bluuebunny/crossref_metadata_2025 huggingface dataset:
Study Protocol: A Scoping Review on Costing Methodologies in Robotic Ventral Hernia Repair
Authors: Nielsen Kristian Als , Kaiser Karsten , Helligsø Per , Nielsen Michael Festersen , Valorenzos Alexandros
Published: August 2024

Background

Healthcare expenditure is increasing at a rate that surpasses the growth of the gross domestic product in most Western nations, emphasizing the need for precise hospital accounting practices. In resource-constrained environments, accurately estimating the costs of hospital services, such as robotic ventral hernia repair, is essential for achieving efficiency and transparency. Despite the existence of several studies reporting on the cost of robotic ventral hernia repair, there is a lack of systematic mapping of current knowledge on the methodological designs used in studies reporting on the costs and resource use.

Methods

This study protocol outlines the methodology for a scoping review aimed at systematically mapping the existing literature on costing methodologies in robotic ventral hernia repair. The scoping review will follow the framework outlined by Arksey and O’Malley and adhere to the PRISMA-ScR guidelines. A systematic search will be conducted in Embase, Medline and Cochrane Library. Studies will be included if they involve patients undergoing robotic ventral hernia repair and report on cost/costing methodologies. The review will extract data on study characteristics, intervention specifics, and detailed costing methodologies. Two independent reviewers will conduct the data extraction, with discrepancies resolved through discussion or by a third reviewer.

Discussion

The review will identify significant variations in costing methodologies, including differences in perspectives (hospital vs. societal), time horizons, and cost components. It aims to highlight gaps and inconsistencies in the current literature, providing a foundation for future research to standardize costing methodologies and improve the accuracy of economic evaluations in robotic surgery. By systematically mapping the existing literature, this scoping review will provide valuable insights into the current state of costing methodologies in robotic ventral hernia repair. It will serve as a foundational reference for researchers, policymakers, and healthcare providers, offering recommendations to enhance the economic evaluation of robotic surgical technologies.
Assessing Population-level Accessibility to Medical College Hospitals in India: A Geospatial Modeling Study
Authors: Thakkar Harsh , Reddy Chaitanya , Passi Varun Raj , Miyajiwala Aamir , Kale Sahil , Raj Ankit , Zadey Siddhesh
Published: August 2024

Background

While studies have investigated the availability of Medical College Hospitals (MCHs) in India, data on geographical accessibility is limited. Our study looks at the current geographical accessibility to these MCHs across 36 states and union territories (UTs) and 735 districts.

Methods and Findings

We provided and validated the MCH data acquired from the National Health Profile Report 2022. We took motorized and walking travel-time friction surface rasters from the Malaria Atlas Project 2019 and high-resolution population estimates from WorldPop 2020. Using these, we examined the density of MCHs per million population and the median travel time to the nearest MCH. We assessed the Access Population Coverage (APC), defined as the proportion of the population within 30, 60, 90, and 120 minutes by motorized transport and within 30 and 60 minutes from the nearest MCH by walking.

In 2022, India had an average density of 0.47 MCHs per million. The median travel time to the nearest MCH was 67.94 minutes by motorized transport and 589.82 minutes by walking. 71.76% of the population could access the nearest MCH by motorized transport within 60 minutes (range across districts: 0-100%). 4.22% of the population could access the nearest MCH by walking within 30 minutes (range across districts: 0-71.86%). The APC was 62.20% within 60 minutes by motorized transport in rural vs. 92.34% in urban areas. The APC within 60 minutes by motorized transport for public MCHs was 63.62%, while that for private was 45.95%. These estimates do not account for resource availability at the hospitals or vehicular ownership in the population.

Conclusions

Median travel time and APC are useful for assessing geographical accessibility. Our study found a wide disparity in MCH access across Indian states and rural vs. urban areas. These analyses can guide the optimal placement of new MCHs.
OzWheat: a genome-to-phenome platform to resolve complex traits for wheat pre-breeding and research
Authors: Hyles Jessica E. , Eagles Howard A. , Ramm Kerrie , Sherman Bjorg , Gock Andrew , Stops Sandra , Phongkham Tanya , Leyne Emmett , Rathjen Tina , Suchecki Radoslaw , Stevens Lauren , Ord Louise , Fradgley Nick S. , McNeil Meredith D. , Marquardt Annelie , Andrew Samuel C. , Forrest Kerrie , Eastwood Russell F. , Norman Adam , Tredrea Annette , Trethowan Richard , Trevaskis Ben , Dillon Shannon K.
Published: August 2024

For over a century, Australian wheat breeders have successfully adapted wheat to a broad range of climatic conditions and crop management practices. The OzWheat genome-to-phenome (G2P) platform was established to capture this breeding history and explore traits, genes, and their interactions with the environment to enable ongoing research and deliver targets for wheat improvement. A panel of 285 cultivars and landraces were chosen through knowledge of breeding pedigrees to represent both global diversity and the historic flow of genetic variation over more than 100 years of selective breeding in Australia. Genetic characterisation of the panel included identification of genome-wide sequence variants and gene expression profiling across environments. Important traits for adaptation (flowering time and plant height) were assayed in controlled environments and at multiple field sites and years, with genome-wide association analyses (GWAS) using linear mixed models detecting both known and novel loci. Here, we report establishment of the OzWheat G2P platform as a powerful tool to integrate wheat genomes and phenomes and demonstrate its use to identify candidate genes and understand gene by environment interactions. This provides the wheat research and breeding community a new resource to support future cultivar development.
Neural Sequences Underlying Directed Turning inC. elegans
Authors: Kramer Talya S. , Wan Flossie K. , Pugliese Sarah M. , Atanas Adam A. , Hiser Alex W. , Luo Jinyue , Bueno Eric , Flavell Steven W.
Published: August 2024

Complex behaviors like navigation rely on sequenced motor outputs that combine to generate effective movement. The brain-wide organization of the circuits that integrate sensory signals to select and execute appropriate motor sequences is not well understood. Here, we characterize the architecture of neural circuits that controlC. elegansolfactory navigation. We identify error-correcting turns during navigation and use whole-brain calcium imaging and cell-specific perturbations to determine their neural underpinnings. These turns occur as motor sequences accompanied by neural sequences, in which defined neurons activate in a stereotyped order during each turn. Distinct neurons in this sequence respond to sensory cues, anticipate upcoming turn directions, and drive movement, linking key features of this sensorimotor behavior across time. The neuromodulator tyramine coordinates these sequential brain dynamics. Our results illustrate how neuromodulation can act on a defined neural architecture to generate sequential patterns of activity that link sensory cues to motor actions.
Interpretable improving prediction performance of general protein language model by domain-adaptive pretraining on DNA-binding protein
Authors: Zeng Wenwu , Dou Yutao , Pan Liangrui , Xu Liwen , Peng Shaoliang
Published: August 2024

DNA-protein interactions exert the fundamental structure of many pivotal biological processes, such as DNA replication, transcription, and gene regulation. However, accurate and efficient computational methods for identifying these interactions are still lacking. In this study, we propose a novel method ESM-DBP through refining the DNA-binding protein (DBP) sequence repertory and domain-adaptive pretraining based the protein language model (PLM). Our method considers the lack of exploration of general PLM for DBP domain-specific knowledge, so we screened out 170,264 DBPs from the UniProtKB database to construct the model that more suitable for learning crucial characteristics of DBP. The evaluation of ESM-DBP is systematically performed in four different DBP-related downstream prediction tasks, i.e., DNA-binding protein, DNA-binding residue, transcription factor, and DNA-binding Cys2His2 zinc-finger predictions. Experimental results show that ESM-DBP provides a better feature representation of DBP compared to the original PLM, resulting in improved prediction performance and outperforming other state-of-the-art prediction methods. In addition, ESM-DBP incorporates the integrated gradient algorithm for interpretable analysis, which usually ignored in the previous methods. It reveals that ESM-DBP possesses high sensitivity to the key decisive DNA-binding domains. Moreover, we find that ESM-DBP can still perform well even for those DBPs with only a few similar homologous sequences, and this generalization performs better than the original PLM. The data and standalone program of ESM-DBP are freely accessible athttps://github.com/pengsl-lab/ESM-DBP.
Characterization of a marine bacteria through a novel metabologenomics approach
Authors: Arini Gabriel Santos , Borelli Tiago Cabral , Ferreira Elthon Góis , de Felício Rafael , Teixeira Paula Rezende , Pedrino Matheus , Rabiço Franciene , de Siqueira Guilherme Marcelino Viana , Mencucini Luiz Gabriel , Tsuji Henrique , Andrade Lucas Sousa Neves , Garrido Leandro Maza , Padilla Gabriel , Gil-de-la-Fuente Alberto , Wang Mingxun , Lopes Norberto Peporine , Trivella Daniela Barretto Barbosa , Costa Lotufo Leticia Veras , Guazzaroni María-Eugenia , da Silva Ricardo Roberto
Published: August 2024

Exploiting microbial natural products is a key pursuit of the bioactive compound discovery field. Recent advances in modern analytical techniques have increased the volume of microbial genomes and their encoded biosynthetic products measured by mass spectrometry-based metabolomics. However, connecting multi-omics data to uncover metabolic processes of interest is still challenging. This results in a large portion of genes and metabolites remaining unannotated. Further exacerbating the annotation challenge, databases and tools for annotation and omics integration are scattered, requiring complex computations to annotate and integrate omics datasets. Here we performed a two-way integrative analysis combining genomics and metabolomics data to describe a new approach to characterize the marine bacterial isolate BRA006 and to explore its biosynthetic gene cluster (BGC) content as well as the bioactive compounds detected by metabolomics. We described BRA006 genomic content and structure by comparing Illumina and Oxford Nanopore MinION sequencing approaches. Digital DNA:DNA hybridization (dDDH) taxonomically assigned BRA006 as a potential new species of theMicromonosporagenus. Starting from LC-ESI(+)-HRMS/MS data, and mapping the annotated enzymes and metabolites belonging to the same pathways, our integrative analysis allowed us to correlate the compound Brevianamide F to a new BGC, previously assigned to other function.
Environmental DNA Surveys of Invertebrate Community on Forest Canopies Using Rainwater Analysis
Authors: Miwa Takumaru , Miyashita Naoya , Numa Chisato , Doi Hideyuki
Published: August 2024

Forest canopies, known for their high biodiversity, are essential for understanding forest ecosystems. Traditional methods for canopy surveys, such as tree climbing and canopy walkways, face challenges related to safety, cost, and time constraints. Environmental DNA (eDNA) analysis, which involves examining DNA from environmental samples, offers a promising alternative for these surveys. This study investigates the feasibility of using rainwater to collect eDNA from forest canopies, utilizing rain’s natural ability to wash away DNA from hard-to-reach areas. By comparing DNA analysis results from rainwater with conventional records obtained through visual and capture surveys, this research aims to validate the effectiveness and reliability of this method. Preliminary findings suggest that eDNA analysis from rainwater could provide an efficient approach to canopy biodiversity surveys, though further validation is required. This study marks an important first step towards developing eDNA analysis as a complementary tool for forest canopy research.
Modeling Microbial Regulatory Feedback in Organic Matter Decomposition Identifies Copiotrophic Traits as Key Drivers of Positive Priming
Authors: Ahamed Firnaaz , Stegen James C. , Graham Emily B. , Scheibe Timothy D. , Song Hyun-Seob
Published: August 2024

Microbial priming, characterized by significant changes in organic matter (OM) decomposition rates due to minor external treatments with the addition of labile OM, exerts a significant impact on biogeochemical cycles in ecosystems. Priming can take many forms, including positive priming (increased OM decomposition rates), negative priming (decreased OM decomposition rates), and everything in between. Currently, we lack generalizable frameworks that can mechanistically explain these diverse patterns of priming, making it challenging to identify its governing factors. In this work, we theorized priming to result from a biogeochemical feedback loop regulated by microorganisms optimizing the balance between cost and benefit towards maximizing their growth rates, i.e., the cost of exoenzyme synthesis for decomposing complex OM and the benefits of energy acquisition from microbial growth on labile OM. Accordingly, we examined the impacts of microbial growth traits and interactions on priming employing a cybernetic approach, which specializes in predicting complex microbial growth patterns through a regulatory feedback loop. Using the cybernetic model, we simulated the occurrence of priming driven by microorganisms in the following four distinct settings: copiotrophic degraders independently, oligotrophic degraders independently, a consortium of copiotrophic degraders and oligotrophic non-degraders, and a consortium of oligotrophic degraders and copiotrophic non-degraders. Comprehensive Monte Carlo simulations using these four models revealed several critical aspects of priming, including: (1) positive priming is a dominant phenomenon in general, while negative priming can also occur sporadically under specific parameter settings, (2) positive priming is more frequently observed in microbial systems with copiotrophic degraders than with oligotrophic degraders, (3) the presence of copiotrophic non-degraders suppresses positive priming, while the presence of oligotrophic non-degraders promotes positive priming, and (4) the evolution of priming over time is also influenced by microbial growth traits and interactions. Most strikingly, all four models predicted a dramatic positive priming effect triggered by the addition of a small amount (i.e., less than 10%) of labile organic matter, with no notable changes observed beyond this point. Together with other findings summarized above, this might represent a key feature of microbial priming that might be commonly observed across microbial systems with diverse growth traits as supported by literature data. Overall, this work combining new theories and models significantly enhances our understanding of priming by providing model-generated and empirically-testable hypotheses on the mechanisms governing priming.
Adversarial learning enables unbiased organism-wide cross-species alignment of single-cell RNA data at scale
Authors: Díaz-Mejía Juan Javier , Williams Elias , Innes Brendan , Focsa Octavian , Mendonca Dylan , Singh Swechha , Nixon Allison , Schuster Ronen , Buechler Matthew B. , Hinz Boris , Cooper Sam
Published: August 2024

Today’s single-cell RNA (scRNA) datasets remain siloed, due to significant challenges associated with their integration at scale. Moreover, most scRNA analysis tools that operate at scale leverage supervised techniques that are insufficient for cell-type identification and discovery. Here, we demonstrate that the alignment of scRNA data using unsupervised models is accurate at an organism-wide scale and between species. To do this, we show adversarial training of a deep-learning model we term batch-adversarial single-cell variational inference (BA-scVI) can be employed to align standardized benchmark datasets comprising dozens of scRNA studies spanning tissues in humans and mice. In the aligned space, we analyze cell types that span tissues in both species and find prevalent complement expressing macrophages and fibroblasts. We provide access to the tools presented via an online interface for atlas exploration and reference-based drag-and-drop alignment of new data.
Nonequilibrium phases of a biomolecular condensate facilitated by enzyme activity
Authors: Coupe Sebastian , Fakhri Nikta
Published: August 2024

Biomolecular condensates represent a frontier in cellular organization, existing as dynamic materials driven out of equilibrium by active cellular processes. Here we explore active mechanisms of condensate regulation by examining the interplay between DEAD-box helicase activity and RNA base-pairing interactions within ribonucleoprotein condensates. We demonstrate how the ATP-dependent activity of DEAD-box helicases—a key class of enzymes in condensate regulation—acts as a nonequilibrium driver of condensate properties through the continuous remodeling of RNA interactions. By combining the LAF-1 DEAD-box helicase with a designer RNA hairpin concatemer, we unveil a complex landscape of dynamic behaviors, including time-dependent alterations in RNA partitioning, evolving condensate morphologies, and shifting condensate dynamics. Importantly, we reveal an antagonistic relationship between RNA secondary structure and helicase activity which promotes condensate homogeneity via a nonequilibrium steady state. By elucidating these nonequilibrium mechanisms, we gain a deeper understanding of cellular organization and expand the potential for active synthetic condensate systems.
Local Synthesis of Reticulon-1C Lessens the Outgrowth of Injured Axons by Controlling Spastin Activity
Authors: Luarte Alejandro , Gallardo Javiera , Corvalán Daniela , Chakraborty Ankush , Gouveia-Roque Cláudio , Bertin Francisca , Contreras Carlos , Ramírez Juan Pablo , Weber Andrè , Acevedo Waldo , Zuschratter Werner , Herrera-Molina Rodrigo , Wyneken Úrsula , Paula-Lima Andrea , Adasme-Rocha Tatiana , Figueroa Antonia , González Carolina , González-Billault Christian , Hengst Ulrich , Couve Andrés
Published: August 2024

The regenerative potential of developing cortical axons following injury depends on intrinsic mechanisms, such as axon-autonomous protein synthesis, that are still not fully understood. An emerging factor in this regenerative process is the bi-directional interplay between microtubule dynamics and structural proteins of the axonal endoplasmic reticulum. Therefore, we hypothesize that locally synthesized structural proteins of the endoplasmic reticulum may regulate microtubule dynamics and the outgrowth of injured cortical axons. This hypothesis is supported by RNA data-mining, which identified Reticulon-1 as the sole ER-shaping protein consistently present in axonal transcriptomes and found it to be downregulated following cortical axon injury. Using compartmentalized microfluidic chambers, we demonstrate that local knockdown of Reticulon-1 mRNA enhances outgrowth while reducing the distal tubulin levels of injured cortical axons. Additionally, live cell imaging shows injury-induced reductions in microtubule growth rate and length, which are fully restored by axonal Reticulon-1 knockdown. Interestingly, axonal inhibition of the microtubule-severing protein Spastin fully prevents the effects of local Reticulon-1 knockdown on outgrowth and tubulin levels, while not affecting microtubule dynamics. Furthermore, we provide evidence supporting that the Reticulon-1C isoform is locally synthesized in injured axons and associates with Spastin to inhibit its severing activity. Our findings reveal a novel injury-dependent mechanism in which a locally synthesized ER-shaping protein lessens microtubule dynamics and the outgrowth of cortical axons.
Identification of a novel resistance gene which provides insight into Vip3Aa mode of action inHelicoverpa armigera
Authors: Bachler Andreas , Padovan Amanda , Anderson Craig J. , Wei Yiyun , Wu Yidong , Pearce Stephen , Downes Sharon , James Bill , Tessnow Ashley , Sword Gregory A. , Williams Michelle , Tay Wee Tek , Gordon Karl H. J. , Walsh Tom K.
Published: August 2024

The global reliance onBacillus thuringiensis(Bt) proteins for controlling lepidopteran pests in cotton, corn, and soybean crops underscores the critical need to understand resistance mechanisms. Vip3Aa, one of the most widely deployed and currently effective Bt proteins in genetically modified crops, plays a pivotal role in pest management. This study identifies the molecular basis of Vip3Aa resistance in AustralianHelicoverpa armigerathrough genetic crosses, and integrated genomic and transcriptomic analyses. We identified a previously uncharacterized gene, LOC110373801 (designatedHaVipR1), as a crucial determinant of Vip3Aa resistance in two field-derived resistant lines. Functional validation using CRISPR-Cas9 knockout in susceptible lines confirmed the gene’s role in conferring resistance.

Despite extensive laboratory selection of Vip3Aa-resistant colonies in Lepidoptera, the biochemical mechanisms underlying resistance have remained elusive. Our research demonstrates thatHaVipR1-mediated resistance operates independently of known resistance genes, including midgut-specific chitin synthase and the transcription factor SfMyb.

The identification ofHaVipR1offers further insights into the Vip3Aa mechanism of action. This discovery is vital for devising strategies to counteract resistance and sustain the efficacy of Bt crops. Future research should focus on elucidating the biochemical pathways involvingHaVipR1and investigating its interactions with other resistance mechanisms. Our findings underscore the utility of analysing field-derived resistant lines in providing biologically relevant insights and stress the necessity for comprehensive management strategies to maintain agricultural productivity.

Significance Statement

This is the first identification of a specific gene inHelicoverpa armigerawhich mediates resistance to theBacillus thuringiensis(Bt) protein Vip3Aa. We identify that this gene is disrupted in two different ways in separate field-derived resistant lines, one being a large transposable element insertion in the first intron of theHaVipR1gene, confirmed using long-read sequencing. Disruption of this gene using CRISPR-Cas9 knockout in a susceptibleH. armigeraline confers Vip3A resistance. The identification of a specific gene is important for molecular monitoring and management ofH. armigeraas well as other global pests of concern likeSpodoptera frugiperda. These findings also offer insights for researchers aiming to understand how Vip3Aa functions, as the action pathway remains unclear.
Avoided and avoidable deaths with the use of COVID-19 convalescent plasma in Italy during the first two years of pandemic
Authors: Franchini Massimo , Casadevall Arturo , Dragotakes Quigly , Focosi Daniele
Published: August 2024

Italy was the first western country to be hit by the COVID-19 pandemic and suffered nearly 200,000 deaths so far during the four years of the pandemic. In March 2020, Italy first deployed COVID-19 convalescent plasma (CCP) to treat hospitalized patients. Despite this initial effort, the proportion of COVID-19 patients treated with CCP during the first two years of the pandemic (2020-2021) was very low (approximately 2% of individuals hospitalized for COVID-19). In this study, we estimated the number of actual inpatient lives saved by CCP treatment in Italy using national mortality data, and CCP mortality reduction data from meta-analyses of randomized controlled trials and real-world data. We also estimated the potential number of lives saved if CCP had been deployed to 100% of hospitalized patients or used in 15% to 75% of outpatients. According to these models, CCP usage in 2020-2021 saved between 385-1304 lives, but this number would have increased to 17,751-60,079 if 100% of inpatients had been transfused with CCP. Similarly, broader (15-75%) usage in outpatients could have prevented 21,187-190,689 hospitalizations (desaturating hospitals) and 6,144-81,926 deaths. These data have important implications for convalescent plasma use in future infectious disease emergencies.
Early Detection of Mental Health Crises through AI-Powered Social Media Analysis: A Prospective Observational Study
Authors: Mansoor Masab A. , Ansari Kashif
Published: August 2024

Background

Early detection of mental health crises is crucial for timely intervention and improved outcomes. This study explores the potential of artificial intelligence (AI) in analyzing social media data to identify early signs of mental health crises.

Methods

We developed a multi-modal deep learning model integrating natural language processing and temporal analysis techniques. The model was trained on a diverse dataset of 996,452 social media posts in multiple languages (English, Spanish, Mandarin, and Arabic) collected from Twitter, Reddit, and Facebook over a 12-month period. Performance was evaluated using standard metrics and validated against expert psychiatric assessment.

Results

The AI model demonstrated high accuracy (89.3%) in detecting early signs of mental health crises, with an average lead time of 7.2 days before human expert identification. Performance was consistent across languages (F1 scores: 0.827-0.872) and platforms (F1 scores: 0.839-0.863). Key digital markers included linguistic patterns, behavioral changes, and temporal trends. The model showed varying accuracy for different crisis types: depressive episodes (91.2%), manic episodes (88.7%), suicidal ideation (93.5%), and anxiety crises (87.3%).

Conclusions

AI-powered analysis of social media data shows promise for early detection of mental health crises across diverse linguistic and cultural contexts. However, ethical challenges including privacy concerns, potential stigmatization, and cultural biases need careful consideration. Future research should focus on longitudinal outcome studies, ethical integration with existing mental health services, and development of personalized, culturally-sensitive models.
A biofilm-tropicPseudomonas aeruginosabacteriophage uses the exopolysaccharide Psl as receptor
Authors: Walton Brenna , Abbondante Serena , Marshall Michaela Ellen , Dobruchowska Justyna M. , Alvi Amani , Gallagher Larry A. , Vallikat Nikhil , Zhang Zhemin , Wozniak Daniel J. , Yu Edward W. , Boons Geert-Jan , Pearlman Eric , Rietsch Arne
Published: August 2024

Bacteria in nature can exist in multicellular communities called biofilms. Biofilms also form in the course of many infections.Pseudomonas aeruginosainfections frequently involve biofilms, which contribute materially to the difficulty to treat these infections with antibiotic therapy. Many biofilm-related characteristics are controlled by the second messenger, cyclic-di-GMP, which is upregulated on surface contact. Among these factors is the exopolysaccharide Psl, which is a critically important component of the biofilm matrix. Here we describe the discovery of aP. aeruginosabacteriophage, which we have called Clew-1, that directly binds to and uses Psl as a receptor. While this phage does not efficiently infect planktonically growing bacteria, it can disruptP. aeruginosabiofilms and replicate in biofilm bacteria. We further demonstrate that the Clew-1 can reduce the bacterial burden in a mouse model ofP. aeruginosakeratitis, which is characterized by the formation of a biofilm on the cornea. Due to its reliance on Psl for infection, Clew-1 does not actually form plaques on wild-type bacteria under standardin vitroconditions. This argues that our standard isolation procedures likely exclude bacteriophage that are adapted to using biofilm markers for infection. Importantly, the manner in which we isolated Clew-1 can be easily extended to other strains ofP. aeruginosaand indeed other bacterial species, which will fuel the discovery of other biofilm-tropic bacteriophage and expand their therapeutic use.
Multi-Targeted Effects of Novel Cycloastragenol Derivatives: Enhancing NRF2, Proteostasis, and Telomerase Pathways with p53 Modulation to Delay Replicative Senescence
Authors: Yilmaz Sinem , Bedir Erdal , Ballar Kirmizibayrak Petek
Published: August 2024

Aging is a complex, multifactorial process driven by various cellular and molecular mechanisms, including telomere shortening, oxidative stress, and the decline of proteostasis, all of which contribute to replicative senescence and age-related diseases. Cycloastragenol (CA), a triterpenoid saponin derived fromAstragalus membranaceus, has shown potential for its ability to activate telomerase, suggesting therapeutic benefits in delaying cellular aging. In this study, we explored the effects of novelCAderivatives, obtained through biotransformation as telomerase activators, on the NRF2/proteasome/telomerase axis and their potential to delay replicative senescence in human primary epidermal keratinocytes (HEKn).

Our findings reveal that theseCAderivatives significantly enhance NRF2 nuclear activity, leading to the upregulation of key cytoprotective enzymes essential for mitigating oxidative stress. Notably, these derivatives exhibited efficacy at much lower concentrations compared toCA, demonstrating their potential for enhanced therapeutic application. The derivatives also markedly increased proteasome activity, particularly in the β1 and β5 subunits, thereby preserving proteostasis—a critical factor in preventing the accumulation of damaged proteins associated with aging. Furthermore, continuous treatment with these derivatives sustained stimulatory effects, which was evidenced by increased NRF2, proteasome, and hTERT protein levels even in senescent cells and extended cellular lifespan.

Additionally, we explored the impact ofCAderivatives on p53-mediated pathways, demonstrating that these compounds effectively modulate the p53/p21 axis, reducing cell cycle arrest and promoting cellular proliferation. Moreover, the derivatives exhibited neuroprotective properties by attenuating glutamate-induced excitotoxicity, further underscoring their potential as multi-targeted anti-aging agents. In conclusion, our study provides strong evidence that novelCAderivatives act on multiple fronts to enhance NRF2 activity, maintain proteostasis, and modulate telomerase and p53 pathways, most at lower doses compared toCA. These actions collectively contribute to the delay of replicative senescence and the promotion of cellular longevity, positioningCAderivatives as potent candidates for developing multi-targeted anti-aging therapies that address the complex interplay of aging-related cellular processes.

Highlights

Telomerase-activeCAderivatives enhance NRF2 activity and proteasome activity, leading to cytoprotection at lower doses thanCA.

CAderivatives modulate the p53 pathway and cell cycle, prolonging cellular lifespan and delaying replicative senescence.

CAderivatives protect cells against glutamate-excitotoxicity along with decreased p53 protein levels.
Attentional priority and limbic activity favor gains over losses
Authors: Hu Kesong , Rosa Eve De , Anderson Adam K
Published: August 2024

Prospect theory has suggested that decisions reflect a bias toward avoidance of loss compared to equivalent gains. In our study we examine whether a similar bias is found in decisions regarding whether a loss associated stimulus or a gain associated stimulus is given priority in perception. We find that for most people, gains are given priority over loss in the decision of which of the two stimuli occurs first. We also ask whether gains are reflected in greater activity in limbic systems related to emotion. In an fMRI study, we find that most people show greater emotional response to gains, not losses. We consider how these findings might be related to risk aversion in studies of decision making.
A fast-acting inhibitor of blood-stageP. falciparumwith mechanism distinct from artemisinin and chloroquine
Authors: Kabeche Stephanie , Meister Thomas , Yeh Ellen
Published: August 2024

Artemisinins are first-line treatment for malaria, prized for their extremely fast reduction of parasite load in patients. New fast-acting antimalarial compounds are urgently needed to counter artemisinin resistance, but the fast parasite reduction observed with artemisinins is rare among antimalarial compounds. Here we show that MMV1580853 has a very fastin vitrokilling rate, comparable to that of dihydroartemisinin. Near-complete parasite growth inhibition was observed within 1 hour of treatment with MMV1580853 and dihydroartemisinin, while chloroquine, another fast-acting antimalarial, showed partial growth inhibition after 1h. MMV1580853 was reported to inhibit prenyltransferases, but its fast killing rate is inconsistent with this mechanism-of-action and we were unable to validate any of 3 annotatedP. falciparumprenyltransferases as MMV1580853 targets. MMV1580853 also did not phenocopy the inhibition phenotype of either chloroquine or dihydroartemisinin. These results indicate that MMV1580853 has a distinct mechanism-of-action leading to a very fast killing rate. MMV1580853 compound development and investigation of its mechanism-of-action will be critical avenues in the search for drugs matching the remarkable clinical efficacy of artemisinin.
Modelling inflammation-induced peripheral sensitization in a dish - more complex than expected?
Authors: Li Yuening , Lock Amy , Fedele Laura , Zebochin Irene , Sabate Alba , Siddle Matthew , Cainarca Silvia , Röderer Pascal , Montag Katharina , Tarroni Paola , Brüstle Oliver , Shaw Tanya , Taams Leonie , Denk Franziska
Published: August 2024

Peripheral sensitization of nociceptors is believed to be a key driver of chronic pain states. Here, we sought to study the effects of a modified version of inflammatory soup on the excitability of human stem-cell derived sensory neurons. For this, we used a pre-existing and a novel stem cell line, modified to stably express the calcium sensor GCamP6f. Upon treatment with inflammatory soup, we observed no changes in neuronal transcription or functional responses upon calcium imaging, and only a very minor increase in resting membrane potential via whole cell patch clamping. Similarly small changes were observed when treating mouse primary sensory neurons with inflammatory soup. A semi-systematic re-examination of past literature further indicated that observed effects of inflammatory mediators on dissociated sensory neuron cultures are generally very small. We conclude that modelling inflammation-induced peripheral sensitization in vitro is non-trivial and will require careful selection of mediators and/or more complex, longitudinal multi-cellular setups. Especially in the latter, our novel GCamP6f induced-pluripotent stem cell line may be of value.
E. coliphylogeny drives co-amoxiclav resistance through variable expression ofblaTEM-1
Authors: Matlock William , Rodger Gillian , Pritchard Emma , Colpus Matthew , Kapel Natalia , Barrett Lucinda , Morgan Marcus , Oakley Sarah , Hopkins Katie L. , Roohi Aysha , Karageorgopoulos Drosos , Avison Matthew B. , Walker A. Sarah , Lipworth Samuel , Stoesser Nicole
Published: August 2024

Co-amoxiclav resistance inE. coliis a clinically important phenotype associated with increased mortality. The class A beta-lactamaseblaTEM-1is often carried by co- amoxiclav-resistant pathogens, but exhibits high phenotypic heterogeneity, making genotype-phenotype predictions challenging. We present a curated dataset ofn=377E. coliisolates representing all 8 known phylogroups, where the only acquired beta- lactamase isblaTEM-1. For all isolates, we generate hybrid assemblies and co-amoxiclav MICs, and for a subset (n=67/377),blaTEM-1qPCR expression data. First, we test whether certainE. colilineages are intrinsically better or worse at expressingblaTEM-1, for example, due to lineage differences in regulatory systems, which are challenging to directly quantify. Using genotypic features of the isolates (blaTEM-1promoter variants and copy number), we develop a hierarchical Bayesian model forblaTEM-1expression that controls for phylogeny. We establish thatblaTEM-1expression intrinsically varies across the phylogeny, with some lineages (e.g. phylogroups B1 and C, ST12) better at expression than others (e.g. phylogroups E and F, ST372). Next, we test whether phylogenetic variation in expression influences the resistance of the isolates. With a second model, we use genotypic features (blaTEM-1promoter variants, copy number, duplications;ampCpromoter variants; efflux pump AcrF presence) to predict isolate MIC, again controlling for phylogeny. Lastly, we use a third model to demonstrate that the phylogenetic influence onblaTEM-1expression causally drives the variation in co- amoxiclav MIC. This underscores the importance of incorporating phylogeny into genotype-phenotype predictions, and the study of resistance more generally.
GroEL/ES chaperonin unfolds then encapsulates a nascent protein on the ribosome
Authors: Roeselová Alžběta , Maslen Sarah L. , He Jessica Zhiyun , Jurkeviciute Gabija , Mark Skehel J. , Enchev Radoslav , Balchin David
Published: August 2024

The bacterial chaperonin GroEL/ES promotes protein folding post-translation by transiently encapsulating substrate proteins within a central chamber. GroEL also binds translating ribosomesin vivo, suggesting an additional role in cotranslational folding. Here, we used biochemical reconstitution, structural proteomics and electron microscopy to study the mechanism by which GroEL/ES engages nascent polypeptides. We show that GroEL binds nascent chains on the inside of its cavity via the apical domains and disordered C-terminal tails, resulting in local structural destabilization of the substrate. Ribosome-tethered nascent proteins are partially encapsulated upon GroES binding to GroEL, and refold in the chaperonin cavity. Reconstitution of chaperone competition at the ribosome shows that both Trigger factor and GroEL can be accommodated on long nascent chains, but GroEL and DnaK are mutually antagonistic. Our findings extend the role of GroEL/ES inde novoprotein folding, and reveal an unexpected plasticity of the chaperonin mechanism that allows cotranslational substrate encapsulation.
Therapeutic Tumor Macrophage Reprogramming in Breast Cancer Through a Peptide-Drug Conjugate
Authors: Lepland Anni , Peranzoni Elisa , Haljasorg Uku , Asciutto Eliana K. , Crespí-Amer Maria , Modesti Lorenzo , Kilk Kalle , Lombardia Manuel , Acosta Gerardo , Royo Miriam , Peterson Pärt , Marigo Ilaria , Teesalu Tambet , Scodeller Pablo
Published: August 2024

In triple negative breast cancer (TNBC), pro-tumoral macrophages promote metastasis and suppress the immune response. To target these cells, we engineered a previously identified CD206 (mannose receptor)-binding peptide, mUNO, to enhance its affinity and proteolytic stability. The new rationally designed peptide, MACTIDE, includes a trypsin inhibitor loop, from the Sunflower Trypsin Inhibitor-I. Binding studies to recombinant CD206 revealed a 15-fold lower KDfor MACTIDE compared to parental mUNO. Additionally, mass spectrometry showed a 5-fold increase in half-life in tumor lysate for MACTIDE compared to mUNO. Homing studies in TNBC-bearing mice showed that fluorescein (FAM)-MACTIDE precisely targeted CD206+tumor-associated macrophages (TAMs) upon intravenous, intraperitoneal and even oral administration, with no significant accumulation in liver. We coupled MACTIDE to the FDA-approved drug Verteporfin, an established photosensitizer for photodynamic therapy and inhibitor of the YAP/TAZ pathway, to generate a conjugate here referred to as MACTIDE-V. In the orthotopic 4T1 TNBC mouse model, non-irradiated MACTIDE-V-treated mice unexpectedly showed a similar anti-tumoral effect and fewer signs of toxicity as irradiated MACTIDE-V-treated mice, leading to subsequent studies on the laser-independent activity of this conjugate.In vitrostudies using bone-marrow derived mouse macrophages showed that MACTIDE-V excluded YAP from the nucleus, increased the phagocytic activity and upregulated several genes associated with cytotoxic anti-tumoral macrophages. In mouse models of TNBC, MACTIDE-V slowed primary tumor growth, suppressed lung metastases, increased markers of phagocytosis and antigen presentation in TAMs and monocytes, increasing the tumor infiltration of several lymphocyte subsets. We therefore propose MACTIDE-V as a useful peptide-drug conjugate to modulate macrophage function in the context of breast tumor immunotherapy.
Test-retest reliability of TMS motor evoked responses and silent periods during explosive voluntary isometric contractions
Authors: Castelli F. , Mian O.S. , Bruton A. , Chembila Valappil A.C. , Tillin N.A.
Published: August 2024

Purpose

This study assessed the intraclass correlation coefficient (ICC) and coefficient of variation (CV) test-retest reliability of TMS responses MEPs and silent periods at early, middle, and late phases of the rising time-torque curve during explosive voluntary contractions. We also investigated how the number of consecutively averaged measurements over 3 to 15 separate contractions influenced reliability.

Methods

On two separate occasions 3-7 days apart, 14 adults completed 48 isometric explosives (1-s) contractions of the knee extensors, superimposed with TMS. The TMS elicited an MEP and silent period in the quadriceps muscles at 45 (early), 115 (middle), or 190 ms (late) during each contraction. TMS was also superimposed at the plateau of 15 separate MVCs. Test-retest ICC and CV were calculated for consecutively averaged MEPs and silent periods.

Results

No one condition was more reliable than another. For MEP amplitude, in all conditions except the explosive late phase, ICCs generally increased, and CV decreased, with an increase in the number of averaged contractions, and were >0.50 ICC and <15% CV within 7 contractions. For silent period, ICCs and CVs were unaffected by the number of consecutively averaged contractions and remained >0.50 ICC and <10% CV.

Conclusion

Test-retest reliability of TMS responses is comparable between phases of explosive contraction and at the plateau of MVC. To enhance MEP reliability, with the increases he number of averaged contractions of except the explosive late phase, we recommend studies average data across > the 3-5 contractions typically reported in the literature for studies using TMS during MVCs.
Preclinical testing of RRx-001 in mouse models of experimental endometriosis reveals promising therapeutic impacts
Authors: McIntyre Iona , Vasilyev Vadim , Perrone Chiara Lia , Dhami Priya , Panir Kavita , Rosser Matthew , Greaves Erin
Published: August 2024

Endometriosis is a chronic inflammatory condition characterised by the presence of ectopic endometrial-like tissue (lesions), associated reduced fertility and chronic pain. Impacting both the health and psycho-social functioning of millions of women worldwide, there is an urgent need for innovative non-hormonal, non-invasive treatments for the disorder. Both peritoneal and lesion-resident macrophages have been strongly implicated in the pathogenesis of endometriosis; key roles include promotion of lesion growth, neuroangiogenesis and nerve sensitization. With such a central role in the disease, macrophages represent a novel therapeutic target. In the current preclinical study, we sought to repurpose the macrophage targeting anti-cancer drug RRx-001 for the treatment of endometriosis. We utilised mouse models of induced endometriosis to demonstrate that RRx-001 acts to reduce endometriosis lesions and attenuate associated pain-like behaviours, without negatively impacting fertility. Using single nuclei multiome analyses, we identified a modification of macrophage subpopulations in the peritoneal cavity, specifically a reduced acquisition of a pro-disease phenotype and an accumulation of a pro-resolving phenotype. These observations signify the potential of RRx-001 as a novel therapeutic for endometriosis management.
Substrate Curvature Influences Cytoskeletal Rearrangement and Modulates Macrophage Phenotype
Authors: Sovar Austin , Patrick Matthew , Annamalai Ramkumar T.
Published: August 2024

Inflammation serves as a critical defense mechanism against pathogens and tissue damage but can lead to chronic diseases, such as cardiovascular disease and diabetes, when dysregulated. Macrophages play a pivotal role in orchestrating inflammatory responses, transitioning from pro-inflammatory M1 to anti-inflammatory M2 phenotypes to resolve inflammation and promote tissue repair. Current approaches to modulate macrophage phenotype predominantly rely on biochemical cues, which may induce systemic side effects. Given the mechanosensitivity of macrophages, this study investigates biophysical cues, specifically substrate curvature, as a localized strategy to regulate macrophage phenotype and minimize systemic repercussions.

We hypothesized that substrate curvature influences macrophage immunophenotype by modulating F-actin polymerization. To test this hypothesis, we fabricated spherical microgels with tunable curvatures and characterized their biophysical properties. Our findings indicate that macrophages adhere to microgel surfaces irrespective of curvature, but the curvature significantly alters F-actin dynamics. Furthermore, manipulating cytoskeletal dynamics via selective actin inhibition partially reversed curvature-induced changes in macrophage phenotype. These results underscore the pivotal role of substrate curvature in modulating macrophage behavior and immunophenotype.

Overall, our study demonstrates that substrate curvature significantly influences macrophage cytoskeletal dynamics and resulting immunophenotype. This simple approach can be utilized as a localized immunomodulatory treatment for inflammatory diseases.
Structural insight into binding site access and ligand recognition by human ABCB1
Authors: Kurre Devanshu , Dang Phuoc X. , Le Le T.M. , Gadkari Varun V. , Alam Amer
Published: August 2024

ABCB1 is a broad-spectrum efflux pump central to cellular drug handling and multidrug resistance in humans. However, its mechanisms of poly-specific substrate recognition and transport remain poorly resolved. Here we present cryo-EM structures of lipid embedded human ABCB1 in its apo, substrate-bound, inhibitor-bound, and nucleotide-trapped states at 3.4-3.9 Å resolution without using stabilizing antibodies or mutations and each revealing a distinct conformation. The substrate binding site is located within one half of the molecule and, in the apo state, is obstructed by transmembrane helix (TM) 4. Substrate and inhibitor binding are distinguished by major differences in TM arrangement and ligand binding chemistry, with TM4 playing a central role in all conformational transitions. Our data offer fundamental new insights into the role structural asymmetry, secondary structure breaks, and lipid interactions play in ABCB1 function and have far-reaching implications for ABCB1 inhibitor design and predicting its substrate binding profiles.