bluuebunny/crossref_metadata_2025 huggingface dataset:
A hybrid computational model of cancer spheroid growth with ribose-induced collagen stiffening
Authors: Botticelli Margherita , Metzcar John , Phillips Thomas , Cox Susan , Keshavanarayana Pradeep , Spill Fabian
Published: October 2024

Metastasis, the leading cause of death in cancer patients, arises when cancer cells disseminate from a primary solid tumour to distant organs. Growth and invasion of the solid tumour often involve collective cell migration, which is profoundly influenced by cell-cell interactions and the extracellular matrix (ECM). The ECM’s biochemical composition and mechanical properties, such as stiffness, regulate cancer cell behaviour and migration dynamics. Mathematical modelling serves as a pivotal tool for studying and predicting these complex dynamics, with hybrid discrete-continuous models offering a powerful approach by combining agent-based representations of cells with continuum descriptions of the surrounding microenvironment. In this study, we investigate the impact of ECM stiffness, modulated via ribose-induced collagen cross-linking, on cancer spheroid growth and invasion. We employed a hybrid discrete-continuous model implemented in PhysiCell to simulate spheroid dynamics, successfully replicating three-dimensionalin vitroexperiments. The model incorporates detailed representations of cell-cell and cell-ECM interactions, ECM remodelling, and cell proliferation. Our simulations align with experimental observations of two breast cancer cell lines, non-invasive MCF7 and invasive HCC1954, under varying ECM stiffness conditions. The results demonstrate that increased ECM stiffness due to ribose-induced cross-linking inhibits spheroid invasion in invasive cells, whereas non-invasive cells remain largely unaffected. Furthermore, our simulations show that higher ECM degradation by the cells not only enables spheroid growth and invasion but also facilitates the formation of multicellular protrusions. Conversely, increasing the maximum speed that cells can reach due to cell-ECM interactions enhances spheroid growth while promoting single-cell invasion. This hybrid modelling approach enhances our understanding of the interplay between cancer cell migration, proliferation, and ECM mechanical properties, paving the way for future studies incorporating additional ECM characteristics and microenvironmental conditions.
Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar
Authors: Miraldo A , Sundh J , Iwaszkiewicz-Eggebrecht E , Buczek M , Goodsell R , Johansson H , Fisher BL , Raharinjanahary D , Rajoelison ET , Ranaivo C , Randrianandrasana C , Rafanomezantsoa J-J , Manoharan L , Granqvist E , van Dijk LJA , Alberg L , Åhlén D , Aspebo M , Åström S , Bellviken A , Bergman P-E , Björklund S , Björkman MP , Deng J , Desborough L , Dolff E , Eliasson A , Elmquist H , Emanuelsson H , Erixon R , Fahlen L , Frogner C , Fürst P , Grabs A , Grudd H , Guasconi D , Gunnarsson M , Häggqvist S , Hed A , Hörnström E , Johansson H , Jönsson A , Kanerot S , Karlsson A , Karlsson D , Klinth M , Kraft T , Lahti R , Larsson M , Lernefalk H , Lestander Y , Lindholm L-T , Lindholm M , Ljung U , Ljung K , Lundberg J , Lundin E , Malmenius M , Marquina D , Martinelli J , Mertz L , Nilsson J , Patchett A , Persson N , Persson J , Prus-Frankowska M , Regazzoni E , Rosander K-G , Rydgård M , Sandblom C , Skord J , Stålhandske T , Svensson F , Szpryngiel S , Tajani K , Tyboni M , Ugarph C , Vestermark L , Vilhelmsson J , Wahlgren N , Wass A , Wetterstrand P , Łukasik P , Tack AJM , Andersson AF , Roslin T , Ronquist F
Published: October 2024

We present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, weekly Malaise trap samples were collected at 203 locations within 100 sites in Sweden and at 50 locations within 33 sites in Madagascar; this was complemented by soil and litter samples from each site. The field samples comprise 4,749 Malaise trap, 192 soil and 192 litter samples from Sweden and 2,566 Malaise trap and 190 litter samples from Madagascar. Samples were processed using mild lysis or homogenization, followed by DNA metabarcoding of COI (418 bp). The data comprise 698,378 non-chimeric sequence variants from Sweden and 687,866 from Madagascar, representing 33,989 (33,046 Arthropoda) and 77,599 (77,380 Arthropoda) operational taxonomic units, respectively. These are the most comprehensive data presented on these faunas so far, allowing unique analyses of the size, composition, spatial turnover and seasonal dynamics of the sampled communities. They also provide an invaluable baseline against which to gauge future changes.
Benchmarking of Low Coverage Sequencing Workflows for Precision Genotyping in Eggplant
Authors: Baraja-Fonseca Virginia , Arrones Andrea , Vilanova Santiago , Plazas Mariola , Prohens Jaime , Bombarely Aureliano , Gramazio Pietro
Published: October 2024

Low-coverage whole-genome sequencing (lcWGS) presents a cost-effective solution for genotyping, particularly in applications requiring high marker density and reduced costs. In this study, we evaluated lcWGS for eggplant genotyping using eight founder accessions from the first eggplant MAGIC population (MEGGIC), testing various sequencing coverages and minimum depth of coverage (DP) thresholds with two SNP callers, Freebayes and GATK. Reference SNP panels were used to estimate the percentage of common biallelic SNPs (i.e, true positives, TP) relative to the low coverage datasets (accuracy) and the SNP panels themselves (sensitivity), along with the percentage of TP with the same genotype across the two datasets (genotypic concordance). Sequencing coverages as low as 1X and 2X achieved high accuracy but lacked sufficient sensitivity and genotypic concordance. However, 3X sequencing reached approximately 10% less sensitivity than 5X while maintaining genotypic concordance above 90% at any DP threshold. Freebayes outperformed GATK in terms of sensitivity and genotypic concordance. Therefore, we used this software to conduct a pilot test with some MEGGIC lines from the fifth generation of selfing (S5), comparing their datasets with a gold standard (GS). Sequencing coverages as low as 1X identified a substantial number of TP, with 3X significantly increasing the yield, particularly at moderate DP thresholds. Additionally, at least 30% of the TP were consistently genotyped in all lines when using coverages greater than 2X, regardless of the DP threshold applied. This study highlights the importance of using a GS to reduce false positives and demonstrates that lcWGS, with proper filtering, is a valuable alternative to high-coverage sequencing for eggplant genotyping, with potential applications to other crops.
Multimodal Freezing of Gait Detection: Analyzing the Benefits of Physiological Data
Authors: Yang Po-Kai , Filtjens Benjamin , Ginis Pieter , Goris Maaike , Nieuwboer Alice , Gilat Moran , Slaets Peter , Vanrumste Bart
Published: October 2024

Freezing of gait (FOG) is a debilitating symptom of Parkinson’s disease (PD), characterized by an absence or reduction in forward movement of the legs despite the intention to walk. Detecting FOG during free-living conditions presents significant challenges, particularly when using only inertial measurement unit (IMU) data, as it must be distinguished from voluntary stopping events that also feature reduced forward movement. Influences from stress and anxiety, measurable through galvanic skin response (GSR) and electrocardiogram (ECG), may assist in distinguishing FOG from normal gait and stopping. However, no study has investigated the fusion of IMU, GSR, and ECG for FOG detection. Therefore, this study introduced two methods: a twostep approach that first identified reduced forward movement segments using a Transformer-based model with IMU data, followed by an XGBoost model classifying these segments as FOG or stopping using IMU, GSR, and ECG features; and an end-to-end approach employing a multi-stage temporal convolutional network to directly classify FOG and stopping segments from IMU, GSR, and ECG data. Results showed that the two-step approach with all data modalities achieved an average F1 score of 0.728 and F1@50 of 0.725, while the end-to-end approach scored 0.771 and 0.759, respectively. However, no significant difference was found compared to using only IMU data in both approaches (p-values: 0.466 to 0.887). In conclusion, adding physiological data does not provide a statistically significant benefit in distinguishing between FOG and stopping.
Longitudinal impact of different treatment sequences of second-generation antipsychotics on metabolic outcomes: a study using targeted maximum likelihood estimation
Authors: Feng Yaning , Wong Kenneth Chi-Yin , Leung Perry Bok-Man , Lee Benedict Ka-Wa , Sham Pak-Chung , Lui Simon Sai-Yu , So Hon-Cheong
Published: October 2024

Background

Second-generation antipsychotics (SGAs) cause metabolic side-effects. However, patients’ metabolic profiles were influenced by many time-invariant and time-varying confounders. Real-world evidence on the long-term, dynamic effects of SGAs (e.g. different treatment sequences) is limited. We employed advanced causal inference methods to evaluate metabolic impact of SGAs in a naturalistic cohort.

Methods

We followed 696 Chinese patients with schizophrenia-spectrum disorders who received SGAs. Longitudinal targeted maximum likelihood estimation (LTMLE) was used to estimate the average treatment effects (ATEs) of continuous SGA treatment versus “no treatment” on metabolic outcomes, including total cholesterol (TC), high-density lipoprotein (HDL), low-density lipoprotein (LDL), triglyceride (TG), fasting glucose (FG), and body-mass-index (BMI), over 6-18 months at 3-month intervals. LTMLE accounted for both time-invariant and time-varying confounders. We also evaluated whether side-effects persisted after SGA discontinuation.

Results

The average treatment effects (ATEs) of continuous SGA treatment on BMI and TG showed an inverted U-shaped pattern, peaking at 12 months and declining afterwards. Similar patterns were observed for TC and LDL, albeit the ATEs peaked at 15 months. For FG and HDL, the ATEs peaked at ∼6 months. The adverse impact of SGAs on BMI persisted even after medication discontinuation, yet other metabolic parameters did not show such lingering side-effects. Compared with other SGAs, clozapine and olanzapine showed greater metabolic side-effects.

Conclusions

Our real-world study suggests that metabolic side-effects may stabilize with prolonged continuous treatment. Clozapine and olanzapine confer greater cardiometabolic risks than other SGAs. The side-effects of SGAs on BMI may persist after drug discontinuation. These insights may guide antipsychotic choice and help improve the management of metabolic side-effects.
Quantification of droplet and contact transmission risks among elementary school students based on network analyses using video-recorded data
Authors: Kikuchi Shuta , Nakajima Keisuke , Kato Yasuki , Takizawa Takeshi , Sugiyama Junichi , Mukai Taisei , Kakizawa Yasushi , Kurahashi Setsuya
Published: October 2024

Elementary schools are environments in which immunologically immature students come into close contact with each other and are susceptible to the spread of infectious diseases. Analyzing the behavior of multiple students has been challenging, and the relationship between infections remains unclear. In this study, we analyzed the relevance between droplet and contact transmission and the behavior of elementary school students using video-recorded data, network analyses, and simulations. The analysis of communication behavior revealed the diverse nature of interactions among students. By calculating the droplet transmission probabilities based on conversation duration, this study quantified the risk of droplet transmission in elementary schools. The analysis of contact behavior introduces a novel approach for constructing contact networks based on contact history. According to this method, items such as desks, shirts, and doors have the potential to be used as fomites for virus transmission. In addition, the reliability of the predictions was demonstrated through micro-simulations. Interestingly, the micro-simulations indicated that the majority of virus copies were transmitted through single items, emphasizing the importance of targeted hygiene measures. This study contributes significantly to the prevention of infectious diseases in elementary schools by providing evidence-based information on transmission pathways and behavior-related risks. Moreover, the insights from this study can guide the development of simulation models for analyzing infection risks in educational settings.
Alpha thalassemia/mental retardation X-linked (ATRX) protein expression in human pituitary neuroendocrine tumours and its reported correlation to prognosis and clinical outcomes: A systematic review
Authors: Wang Edward , Rotondo Fabio , Cusimano Michael D.
Published: October 2024

Mutations in Alpha thalassemia/mental retardation X-linked (ATRX) have been implicated in several cancers, including gliomas, sarcomas, neuroendocrine tumors, and other mesenchymal malignancies. ATRX loss contributes to oncogenesis, accelerates tumor growth, and reduces survival by disrupting epigenetic and telomere mechanisms. Additionally, ATRX loss can increase tumor sensitivity to treatment therapies. While research has explored ATRX expression in many cancers, data on its relationship to prognosis in pituitary neuroendocrine tumors (PitNETs) remain inconsistent. This systematic review aims to summarize all available studies on ATRX mutations and expression in PitNETs. A systematic search of PubMed, Scopus, and EMBASE databases was conducted to identify publications between 2014 and 2024 that investigated ATRX mutations or expression in PitNETs, following PRISMA 2020 guidelines. Of 30 identified studies, nine met the inclusion criteria, covering a total of 500 PitNETs. Only 19 tumors (3.6%) showed a loss of ATRX expression. Among these, 58% exhibited corticotropic pathology, while 26% displayed lactotrophic pathology. A small subset of tumors (32%) was classified as pituitary carcinomas with aggressive and proliferative characteristics. Additionally, 16% demonstrated the alternative lengthening of telomeres (ALT) phenotype, 53% had concurrent TP53 mutations, and 21% had elevated Ki67 indices, indicating a higher proliferative index. Although ATRX mutations are rare in PitNETs, tumors with ATRX loss tend to be more aggressive and exhibit proliferative and transformative properties. Due to the limited number of cases, further studies with larger, prospective cohorts are needed to better understand the role of ATRX loss in PitNET progression and aggressiveness.
Real-life observation of wildfire-smoke impaired COVID-19 vaccine immunity
Authors: Sanghar Gursharan K , Teuber Melissa , Ravindran Resmi , Keller Emma Jean , Raffuse Sean M , Hernandez Pedro A , Linderholm Angela , Echt Gabrielle , Franzi Lisa , Tuermer-Lee Kaelyn , Juarez Maya , Albertson Timothy E , Khan Imran , Haczku Angela
Published: October 2024

Background: Wildfires are increasingly common with wildfire smoke affecting millions globally, yet its impact on immune responses is poorly understood. Natural Killer (NK) cells play a role in mediating air pollutant effects and regulating vaccine immunity. Objective: This real-world study, conducted on participants in the Pfizer BNT162b2 COVID-19 vaccine trial, studied the effects of wildfire smoke exposure on long-term vaccine effects. Methods: We collected blood samples from 52 healthy, non-smoking participants (ages 26-83) before and 1 month after placebo or vaccine injections during heavy wildfire smoke events in Sacramento. The study included 28 vaccinated (Group 1) and 24 placebo-injected (Group 2) individuals, the latter vaccinated several months later, outside wildfire season. Blood samples from both Group 1 and 2 were also investigated 6 months after the second dose of vaccine. We analyzed intracellular cytokines, B and NK cell markers by flow cytometry, and serum immunoglobulin levels against common coronaviruses using multiplex assays. Results: A robust S-RBD-specific IgG response observed 1 month post booster, declined variably 6 months later. Wildfire smoke acutely increased IL-13 expression by CD56bright NK cells. IL-13+CD56bright NK cells at the time of vaccination negatively correlated with anti-S-RBD IgG (r=-0.41, p<0.05) one month later. Total IgG levels on the other hand, positively correlated with the air quality index (AQI) measured during vaccination (r=0.96, p<0.01). Similarly to age (but not sex, BMI or race/ethnicity), the two-week AQI averages during vaccination showed a significant negative correlation with anti-S-RBD IgG levels 6 months later (r=-0.41, p<0.05). Conclusion: Wildfire smoke may lead to inappropriate immunoglobulin production and diminished vaccine immunity. Our novel findings highlight a previously unrecognized pathway involving NK-cell derived IL-13 and non-specific B-cell activation and underscore the significance of environmental exposures in shaping immunity.
A nationwide joint spatial modelling of simultaneous epidemics of dengue, chikungunya, and Zika in Colombia
Authors: Picinini Freitas Laís , Carabali Mabel , Schmidt Alexandra M. , Salazar Flórez Jorge Emilio , Ávila Monsalve Brayan , García-Balaguera César , Restrepo Berta N. , Jaramillo-Ramirez Gloria I. , Zinszer Kate
Published: October 2024

Background

Chikungunya, and Zika emerged in the 2010s in the Americas, causing simultaneous epidemics with dengue. However, little is known of theseAedes-borne diseases (ABDs) joint patterns and contributors at the population-level.

Methods

We applied a novel Poisson-multinomial spatial model to the registered cases of dengue (n=291,820), chikungunya (n=75,913), and Zika (n=72,031) by municipality in Colombia, 2014-2016. This model estimates the relative risk of total ABDs cases and associated factors, and, simultaneously, the odds of presence and contributors of each disease using dengue as a baseline category. This approach allows us to identify combined characteristics of ABDs, since they are transmitted by the same mosquitoes, while also identifying differences between them.

Findings

We found an increased ABDs risk in valleys and south of the Andes, the Caribbean coast, and borders, with temperature as the main contributor (Relative Risk 2.32, 95% Credible Interval, CrI, 2.05-2.64). Generally, dengue presence was the most probable among the ABDs, although that of Zika was greater on Caribbean islands. Chikungunya and Zika were more likely present than dengue in municipalities with less vegetation (Odds Ratio, OR, 0.75, 95%CrI 0.65-0.86, and 0.85, 95%CrI 0.74-0.99, respectively). Chikungunya tended to be present in more socially vulnerable areas than dengue (OR 1.20, 95%CrI 0.99-1.44) and Zika (OR 1.19, 95%CrI 0.95-1.48).

Interpretation

Important differences between the ABDs were identified and can help guide local and context-specific interventions, such as those aimed at preventing cases importation in border and tourism locations and reducing chikungunya burden in socially vulnerable regions.
Telemedicine in Eye Care During the COVID-19 Pandemic: A Review of Patient & Physician Perspectives
Authors: Halajyan Christina Perjuhi , Thomas Jonathan , Xu Benjamin , Gluckstein Jeffrey , Jiang Xuejuan
Published: October 2024

Purpose

There has been an increase in the adoption of telemedicine during the COVID-19 pandemic. This review used systematic search and review criteria to assess the literature on patient and physician perspectives toward telemedicine for vision care during the pandemic.

Methods

We conducted a comprehensive search on PubMed, Embase, and Scopus using relevant MeSH terms to identify peer-reviewed studies examining telemedicine use in eye care during the pandemic. The search strategy encompassed three key concepts: COVID-19 or pandemic, telehealth or telemedicine, and eye care. Further screening of references and similar articles was conducted to identify additional relevant studies.

Results

We identified 24 relevant studies published between 2020 and 2022. Of these, 15 focused on patients’ perspectives, while 12 explored physicians’ perspectives. Predominantly cross-sectional in design, these studies were mainly conducted during the initial wave of the pandemic (March 2020 to June 2020), primarily in urban locations and hospital settings. Patients were satisfied with telemedicine and considered it equally effective to in-person visits. Patients believed telemedicine was convenient, improved eye care access, and a beneficial triage tool. Physicians acknowledged telemedicine’s convenience for follow-up assessment and its ability to expand the capacity for emergency cases. However, both patients and physicians voiced concerns about the absence of ancillary examination and technological challenges.

Conclusion

Our review highlights the positive impact of telemedicine in eye care during the pandemic. Nonetheless, most studies were limited in sample size. They did not delve into potential disparities based on race/ethnicity, socioeconomic status, and geographic location, factors that could influence patient attitudes toward telemedicine. Further research is warranted to validate the findings from our selected studies and explore factors that influence the implementation of telemedicine, particularly across various eye care subspecialties.
miRNA Biomarkers in Prostate Cancer: Leveraging Machine Learning for Improved Diagnostic Accuracy
Authors: Singh Shweta , Pathak Abhay Kumar , Kural Sukhad , Kumar Lalit , Bhardwaj Madan Gopal , Yadav Mahima , Trivedi Sameer , Das Parimal , Gupta Manjari , Jain Garima
Published: October 2024

Prostate cancer (PCa) diagnosis often relies on prostate-specific antigen (PSA) testing, but its high false-positive rates often lead to unnecessary biopsies. MicroRNAs (miRNAs) have emerged as promising non-invasive biomarkers for cancer detection due to their stability in biological fluid and disease specificity. Despite their potential, the clinical translation of miRNAs as non-invasive cancer biomarkers is hindered by several challenges - population-based variability, environmental Factors, methodological Inconsistencies, lack of standardization, normalization Issues, and complexity of the biological System. These factors significantly impact the consistency of miRNA expression readouts, particularly in terms of Ct-values, across different studies, which in turn affects the determination of cutoff values that are crucial in a diagnostic setup. This preliminary study offers a pilot demonstration for integrating miRNA biomarker expression with machine learning (ML), which can help identify patterns and improve classification, potentially reducing the reliance on fixed cutoff values in certain contexts and pave the path to wider clinical translation.

We analyzed the expression of key miRNAs (miR-21-5p, miR-221-3p, and miR-141-3p) in blood samples from patients with PCa and benign prostatic hyperplasia (BPH). Utilizing a Random Forest classifier, we achieved an accuracy of 77.42%, a precision of 86.21%, a recall of 71.43%, and an AUC-ROC score of 0.78. The application of ML enabled us to leverage complex features, such as combinations and ratios of miRNA expression data, which enhanced the robustness and reliability of the diagnostic model. Additionally, bioinformatics analysis of the preferential features identified by the ML model confirmed the biological relevance of these miRNAs in PCa-related pathways, further supporting their potential as clinical biomarkers.

In the future, ML is poised to significantly enhance diagnostic performance compared to traditional linear analyses of a limited set of biomarkers. While our study did not explore multiple populations or the effects of methodological variables, it highlights the potential of ML by demonstrating improved accuracy and eliminating the need for cutoff values. This capability could broaden the applicability of miRNA-based diagnostics, making them more reliable and actionable in clinical settings. However, to fully realize this potential, further validation with larger and more diverse cohorts is essential. Overall, this study lays the groundwork for utilizing ML-enhanced miRNA panels as powerful tools for the early and non-invasive diagnosis of PCa in future clinical practice.

Graphical Abstract
Nuclear and organelle genome assemblies of fiveCucumis meloL. accessions, Ananas, Canton, PI 414723, Vedrantais and Zhimali, belonging to diverse botanical groups
Authors: Belinchon-Moreno Javier , Berard Aurelie , Canaguier Aurelie , Le-Clainche Isabelle , Rittener-Ruff Vincent , Lagnel Jacques , Hinsinger Damien , Boissot Nathalie , Faivre-Rampant Patricia
Published: October 2024

The construction of accurate whole genome sequences is pivotal for characterizing the genetic diversity of plant species, identifying genes controlling important traits, or understanding their evolutionary dynamics. Here, we generated the nuclear, mitochondrial and chloroplast high- quality assemblies of five melon (Cucumis meloL.) accessions representing five diverse botanical groups, using the Oxford Nanopore sequencing technology. The accessions here studied included varied origins, fruit shapes, sizes, and resistance traits, providing a holistic view of melon genomic diversity.

The final chromosome-level genome assemblies ranged in size from 359 to 365 Mb, with approximately 25x coverage for four of them multiplexed in half of a PromethION flowcell, and 48x coverage for the fifth, sequenced individually in another half of a PromethION flowcell. Contigs N50 ranged from seven to 15 Mb for all the assemblies, and very long contigs reaching sizes of 20-25 Mb, almost compatible with complete chromosomes, were assembled in all the accessions. Quality assessment through BUSCO and Mercury indicated the high completeness and accuracy of the assemblies, with BUSCO values exceeding 96% for all accessions, and Mercury QV values ranging between 32 and 47.

We focused on the complex NLR resistance gene clusters to validate the accuracy of the assemblies in highly complex and repetitive regions. Through Nanopore adaptive sampling, we generated accurate targeted assemblies of these regions with a significantly higher coverage, enabling the comparison to our whole genome assemblies.

Overall, these chromosome-level assembled genomes constitute a valuable resource for research focused on melon diversity, disease resistance, evolution, and breeding applications.

Article Summary

This study presents high-quality nuclear, mitochondrial, and chloroplast genome assemblies for five diverse melon (Cucumis meloL.) accessions, using Oxford Nanopore sequencing. The assemblies represent a broad spectrum of melon diversity, including differences in origin, fruit morphology, or resistance traits. The genomes, ranging from 359 to 365 Mb, were assembled at a chromosome level with high contiguity, and verified using different validation approaches. This study provides valuable insights for research on melon genetic diversity, disease resistance, and breeding applications. The genome data will be especially valuable for plant geneticists, breeders, and researchers working on crop improvement and resistance traits.
Spatiotemporal coordination of actin regulators generates invasive protrusions in cell-cell fusion
Authors: Lu Yue , Walji Tezin , Ravaux Benjamin , Pandey Pratima , Yang Changsong , Li Bing , Luvsanjav Delgermaa , Lam Kevin H. , Zhang Ruihui , Luo Zhou , Zhou Chuanli , Habela Christa W. , Snapper Scott B. , Li Rong , Goldhamer David J. , Schmidtke David W. , Pan Duojia , Svitkina Tatyana M. , Chen Elizabeth H.
Published: October 2024

Invasive membrane protrusions play a central role in a variety of cellular processes. Unlike filopodia, invasive protrusions are mechanically stiff and propelled by branched actin polymerization. However, how branched actin filaments are organized to create finger-like invasive protrusions is unclear. Here, by examining the mammalian fusogenic synapse, where invasive protrusions are generated to promote cell membrane juxtaposition and fusion, we have uncovered the mechanism underlying invasive protrusion formation. We show that two nucleation promoting factors (NPFs) for the Arp2/3 complex, WAVE and N-WASP, exhibit different localization patterns in the protrusions. While WAVE is closely associated with the plasma membrane at the leading edge of the protrusive structures, N-WASP is enriched with WIP along the actin bundles in the shafts of the protrusions. During protrusion initiation and growth, the Arp2/3 complex nucleates branched actin filaments to generate low density actin clouds, in which the large GTPase dynamin organizes the new branched actin filaments into bundles, followed by actin-bundle stabilization by WIP, the latter functioning as a novel actin-bundling protein. Disrupting any of these components results in defective protrusions and failed myoblast fusion in cultured cells and mouse embryos. Taken together, our study has revealed the intricate spatiotemporal coordination between two NPFs and two actin-bundling proteins in building invasive protrusions at the mammalian fusogenic synapse, and has general implications in understanding invasive protrusion formation in cellular processes beyond cell-cell fusion.
A liver function test score identifies high-risk MASLD patients based on the pattern of liver enzymes
Authors: Hajaj Emma , Bendersky Ahinoam Glusman , Braun Marius , Shlomai Amir
Published: October 2024

Background & Aims

A cholestatic pattern of liver enzymes is associated with progressive liver disease and major adverse liver-related outcomes (MALO) among patients with Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD). We aimed to authenticate the efficacy of a newly formulated liver function test (LFT) score for distinguishing patients with cholestatic vs. hepatocellular patterns and to evaluate its prognostic utility in MASLD patients.

Methods

A retrospective longitudinal study on a dataset of over 250,000 individuals diagnosed with MASLD and/or obesity with cardiovascular risk factors. Patients were categorized into cholestatic (C), mixed (M), or hepatocellular (H) patterns according to the LFT score, or the well-known R score. Long-term MALO, major adverse cardiovascular events (MACE), and all-cause mortality were tracked.

Results

The LFT score excelled in differentiating patients into C, M, or H groups accurately. While about two-thirds of our cohort initially showed a low FIB4 (<1.3), patients in the C category experienced a higher incidence of MALO and MACE compared to those in the H category (0.5% vs. 0.2% and 7.1% vs. 3.6%, respectively) over the span of 10 years post-diagnosis. Additionally, the 15-year overall survival rate was notably lower for C patients compared to their H counterparts (63% vs. 77%, p<0.0001). The LFT score was more effective than the R score in distinguishing between H and C patients for prognostic purposes, and a baseline cholestatic pattern indicates poorer outcomes regardless of subsequent LFT changes.

Conclusions

The LFT score accurately categorizes cholestatic MASLD patients and may serve as a useful prognostic tool.
Integrating explainable machine learning and transcriptomics data reveals cell-type specific immune signatures underlying macular degeneration
Authors: Ma Khang , Nakajima Hosei , Basak Nipa , Barman Arko , Ratnapriya Rinki
Published: October 2024

Genome-wide association studies (GWAS) have established a key role of dysfunctional immune response in the etiology of Age-related Macular Degeneration (AMD). However, immune cells constitute a small proportion of the retina, and their role in AMD is not completely resolved. Here we develop an explainable machine learning pipeline using transcriptome data 453 donor retinas, identifying 81 genes distinguishing AMD from controls with an AUC-ROC of 0.80 (CI 0.70-0.92). These genes show enrichment for pathways involved in immune response, complement and extracellular matrix and connected to known AMD genes through co-expression networks and gene expression correlation. The majority of these genes were enriched in their expression within retinal glial cells, particularly microglia and astrocytes. Their role in AMD was further strengthened by cellular deconvolution, which identified distinct differences in microglia and astrocytes between normal and AMD. We corroborated these findings using independent single-cell data, where several of these candidate genes exhibited differential expression. Finally, the integration of AMD-GWAS data identified a common regulatory variant, rs4133124 atPLCG2, as a novel AMD-association. Collectively, our study provides molecular insights into the recurring theme of immune dysfunction in AMD and highlights the significance of glial cell differences as an important determinant of AMD progression.
Systematic standardization of organ-on-a-chip under controlled flow conditions: use case with Caki-1 and A549 cell lines
Authors: Balsa-Díaz Andrea , Vázquez-Vázquez Laura , Ferreiro-Vila Elías , Rivas-Meizoso Lois , Martínez Antón L. , Brea José Manuel , Loza María Isabel , Rodriguez Santiago Pérez , Sinde Esteban , Alvarez Ezequiel , Rodiño-Janeiro Bruno K.
Published: October 2024

Newin vitromodels are an urgent need for to improve both the research data and the preclinical development of new drugs. Current standardized cellular models are mainly based in 2D cell culture, which lacks flow conditions and with complex co-culture settings. In this way, advanced cell culture models, such as organ-on-a-chip (OoC), aim to solve these limitations. OoC systems are composed by a microfluidic chip functionalized with different combinations of extracellular matrixes, coatings and cell cultures to mimic the physiological conditions of human organs. Advantages of OoC include the possibility to add 3D structures, delimited regions for co-culture and dynamic flow conditions to cell cultures. However, to perform reproducible and controlled experiments with OoC, it is necessary to systematically standardize the cell culture conditions in the microfluidic channels. For this is necessary to test both the combination of flow and extracellular matrix (ECM) coating to reliably mimic the human organ physiology. In this work, we standardized both conditions, ECM coating and the flow conditions to functionalize OoC with cell lines from kidney (Caki-1) and from lung (A549) to develop OoC systems beyond the Vessel-on-a-chip setting. In this way, the protocol detailed in this work will allow to standardize cell culture on different optimized OoC types with different cell types from different origins.
Autocatalytic assembly of a chimeric aminoacyl-RNA synthetase ribozyme
Authors: Radakovic Aleksandar , Todisco Marco , Mishra Anmol , Szostak Jack W.
Published: October 2024

Autocatalytic reactions driving the self-assembly of biological polymers are important for the origin of life, yet few experimental examples of such reactions exist. Here we report an autocatalytic assembly pathway that generates a chimeric, amino acid-bridged aminoacyl-RNA synthetase ribozyme. The noncovalent complex of ribozyme fragments initiates low level aminoacylation of one of the fragments, which after loop-closing ligation generates a highly active covalently-linked chimeric ribozyme. The generation of this ribozyme is increasingly efficient over time due to the autocatalytic assembly cycle that sustains the ribozyme over indefinite cycles of serial dilution. Due to itstransactivity, this ribozyme also assembles ribozymes distinct from itself, such as the hammerhead, suggesting that RNA aminoacylation, coupled with nonenzymatic ligation, could have facilitated the emergence and propagation of ribozymes.
Personalized azithromycin treatment rules for children with watery diarrhea using machine learning
Authors: Kim Sara S , Codi Allison , Platts-Mills James A. , Pavlinac Patricia , Manji Karim , Sudfeld Chris , Duggan Christopher P. , Dube Queen , Bar-Zeev Naor , Kotloff Karen , Sow Samba O , Sazawal Sunil , Singa Benson O , Walson Judd , Qamar Farah , Ahmed Tahmeed , De Costa Ayesha , Benkeser David , Rogawski McQuade Elizabeth T
Published: October 2024

Introduction

We used machine learning to identify novel strategies to target azithromycin to the children with watery diarrhea who are most likely to benefit.

Methods

Using data from a randomized trial of azithromycin for watery diarrhea, we developed personalized treatment rules given sets of diagnostic, child, and clinical characteristics, employing a robust ensemble machine learning-based procedure. For each rule, we estimated the proportion treated under the rule and the average benefits of treatment.

Results

Among 6,692 children, treatment was recommended on average for approximately one third of children. The risk of diarrhea on day 3 was 10.1% lower (95% CI: 5.4, 14.9) with azithromycin compared to placebo among children recommended for treatment. For day 90 re-hospitalization and death, risk was 2.4% lower (95% CI: 0.6, 4.1) with azithromycin compared to placebo among those recommended for treatment. While pathogen diagnostics were strong determinants of azithromycin effects on diarrhea duration, host characteristics were more relevant for predicting benefits for re-hospitalization or death.

Conclusion

The ability of host characteristics to predict which children benefit from azithromycin with respect to the most severe outcomes suggests appropriate targeting of antibiotic treatment among children with watery diarrhea may be possible without access to pathogen diagnostics.
Targeting ADORA-PDE10 cAMP Microdomain: A Novel Therapeutic Approach for Pulmonary Hypertension
Authors: Valasarajan Chanil , Hesami Golnaz , Maroli Giovanni , Cherian Anoop V. , Laria Julio Castro-palomino , Laria Nahomi Castro-Palomino , Wietelmann Astrid , Gnatzy-Feik Leoni , Rosenkranz Stephan , Savai Rajkumar , Seeger Werner , Pullamsetti Soni Savai
Published: October 2024

Despite substantial advancements in the treatment of pulmonary arterial hypertension (PAH), obstacles remain in achieving optimal outcomes. In this study, we focus on understanding the therapeutic effect of targeting the ADORA1/PDE10A-regulated cyclic AMP (cAMP) microenvironment in treating pulmonary hypertension. Screening of differentially expressed adenosine receptors in samples derived from healthy individuals and patients with idiopathic pulmonary arterial hypertension (IPAH) showed that ADORA1 expression was significantly upregulated under disease conditions. Functional studies revealed that, upon ADORA1 inhibition, donor hPASMCs showed anti-proliferative, pro-apoptotic features and increased intracellular cAMP levels. Surprisingly, the same effects were not replicated in IPAH PASMCs, suggesting the presence of another cAMP regulatory factor in close proximity to ADORA1 in IPAH PASMCs. To investigate this point, we performed protein-protein interaction studies in IPAH PASMCs and found that Phosphodiestrase 10A (PDE10A) co-localizes with ADORA1 under disease conditions. Moreover, we observed that ADORA1 and PDE10A form a regulatory complex in the A kinase anchoring protein 5 (AKAP5) microdomain. Silencing or dual inhibition of both ADORA1 and PDE10A in IPAH PASMCs induced anti-proliferative and pro-apoptotic effects with increased intracellular cAMP levels. To investigate the effects of the dual inhibitor in vivo, we administered it to both MCT and Sugen5416/hypoxia (SuHx) rat models of PAH, showing improved right ventricle function, reduced pulmonary vascular resistance and decreased lung vascular remodeling. In conclusion, we provide evidence that dual pharmacological targeting of ADORA1 and PDE10A has high therapeutic potential against PAH.
PXGS: a Poly-Transgene Expression System based on Mutually Exclusive Splicing of Dscam
Authors: Yu Renee Yin , Bucio-Mendez Alyeri , Chen Brian E
Published: October 2024

Biologists often need to investigate multiple genes simultaneously in an organism. However, it is currently not possible to express more than a few transgenes in an animal under conditional control. Here, we developed a technique based on the mutually exclusive splicing of the Down Syndrome Cell Adhesion Molecule1 (Dscam1) gene in Drosophila melanogaster to achieve simultaneous transgene expression of 12 genes at a time. We show that the hypervariable Dscam1 exon 4 region maintains its alternative splicing when placed in a UAS expression vector. Each of the twelve exon 4 alternates can be replaced with an exogenous gene of at least 10 kilobases and will express properly in vivo all under conditional genetic control. We demonstrate the expression of four different fluorophores placed in different exon 4 alternate positions in neural and non-neural cells in vivo. We validated the technique by rewiring Drosophila sensory neuron axons in vivo by simultaneously expressing several cell surface receptors within the neuron. This technology will also enable Drosophila melanogaster as a model system for synthetic biology research.
TheNematostellaWnt/β-catenin destruction complex provides insight into the evolution of the regulation of a major metazoan signal transduction pathway
Authors: Sun Hongyan , Zidek Radim , Martindale Mark Q. , Wikramanayake Athula
Published: October 2024

The Wnt/β-catenin (cWnt) signaling pathway is one of the most important intercellular signaling pathways in animals. How cWnt components regulate the pathway in bilaterians is well understood, but these processes are poorly characterized in the earliest branching animal clades. We used the cnidarianNematostella(cnidarians are the closest bilaterian outgroup) to study the cWnt destruction complex (DC) which is the primary mechanism for regulating cytoplasmic concentrations of β-catenin. In bilaterians the DC scaffolding proteins Axin and APC directly interact and bind β-catenin to target it for proteolysis, but all non-bilaterian Axin and APC homologs lack the conserved domains required for bilaterian DC function. Using functional approaches, we show that inNematostellaAxin and APC-like proteins scaffold an active DC that is regulated differently than the bilaterian DC. Additionally, using AlphaFold software we discovered a sequence embedded in the Axin-RGS domain of non-bilaterian Axin that has homology to the bilaterian Axin β-catenin-binding motif (βcatBM). We propose that the bilaterian βcatBM evolved as a low-affinity β-catenin-interacting sequence in the Axin-RGS domain in pre-bilaterians and moved C-terminally in bilaterians where it acquired higher affinity for β-catenin. Our work provides novel insight into how regulatory modules can evolve in metazoan signaling pathways.
Transcriptional profiles of murine oligodendrocyte precursor cells across the lifespan
Authors: Heo Dongeun , Kim Anya A. , Neumann Björn , Doze Valerie N. , Xu Yu Kang T. , Mironova Yevgeniya A. , Slosberg Jared , Goff Loyal A. , Franklin Robin J. M. , Bergles Dwight E.
Published: October 2024

Oligodendrocyte progenitor cells (OPCs) are highly dynamic, widely distributed glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. By also generating new oligodendrocytes in the adult CNS, OPCs allow formation of new myelin sheaths in response to environmental and behavioral changes and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, which may impair homeostasis, remyelination, and adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses membrane-anchored EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP) and performed high-throughput single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation across the lifespan. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1α and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged animals restored their ability to differentiate, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. ThisMatn4-mEGFPmouse line and single-cell mRNA datasets of cortical OPCs across ages help to define the molecular changes guiding their behavior in various physiological and pathological contexts.
Insights on macrosynteny, ′rebel′ genes, and a new sex-linked region in anurans from comparative genomics and a new chromosome-level genome for the western chorus frog
Authors: Chen Ying , Lougheed David R. , Sun Zhengxin , Ethier Jeffrey , Trudeau Vance L , Lougheed Stephen C.
Published: October 2024

Amphibians have unique genome characteristics including slow karyotypic evolution and cytogenetically undifferentiated sex chromosomes. Yet our understanding of amphibian genomes has not kept pace with that of mammals and birds, partially due to scarce genomic resources and challenges associated with large genome sizes and high repetitiveness. We assembled and annotated a chromosome-level genome for the western chorus frog (Pseudacris triseriata), a species of conservation concern and importance in evolutionary research. Comparison of our new genome with other chromosome-level frog genomes reveals exceptionally conserved evolution of 13 chromosomal elements and gene orders across over 200 million years of anuran evolution. We uncovered ′rebel′ Benchmarking Universal Single-Copy Orthologs (BUSCO) genes that have been duplicated in almost all frog species, have been transposed, and showed lineage-specific synteny patterns – possibly relating to key traits such as frog advertisement calls and mitochondrial genome evolution. We also assembled a complete mitochondrial genome and found heteroplasmy of both point polymorphisms and length variation in the tandem repeat arrays in the control region. Double-digest restriction-site associated DNA sequencing analysis indicates that the western chorus frog has an XY sex system and the sex-linked region involved an ~1Mb indel structural variant. Overall, our study provides important genomic resources for treefrogs and other anurans, documents highly conserved chromosomal evolution and gene orders in anurans, identifies ′rebel′ genes that might be important for frog evolution, and reveals a new sex-linked region with indel structural variants in anurans.
The Floquet Fluxonium Molecule: Driving Down Dephasing in Coupled Superconducting Qubits
Authors: Thibodeau Matthew , Kou Angela , Clark Bryan K.
Published: October 2024

High-coherence qubits, which can store and manipulate quantum states for long times with low error rates, are necessary building blocks for quantum computers. Here we propose a driven superconducting erasure qubit, the Floquet fluxonium molecule, which minimizes bit-flip rates through disjoint support of its qubit states and suppresses phase flips by a novel second-order insensitivity to flux-noise dephasing. We estimate the bit-flip, phase-flip, and erasure rates through numerical simulations, with predicted coherence times of approximately 50 ms in the computational subspace and erasure lifetimes of about 500μs. We also present a protocol for performing high-fidelity single-qubit rotation gates via additional flux modulation, on timescales of roughly 500 ns, and propose a scheme for erasure detection and logical readout. Our results demonstrate the utility of drives for building new qubits that can outperform their static counterparts.

Published by the American Physical Society
2024