali Nasiri-Sarvi, Mahdi S. Hosseini, Damien Garcia, Adrian Basarab, Mathieu Boily, Hassan Rivaz


Enhancing Denoising Models Performance Through Timestep-Aware Predictor for Latent Diffusion-Based Image Generation

2023 23rd International Conference on Control, Automation and Systems (ICCAS)

Pusan National University,Department of Mechanical Engineering,Busan,Korea

National Research Foundation of Korea(NRF)


Progressive Diffusion Model for UAVs Image Generation

Proceedings of the 18th International Conference on Agents and Artificial Intelligence

Hèdi Fkih, Abdelaziz Kallel, Zied Chtourou


Self-Discovering Interpretable Diffusion Latent Directions for Responsible Text-to-Image Generation

Hang Li, Chengzhi Shen, Philip Torr, Volker Tresp, Jindong Gu


Conditional Molecule Generation with 2D Latent Diffusion

Budapest University of Technology and Economics


Guess What I Think: Streamlined EEG-to-Image Generation with Latent Diffusion Models

ICASSP 2025 - 2025 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)

Eleonora Lopez, Luigi Sigillo, Federica Colonnese, Massimo Panella, Danilo Comminiello

Sapienza University of Rome,Dept. Information Engineering, Electronics and Telecommunications (DIET),Italy


Conditional diffusion guided by part-level latent for dental crown point cloud generation

International Conference on Image, Signal Processing, and Pattern Recognition (ISPP 2024)

Ao Zhang, Zhen Shen, Jian Yang, Qihang Fang, Gang Xiong, Xisong Dong


LSSGen: Leveraging Latent Space Scaling in Flow and Diffusion for Efficient Text to Image Generation

2025 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)

Jyun-Ze Tang, Chih-Fan Hsu, Jeng-Lin Li, Ming-Ching Chang, Wei-Chao Chen


Synthetic Image Generation With a Fine-Tuned Latent Diffusion Model for Organ on Chip Cell Image Classification

2023 Signal Processing: Algorithms, Architectures, Arrangements, and Applications (SPA)

Maksims Ivanovs, Laura Leja, Kārlis Zviedris, Roberts Rimsa, Karina Narbute, Valerija Movcana, Felikss Rumnieks, Arnis Strods, Kevin Gillois, Gatis Mozolevskis, Arturs Abols, Roberts Kadikis

Institute of Electronics and Computer Science,Riga,Latvia


Latent Diffusion for Language Generation

Advances in Neural Information Processing Systems 36

Justin Lovelace, Varsha Kishore, Chao Wan, Eliot Shekhtman, Kilian Weinberger


Echosync++: Clinically Conditioned Cardiac Ultrasound Video Generation with Latent Diffusion and Ejection Fraction Consistency

2026 International Conference on Image, Signal Processing and Pattern Recognition (ISPP)

Ziwen Zhou, Yuhan Zhao, Zhongyang Fang, Haochen Lin, Rongtao Li, Wentao Fan

Beijing Normal-Hong Kong, Baptist University,Department of Computer Science,Zhuhai,China

National Natural Science Foundation of China


Sat2City: 3D City Generation from a Single Satellite Image with Cascaded Latent Diffusion

2025 IEEE/CVF International Conference on Computer Vision (ICCV)

Tongyan Hua, Lutao Jiang, Ying-Cong Chen, Wufan Zhao

The Hong Kong University of Science and Technology (Guangzhou),Guangzhou,China

National Natural Science Foundation of China, Ministry of Natural Resources


Intermediate-image-guided unsupervised deformable image registration using a latent diffusion model

Jiong Wu, Heng Zhou, Ziqian Huang, Boxiao Yu, Sangjin Bae, Wei Shao, Kuang Gong


MolBB: Molecular Graph Generation via Latent Brownian Bridge Diffusion Model

2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Macau University of Science and Technology


Unifying Generation and Prediction on Graphs with Latent Graph Diffusion


Floorplan-Diffusion: Automatic Floor Plan Generation via Pre-trained Large Latent Diffusion Model

Proceedings of the 2025 International Conference on Multimedia Retrieval

Minyang Xu, Yunzhong Lou, Xiang Gao, Xiangdong Zhou

School of Computer Science, Fudan University, Shanghai, China


Exploring Inherent Image Priors and Regulazation in Pretrained Latent Diffusion Model for Zero-Shot Image Restoration

2025 4th International Conference on Image Processing, Computer Vision and Machine Learning (ICICML)

Hefei University of Technology,School of Mathematics,Hefei,China


Comparative Analysis of Image Generation Based on GAN, VAE, and Diffusion Models

Proceedings of the 3rd International Conference on Data Science, Advanced Algorithms, and Intelligent Computing

Hainan Queen Mary School Beijing University of Posts and Telecommunications, Beijing, China


Diffusion-Based Neural Architectures for Image and Video Generation

Proceedings of the 1st International Conference on Interdisciplinary Research in Science, Engineering, and Technology

Suja P., S. Vijitha, B. Supriya, Mukesh Tripathi, S. Muthuselvan, Swagata Panchadhyayee

Department of Computer Science, Muslim Arts College, Thiruvithancode, Kanniyakumari, Tamil Nadu, India


Latent Diffusion Models with Correlation Loss for Tabular Data Generation

2025 5th International Conference on Neural Networks, Information and Communication Engineering (NNICE)

School of Computer Science and Technology, University of Science and Technology of China,Hefei,China


Text-to-Video Generation Using Latent Diffusion Models: Structural and Temporal Analysis

2025 IEEE Madhya Pradesh Section Conference (MPCON)

Utkarssh Sehgal, Navroop Kaur Ballagan, Anuranjana

Amity University,Department of Information Technology,Noida,Uttar Pradesh,India


Latent age attribute modulation guided continuous aging facial image generation

Sixteenth International Conference on Graphics and Image Processing (ICGIP 2024)

Jinglei Qu, Chen Chen, Yichao Zhou, Xiyuan Hu


Bass Accompaniment Generation Via Latent Diffusion

ICASSP 2024 - 2024 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)

Marco Pasini, Maarten Grachten, Stefan Lattner

Sony Computer Science Laboratories,Paris,France


Language-Guided Trajectory Traversal in Disentangled Stable Diffusion Latent Space for Factorized Medical Image Generation

2025 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)

Zahra Tehrani Nasab, Amar Kumar, Tal Arbel

Natural Sciences and Engineering Research Council of Canada, Canadian Institute for Advanced Research (CIFAR)


Cytofusion: A Latent Diffusion-Based Framework for Cytology Classification

2025 IEEE International Conference on Image Processing (ICIP)

Linyi Qian, Qian Huang, Yulin Chen, Shaoling Qin

Hohai University,College of Computer Science and Software Engineering,China


Latent Swap Joint Diffusion for 2D Long-Form Latent Generation

Yusheng Dai, Chenxi Wang, Chang Li, Chen Wang, Kewei Li, Jun Du, Lei Sun, Jianqing Gao, Ruoyu Wang, Jiefeng Ma

University of Science and Technology of China,Hefei,China


LADIMO: Face Morph Generation through Biometric Template Inversion with Latent Diffusion

2024 IEEE International Joint Conference on Biometrics (IJCB)

Norwegian University of Science and Technology,Gjøvik,Norway


The Photoredox Paradox: Electron and Hole Upconversion as the Hidden Secrets of Photoredox Catalysis

Journal of the American Chemical Society

Igor V. Alabugin, Paul Eckhardt, Kimberley M. Christopher, Till Opatz

Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States