bluuebunny/crossref_metadata_2025 huggingface dataset:
TRGT-denovo: accurate detection ofde novotandem repeat mutations
Authors: Mokveld T. , Dolzhenko E. , Dashnow H. , Nicholas T. J. , Sasani T. , van der Sanden B. , Jadhav B. , Pedersen B. , Kronenberg Z. , Tucci A. , Sharp A. J. , Quinlan A. R. , Gilissen C. , Hoischen A. , Eberle M. A.
Published: July 2024

Motivation

Identifyingde novotandem repeat (TR) mutations on a genome-wide scale is essential for understanding genetic variability and its implications in rare diseases. While PacBio HiFi sequencing data enhances the accessibility of the genome’s TR regions for genotyping, simplede novocalling strategies often generate an excess of likely false positives, which can obscure true positive findings, particularly as the number of surveyed genomic regions increases.

Results

We developed TRGT-denovo, a computational method designed to accurately identify all types ofde novoTR mutations—including expansions, contractions, and compositional changes— within family trios. TRGT-denovo directly interrogates read evidence, allowing for the detection of subtle variations often overlooked in variant call format (VCF) files. TRGT-denovo improves the precision and specificity ofde novomutation (DNM) identification, reducing the number ofde novocandidates by an order of magnitude compared to genotype-based approaches. In our experiments involving eight rare disease trios previously studied TRGT-denovo correctly reclassified all false positive DNM candidates as true negatives. Using an expanded repeat catalog, it identified new candidates, of which 95% (19/20) were experimentally validated, demonstrating its effectiveness in minimizing likely false positives while maintaining high sensitivity for true discoveries.

Availability and implementation

Built in Rust, TRGT-denovo is available as source code and a pre-compiled Linux binary along with a user guide at:https://github.com/PacificBiosciences/trgt-denovo.
Transcriptome-wide alternative mRNA splicing analysis reveals post-transcriptional regulation of neuronal differentiation
Authors: Zhou Yuan , Rashad Sherif , Niizuma Kuniyasu
Published: July 2024

Alternative splicing (AS) plays important roles in neuronal development, function, and diseases. Efforts to analyze AS transcriptome-wide in neurons remain limited. We characterized the transcriptome-wide AS changes in SH-SY5Y neuronal differentiation model, which is widely used to study neuronal function and disorders. Our analysis revealed global changes in five AS programs that drive neuronal differentiation. Motif analysis revealed the contribution of RNA binding proteins (RBPs) to the regulation of AS during neuronal development. We focused on the predominant AS program during differentiation, exon skipping (SE) events. Motif analysis revealed motifs for PTB and HuR/ELAVL1 to be the top enriched in SE events, and their protein levels were downregulated after differentiation. shRNA Knockdown of either PTB and HuR were associated with enhanced neuronal differentiation and transcriptome-wide exon skipping events driving the process of differentiation. At the level of gene expression, we observed only modest changes, indicating predominant post-transcriptional effects of PTB and HuR. We also observed that both RBPs altered cellular responses to oxidative stress, in line with the differentiated phenotype observed after KD. Our work characterizes the AS changes in a widely used and important model of neuronal development and neuroscience research and reveals intricate post-transcriptional regulation of neuronal differentiation.
Tbx1stabilizes differentiation of the cardiopharyngeal mesoderm and drives morphogenesis in the pharyngeal apparatus
Authors: Lanzetta Olga , Bilio Marchesa , Liebig Johannes , Jechow Katharina , Ten Foo Wei , Ferrentino Rosa , Aurigemma Ilaria , Illingworth Elizabeth , Conrad Christian , Lukassen Soeren , Angelini Claudia , Baldini Antonio
Published: July 2024

Background

TBX1 is required for the development of the pharyngeal apparatus. In the mouse, fish, and ascidian,Tbx1is a marker of cardiopharyngeal mesoderm (CPM), a cell population that provides progenitors to the heart and branchiomeric muscles. However, in mammals: a) the molecular cascade that drives the diversification of this multipotent cell population, and b) the role ofTbx1therein, are not well defined.

Material and methods

We usedin vitrodifferentiation of WT andTbx1−/−mouse embryonic stem cells into precardiac mesoderm, and performed single cell RNA-seq and ATAC-seq at two differentiation stages. We then used WT andTbx1−/−mouse embryos forin vivovalidation of the key findings.

Results and conclusions

We found that the response to loss of TBX1 is cell sub-population-specific, both in terms of gene expression and chromatin remodeling. We show thatTbx1regulates chromatin accessibility and gene expression of an ancient transcriptional module that orchestrates the development of the trunk, pharynx and heart across evolution. This module is co-regulated and includes genes encoding the conserved transcription factor families of Tea Shirt (Tshz), Sine Oculis (Six), Eye absent (Eya), and Ebf/Collier. Analysis of putative regulatory regions of these genes, which were selected using a machine-learning computational procedure, predicted a feed-forward regulatory relationship between TBX1 and SIX factors that drives or stabilizes the module. Most surprisingly, we found a drift in the differentiation trajectory of theTbx1mutant CPM that led to a relative expansion of cells with epithelial-like transcriptional features in the cell culture model and in mouse embryos. We conclude that TBX1 is a critical factor for maintaining the transcriptional profile of the CPM.
Trained Immunity Causes Myeloid Cell Hypercoagulability
Authors: Rehill Aisling M. , McCluskey Seán , Ledwith Anna E. , Ryan Tristram A.J. , Leon Gemma , Charles-Messance Hugo , Gilbert Edmund H. , Day Emily A. , McMahon Corrina , O’Donnell James S. , Curtis Annie M. , O’Neill Luke A.J. , Sheedy Frederick J. , Preston Roger J.S.
Published: July 2024

Venous thromboembolism is common in individuals with chronic inflammatory diseases, but the pathogenic basis for this increased thrombotic risk remains poorly understood. Myeloid cell ‘trained immunity’ describes persistent innate immune cell memory arising from prior exposure to an inflammatory stimulus, leading to an enhanced immune response to subsequent unrelated stimuli. We identify enhanced myeloid cell prothrombotic activity as a novel maladaptive consequence of trained immunity. LPS stimulation of murine bone marrow-derived macrophages trained previously with either β-glucan or free haem exhibited significantly enhanced procoagulant and antifibrinolytic gene expression and activity compared to macrophages stimulated with LPS alone. The β-glucan training-mediated increase in activated myeloid cell procoagulant activity was mediated by enhanced acid sphingomyelinase-mediated tissue factor (TF) functional decryption. Furthermore, pre-treatment with methyltransferase and acetyltransferase inhibitors to erase epigenetic marks associated with innate immune memory diminished trained macrophage TF gene expression in β-glucan-trained macrophages. Functional analysis of splenic monocytes isolated from β-glucan-trained mice revealed enhanced procoagulant activity up to 4 weeks after β-glucan administration compared to monocytes from control mice over the same time period. Remarkably, monocyte procoagulant activity increased proportionately with time since β-glucan administration, before plateauing at 4 weeks. Furthermore, haematopoietic progenitor cells and bone marrow interstitial fluid isolated from β-glucan-trained mice possessed enhanced procoagulant activity compared to control mice. Trained immunity and associated metabolic perturbations may therefore represent novel therapeutic vulnerabilities in immunothrombotic disease development, opening new avenues for targeted intervention.
Inference of gene regulatory networks for overcoming low performance in real-world data
Authors: Hiki Yusuke , Tokuoka Yuta , Yamada Takahiro G. , Funahashi Akira
Published: July 2024

The identification of gene regulatory networks is important for understanding the mechanisms of various biological phenomena. Many methods have been proposed to infer networks from time-series gene expression data obtained by high-throughput next-generation sequencings. Such methods can effectively infer gene regulatory networks forin silicodata, but inferring the networks accurately fromin vivodata remiains a challenge because of the large noise and low time sampling rate. Here, we proposed a novel unsupervised learning method, Multi-view attention Long-short term memory for Network inference (MaLoN). It can infer gene regulatory networks with temporal changes in gene regulation using the multi-view attention Long Short-term memory model. Usingin vivobenchmark datasets inSaccharomyces cerevisiaeandEscherichia coli, we showed that MaLoN can infer gene regulatory networks more accurately than existing methods. The ablated models indicated that the multi-view attention mechanism suppressed false positives. The order of activation of gene regulations inferred by MaLoN was consistent with existing knowledge.
Analysis of the Modulation of RAF Signaling by 14-3-3 Proteins
Authors: Carlip Peter , Stites Edward C.
Published: July 2024

The regulation of cellular biochemical signaling reactions includes the modulation of protein activity through a variety of processes. For example, signaling by the RAF kinases, which are key transmitters of extracellular growth signals downstream from the RAS GTPases, is modulated by dimerization, protein conformational changes, post-translational modifications, and protein-protein interactions. 14-3-3 proteins are known to play an important role in RAF signal regulation, and have the ability to stabilize both inactive (monomeric) and active (dimeric) states of RAF. It is poorly understood how these antagonistic roles ultimately modulate RAF signaling. To investigate, we develop a mathematical model of RAF activation with both roles of 14-3-3, perform algebraic and numeric analyses, and compare with available experimental data. We derive the conditions necessary to explain experimental observations that 14-3-3 overexpression activates RAF, and we show that strong binding of 14-3-3 to Raf dimers alone is not generally sufficient to explain this observation. Our integrated analysis also suggests that RAF–14-3-3 binding is relatively weak for the reasonable range of parameter values, and suggests the Raf dimer–14-3-3 interactions are stabilized primarily by avidity. Lastly we find that in the limit of paired weak/avidity driven interactions between RAF and 14-3-3, the paired binding interactions may be reasonably approximated with a strong, single, equilibrium reaction. Overall, our work presents a mathematical model that can serve as a foundational piece for future, extended, studies of signaling reactions involving regulated RAF kinase activity.
SIngle cell level Genotyping Using scRna Data (SIGURD)
Authors: Graßhoff Martin , Kalmer Milena , Chatain Nicolas , Kricheldorf Kim , Maurer Angela , Weiskirchen Ralf , Koschmieder Steffen , Costa Ivan G.
Published: July 2024

Motivation

By accounting for variants within measured transcripts, it is possible to evaluate the status of somatic variants using single-cell RNA-sequencing (scRNA-seq) and to characterize their clonality. However, the sparsity (very few reads per transcript) or bias in protocols (favoring 3’ ends of the transcripts) makes the chance of capturing somatic variants very unlikely. This can be overcome by targeted sequencing or the use of mitochondrial variants as natural barcodes for clone identification. Currently, available computational tools focus on genotyping, but do not provide functionality for combined analysis of somatic and mitochondrial variants and functional analysis such as characterization of gene expression changes in detected clones.

Results

Here, we propose SIGURD, which is an R-based pipeline for the clonal analysis of single-cell RNA-seq data. This allows the quantification of clones by leveraging both somatic and mitochondrial variants. SIGURD also allows for functional analysis after clonal detection: association of clones with cell populations, detection of differentially expressed genes across clones and association of somatic and mitochondrial variants. Here, we demonstrate the power of SIGURD by analyzing single-cell data of colony-forming cells derived from patients with myeloproliferative neoplasms.

Availability

Code and tutorial of SIGURD are available at GitHubhttps://github.com/CostaLab/sigurd.

Contact

ivan.costa@rwth-aachen.de,skoschmieder@ukaachen.de

Supplementary Information

Supplementary data are available online.
High-motility pro-tumorigenic monocytes drive macrophage enrichment in the tumor microenvironment
Authors: Du Wenxuan , Zhou Bryan , Forjaz André , Shin Sarah M. , Wu Fan , Crawford Ashleigh J. , Nair Praful R. , Johnston Adrian C. , West-Foyle Hoku , Tang Ashley , Kim Dongjoo , Fan Rong , Kiemen Ashley L. , Wu Pei-Hsun , Phillip Jude M. , Ho Won Jin , Sanin David E. , Wirtz Denis
Published: July 2024

Enrichment of tumor-associated macrophages (TAMΦs) in the tumor microenvironment correlates with worse clinical outcomes in triple-negative breast cancer (TNBC) patients, prompting the development of therapies to inhibit TAMΦ infiltration. However, the lackluster efficacy of CCL2-based chemotaxis blockade in clinical trials suggests that a new understanding of monocyte/macrophage infiltration may be necessary. Here we demonstrate that random migration, and not only chemotaxis, drives macrophage tumor infiltration. We identified tumor- associated monocytes (TAMos) that display a dramatically enhanced migration capability, induced rapidly by the tumor microenvironment, that drives effective tumor infiltration, in contrast to low-motility differentiated macrophages. TAMo, not TAMΦ, promotes cancer cell proliferation through activation of the MAPK pathway. IL-6 secreted both by cancer cells and TAMo themselves enhances TAMo migration by increasing dendritic protrusion dynamics and myosin- based contractility via the JAK2/STAT3 signaling pathway. Independent from CCL2 mediated chemotaxis, IL-6 driven enhanced migration and pro-proliferative effect of TAMo were validated in a syngeneic TNBC mouse model. Depletion of IL-6 in cancer cells significantly attenuated monocyte infiltration and reversed TAMo-induced cancer cell proliferation. This work reveals the critical role random migration plays in monocyte driven TAMΦ enrichment in a tumor and pinpoints IL-6 as a potential therapeutic target in combination with CCL2 to ameliorate current strategies against TAMΦ infiltration.
Within-species variation eclipses between-species differences inPanconsolation
Authors: Brooker Jake S. , Webb Christine E. , Kordon Stephanie , de Waal Frans B. M. , Clay Zanna
Published: July 2024

Empathy and its subcomponents are well documented throughout the animal kingdom, indicating the deep evolutionary origins of this socioemotional capacity. A key behavioural marker of empathy is consolation, or unsolicited bystander affiliation directed towards distressed others. Consolation has been observed in our closest living relatives, bonobos (Pan paniscus) and chimpanzees (P. troglodytes). However, systematic comparisons are absent, despite potential for interspecific differences. Bonobos are often considered less aggressive, more emotionally sensitive, and more socially tolerant than chimpanzees—key characteristics purported to drive consolation. Furthermore, social and individual factors also appear to drive intraspecific variation in empathy. To address within- and between-species variability inPanconsolation, we systematically tested the consolatory tendencies of large sanctuary-living groups of both species. Bonobos and chimpanzees exhibited similar consolation tendencies; however, within-species analyses revealed further similarities and variation. Bonobo consolation was most often directed towards and received by younger individuals, while chimpanzee consolation was most often directed towards close social partners. In addition, males and females of both species showed decreased consolation with age, with some evidence for chimpanzee males consoling more than young females. Our findings support the notion that within-species variation inPansocio-emotional abilities is greater than between-species differences, highlighting the presence of striking behavioural diversity across our two closest cousins.
NR2F2 is required in the embryonic testis for Fetal Leydig Cell development
Authors: Perea-Gomez Aitana , Bellido-Carreras Natividad , Dhellemmes Magali , Tang Furong , Le Gallo Coralie , Chaboissier Marie-Christine
Published: July 2024

Male genital development in XY mammalian fetuses is triggered by the action of hormones, including testosterone, secreted by the developing testes. Defects in this process are a cause for Differences in Sex Development (DSD), one of the most common congenital abnormalities in humans. Fetal Leydig Cells (FLC) play a central role for the synthesis of masculinizing hormones in the developing testes. Yet, the genetic cascade controlling their differentiation is poorly understood. Here we investigate the role of the orphan nuclear receptor NR2F2 (COUP-TFII) in FLC development. We report that NR2F2 is expressed in interstitial progenitor cells of the mouse embryonic testes and is downregulated upon their differentiation into FLC. By using two mouse models for conditional mutation ofNr2f2in the developing testes, we demonstrate that NR2F2 is required for testis morphogenesis and FLC development. NR2F2 acts in interstitial progenitors to regulate the initiation and progression of FLC differentiation. These results establish NR2F2 as an essential regulator of FLC development and steroid hormone synthesis in the mouse fetal testis and provide an entry point to understand the etiology of 46, XY DSD associated with pathogenic NR2F2 variants.
Unraveling Structural Disparities in Human and Mycobacterium Tuberculosis Type-I Fatty Acid Synthase
Authors: Kumar Akhil , Rama Priyanka , Katkar Harshwardhan H.
Published: July 2024

Type-I Fatty acid synthase is an essential enzyme present in diverse species including humans (hFAS-I) and mycobacterium tuberculosis (MtbFAS-I), and is an attractive antibacterial drug target. A structural comparison of the two enzymes is essential in order to identify selective drug targets in MtbFAS-I. In this work, we have analyze equilibrium average structures of hFAS-I and MtbFAS-I obtained from 100 ns long molecular dynamics simulation trajectories. Our structural analysis revealed that two of the seven domains present in both hFAS-I and MtbFAS-I,viz. dehydratase (DH) and enoyl reductase (ER), are significantly dissimilar. We further compared corresponding catalytic pockets in these two domains and analyzed their physicochemical characteristics. In addition to being large in MtbFAS-I, the pockets are significantly different in their physicochemical characteristics and water content.
Establishing a Male-Positive Genetic Sexing Strain in the Asian Malaria VectorAnopheles stephensi
Authors: Weng Shih-Che , Chen Fangying , Li Ming , Lee Sammy , Gerry Connor , Turksoy Dylan Can , Akbari Omar S.
Published: July 2024

Genetic biocontrol interventions targeting mosquito-borne diseases require the release of male mosquitoes exclusively, as only females consume blood and transmit human pathogens. This reduces the risk of spreading pathogens while enabling effective population control. Robust sex sorting methods to enable early larval sorting in mosquitoes need to be developed to allow for scalable sex sorting for genetic biocontrol interventions. This study applies the SEPARATOR (Sexing Element Produced by Alternative RNA-splicing of A Transgenic Observable Reporter) system, previously developed forAedes aegypti, to the Asian malaria vectorAnopheles stephensi. We hypothesized that the intron from thedoublesexgene inAnopheles gambiaewould function inAn. stephensidue to evolutionary conservation. Our results confirm that the splicing module fromAn. gambiaeoperates effectively inAn. stephensi, demonstrating evolutionary conservation in sex-specific splicing events between these species. This system enables reliable positive male selection from first instar larval to pupal stages. RT-PCR analysis demonstrates that male-specific EGFP expression is dependent ondoublesexsex-specific splicing events. The SEPARATOR system’s independence from sex-chromosome linkage confers resistance to meiotic recombination and chromosomal rearrangements. This approach may facilitate the mass release of males, and the cross-species portability of SEPARATOR establishes it as a valuable tool for genetic biocontrol interventions across various pest species.
MLSPred-Bench: ML-Ready Benchmark Leveraging Seizure Detection EEG data for Predictive Models
Authors: Mohammad Umair , Saeed Fahad
Published: July 2024

Predicting epileptic seizures is a significantly challenging task as compared to detection. While electroen-cephalography (EEG) data annotated for detection is available from multiple repositories, they cannot readily be used for predictive modeling. In this paper, we designed and developed a strategy that can be used for converting any EEG big data annotated for detection into ML-ready data suitable for prediction. The generalizability of our strategy is demonstrated by executing it on Temple University Seizure (TUSZ) corpus which is annotated for seizure detection. This execution results in 12 ML-ready datasets, collectively calledMLSPred-Benchbenchmark, which constitutes data for training, validating and testing seizure prediction models. Our strategy uses different variations of seizure prediction horizon (SPH) and the seizure occurrence period (SOP) to make more than 150GB of ML-ready data. To illustrate that the generated data can be used for predictive modeling, we executed an ML model on all the benchmarks which resulted in variable performances when compared with the original model and its performance. We expect that our strategy can be used as a general method to transform seizure detection EEG big data into ML-ready datasets useful for seizure prediction. Our code and related materials will be made available athttps://github.com/pcdslab/MLSPred-Bench.
Oral citrate supplementation mitigates age-associated pathological intervertebral disc calcification in LG/J mice
Authors: Ottone Olivia K. , Mundo Jorge J. , Kwakye Boahen N. , Slaweski Amber , Collins John A. , Wu Qinglin , Connelly Margery A. , Niaziorimi Fatemeh , van de Wetering Koen , Risbud Makarand V.
Published: July 2024

Despite the high prevalence of age-dependent intervertebral disc calcification, there is a glaring lack of treatment options for this debilitating pathology. Here, we investigate the efficacy of long-term oral K3Citrate supplementation in ameliorating disc calcification in LG/J mice, a model of spontaneous age-associated disc calcification. K3Citrate successfully reduced the incidence of disc calcification in LG/J mice without deleterious effects on vertebral bone structure, plasma chemistry, and locomotion. Notably, a positive effect on grip strength was evident in treated mice. Spectroscopic investigation of the persisting calcified nodules indicated K3Citrate did not alter the mineral composition and revealed that reactivation of an endochondral differentiation program in endplates may drive LG/J disc calcification. Importantly, K3Citrate reduced calcification incidence without altering the pathological endplate chondrocyte hypertrophy, suggesting mitigation of disc calcification primarily occurred through Ca2+chelation, a conclusion supported by chondrogenic differentiation and Seahorse metabolic assays. Overall, this study underscores the therapeutic potential of K3Citrate as a systemic intervention strategy for disc calcification.

Teaser

Oral citrate mitigates intervertebral disc mineralization in a mouse model of age-dependent spontaneous disc calcification.
Compliance to Iron Folic Acid Supplementation and its associated factors among post-partum mothers of Bharatpur Metropolitan
Authors: Pokhrel Amshu , Bhatta Bimala , Adhikari Anup
Published: July 2024

Background

Anemia is a major global health issue, especially affecting young children, pregnant and postpartum women, and adolescent girls, with 1.92 billion affected in 2021, notably in sub-Saharan Africa and South Asia. Iron deficiency is a key cause, requiring interventions like iron and folic acid supplementation. Despite efforts in Nepal, anemia prevalence fluctuates, with compliance a concern. This study assesses iron and folic acid supplementation compliance among postpartum mothers in Bharatpur Metropolitan City.

Method

A community-based cross-sectional study was conducted among 303 postpartum mothers with babies aged 45days to 1 year in Bharatpur Metropolitan City. Data were collected through face-to-face interviews using a pre-tested questionnaire.

Results

The compliance rate for iron and folic acid supplementation among postpartum mothers was 48.2%. Among different sociodemographic variables, religion of participants was found to be significantly associated with compliance to iron folic acid supplementation (OR 5.367, 95% CI 1.173-16.636). Moreover, participants having more than four antenatal visits (OR 3.465, 95% CI 1.366-8.792), participants having good knowledge about anemia (OR 5.554, 95% CI 2.485-12.415), and participants having good knowledge about iron and folic acid supplementation (OR 2.442, 95% CI 1.064-5.60) were also significantly associated with higher compliance.

Conclusion

To improve IFAS adherence, healthcare providers should focus on health education on the postpartum importance of iron and folic acid supplementation, along with diligent follow-up using culturally tailored strategies. Enhanced compliance will lead to better health outcomes for mothers and their babies.
Radiotherapy continuity for cancer treatment: lessons learned from natural disasters
Authors: Müller-Polyzou Ralf , Reuter-Oppermann Melanie
Published: July 2024

Background: The contemporary world is challenged by natural disasters accelerated by climate change, affecting a growing world population. Simultaneously, cancer remains a persistent threat as a leading cause of death, killing 10~million people annually. The efficacy of radiotherapy, a cornerstone in cancer treatment worldwide, depends on an uninterrupted course of therapy. However, natural disasters cause significant disruptions to the continuity of radiotherapy services, posing a critical challenge to cancer treatment. This paper explores how natural disasters impact radiotherapy practice, compares them to man-made disasters, and outlines strategies to mitigate adverse effects of natural disasters. Through this analysis, the study seeks to contribute to developing resilient healthcare frameworks capable of sustaining essential cancer treatment amidst the challenges posed by natural disasters. Method: We conducted a Structured Literature Review to investigate this matter comprehensively, gathering and evaluating relevant academic publications. We explored how natural disasters affected radiotherapy practice and examined the experience of radiotherapy centres worldwide in resuming operations after such events. Subsequently, we validated and extended our research findings through a global online survey involving radiotherapy professionals. Results: The Structured Literature Review identified twelve academic publications describing hurricanes, floods, and earthquakes as the primary disruptors of radiotherapy practice. The analysis confirms and complements risk mitigation themes identified in our previous research, which focused on the continuity of radiotherapy practice during the COVID-19 pandemic. Our work describes nine overarching themes, forming the basis for a taxonomy of 36 distinct groups. The subsequent confirmative online survey supported and solidified our findings and served as a basis for developing a conceptual framework for natural disaster-resilient radiotherapy. Discussion: The growing threat posed by natural disasters underscores the need to develop business continuity programs and define risk mitigation measures to ensure the uninterrupted provision of radiotherapy services. By drawing lessons from past disasters, we can better prepare for future hazards, supporting disaster management and planning efforts, particularly enhancing the resilience of radiotherapy practice. Additionally, our study can serve as a resource for shaping policy initiatives aimed at mitigating the impact of natural hazards.
Protocol for: A Simple, Accessible, Literature-based Drug Repurposing Pipeline
Authors: Lange Maximin , Martyn Meredith , Gogarty Eoin , Braude Philip , Fayez Feras , Carter Ben
Published: July 2024

We will develop a novel approach to drug repurposing, utilising Natural Language Processing (NLP) and Literature Based Discovery (LBD) techniques. This will present a simplified, accessible drug repurposing pipeline using Word2Vec embeddings trained on PubMed abstracts to identify potential new medications to be repurposed. We present this approach in the context of antipsychotics, but it could be repeated for any available medication.

The research is structured in three stages:

Identification of candidate medications using Word2Vec algorithm trained on scientific literature.

Empirical testing of identified candidates using a large hospital dataset to explore protective effects against disease onset.

Validation of findings using a second, independent dataset to assess generalizability.

This method addresses limitations in current machine learning-based drug repurposing approaches, including lack of external validation and limited accessibility. By leveraging Word2Vec’s ability to capture semantic relationships between words, the study aims to uncover hidden connections in medical literature that may lead to novel therapeutic discoveries.

The protocol emphasizes transparency and reproducibility, utilizing publicly available electronic health record (EHR) databases for validation. This approach allows for tangible results even for researchers with limited machine learning expertise, bridging the gap between biomedical and information systems communities.
Genetic Transformer: An Innovative Large Language Model Driven Approach for Rapid and Accurate Identification of Causative Variants in Rare Genetic Diseases
Authors: Liang Lungang , Chen Yulan , Wang Taifu , Jiang Dan , Jin Jishuo , Pang Yanmeng , Na Qin , Liu Qiang , Jiang Xiaosen , Dai Wentao , Tang Meifang , Du Yutao , Peng Dirong , Jin Xin , Zhao Lijian
Published: July 2024

Background

Identifying causative variants is crucial for the diagnosis of rare genetic diseases. Over the past two decades, the application of genome sequencing technologies in the field has significantly improved diagnostic outcomes. However, the complexity of data analysis and interpretation continues to limit the efficiency and accuracy of these applications. Various genotype and phenotype-driven filtering and prioritization strategies are used to generate a candidate list of variants for expert curation, with the final report variants determined through knowledge-intensive and labor-intensive expert review. Despite these efforts, the current methods fall short of meeting the growing demand for accurate and efficient diagnosis of rare disease. Recent developments in large language models (LLMs) suggest that LLMs possess the potential to augment or even supplant human labor in this context.

Methods

In this study, we have developed Genetic Transformer (GeneT), an innovative large language model (LLM) driven approach to accelerate identification of candidate causative variants for rare genetic disease. A comprehensive evaluation was conducted between the fine-tuned large language models and four phenotype-driven methods, including Xrare, Exomiser, PhenIX and PHIVE, alongside six pre-trained LLMs (Qwen1.5-0.5B, Qwen1.5-1.8B, Qwen1.5-4B, Mistral-7B, Meta-Llama-3-8B, Meta-Llama-3-70B). This evaluation focused on performance and hallucinations.

Results

Genetic Transformer (GeneT) as an innovative LLM-driven approach demonstrated outstanding performance on identification of candidate causative variants, identified the average number of candidate causative variants reduced from an average of 418 to 8, achieving recall rate of 99% in synthetic datasets. Application in real-world clinical setting demonstrated the potential for a 20-fold increase in processing speed, reducing the time required to analyze each sample from approximately 60 minutes to around 3 minutes. Concurrently, the recall rate has improved from 94.36% to 97.85%. An online analysis platform iGeneT was developed to integrate GeneT into the workflow of rare genetic disease analysis.

Conclusion

Our study represents the inaugural application of fine-tuned LLMs for identifying candidate causative variants, introducing GeneT as an innovative LLM-driven approach, demonstrating its superiority in both simulated data and real-world clinical setting. The study is unique in that it represents a paradigm shift in addressing the complexity of variant filtering and prioritization of whole exome or genome sequencing data, effectively resolving the challenge akin to finding a needle in a haystack.
Human reproduction comes at the expense of faster aging and a shorter life
Authors: Hukkanen Mikaela , Kankaanpää Anna , Heikkinen Aino , Kaprio Jaakko , Cristofari Robin , Ollikainen Miina
Published: July 2024

Evolutionary theories suggest a trade-off between resources allocated to reproduction and those allocated to self-maintenance, and predict that higher reproductive output entails a shorter lifespan. This study investigates the impact of childbearing on aging and lifespan using data from contemporary Finnish twin women. We model the association between reproductive trajectories and survival in 17,080 women, and assess biological aging in a subset of participants (N=1,117) using the PCGrimAge clock, an algorithm trained to predict biological aging and mortality risk from DNA methylation. Our findings suggest that early childbearing, numerous pregnancies or nulliparity all contribute to accelerated aging and increased mortality risk. These results provide strong evidence for the existence of a trade-off between reproduction, aging and lifespan in modern humans, and provide novel insights into the genetic and lifestyle determinants of healthspan.
Structural basis for the interaction between the bacterial cell division proteins FtsZ and ZapA
Authors: Fujita Junso , Hibino Kota , Kagoshima Gota , Kamimura Natsuki , Kato Yuki , Uehara Ryo , Namba Keiichi , Uchihashi Takayuki , Matsumura Hiroyoshi
Published: July 2024

Cell division in most bacteria is regulated by the tubulin homolog FtsZ as well as ZapA, a FtsZ-associated protein. However, how FtsZ and ZapA function coordinately has remained elusive. Here we report the cryo-electron microscopy structure of the ZapA-FtsZ complex. The complex forms an asymmetric ladder-like structure, in which the double antiparallel FtsZ protofilament on one side and a single protofilament on the other side are tethered by ZapA tetramers. In the complex, the extensive interactions of FtsZ with ZapA cause a structural change of the FtsZ protofilament, and the formation of the double FtsZ protofilament increases electrostatic repulsion. High-speed atomic force microscopy analysis revealed cooperative interactions of ZapA with FtsZ at a molecular level. Our findings not only provide a structural basis for the interaction between FtsZ and ZapA but also shed light on how ZapA binds to FtsZ protofilaments without disturbing FtsZ dynamics to promote cell division.
FLOW CYTOMETRIC PROCEDURES FOR DEEP CHARACTERIZATION OF NANOPARTICLES
Authors: Tirelli Valentina , Grasso Felicia , Barreca Valeria , Polignano Deborah , Gallinaro Alessandra , Cara Andrea , Sargiacomo Massimo , Fiani Maria Luisa , Sanchez Massimo
Published: July 2024

In recent years, there has been a notable increasing interest surrounding the identification and quantification of nanosized particles, including extracellular vesicles (EVs) and viruses. The challenge posed by the nano-sized dimension of these particles makes precise examination a significant undertaking.

Among the different techniques for the accurate study of EVs, Flow cytometry (FCM) stands out as the ideal method. It is characterized by high sensitivity, low time consumption, non-destructive sampling, and high throughput.

In this article, we propose the optimization of FCM procedures to identify, quantify, and purify EVs and virus like particles (VLPs).

The protocol aims to reduce artifacts and errors in nano-sized particles counting, overall caused by the swarming effect. Different threshold strategies were compared to ensure result specificity. Additionally, the critical parameters to consider when using conventional FCM outside of the common experimental context of use have also been identified. Finally, fluorescent-EVs sorting protocol was also developed with highly reliable results using a conventional cell sorter.
An Omni-Mesoscope for multiscale high-throughput quantitative phase imaging of cellular dynamics and high-content molecular characterization
Authors: Ma Hongqiang , Chen Maomao , Xu Jianquan , Zhao Yongxin , Liu Yang
Published: July 2024

The mesoscope has emerged as a powerful imaging tool in biomedical research, yet its high cost and low resolution have limited its broader application. Here, we introduce the Omni-Mesoscope, a cost-effective high-spatial-temporal, multimodal, and multiplex mesoscopic imaging platform built from cost-efficient off-the-shelf components. This system uniquely merges the capabilities of quantitative phase microscopy to capture live-cell dynamics over a large cell population with highly multiplexed fluorescence imaging for comprehensive molecular characterization. This integration facilitates simultaneous tracking of live-cell morphodynamics across thousands of cells, alongside high-content molecular analysis at the single-cell level. Furthermore, the Omni-Mesoscope offers a mesoscale field of view of approximately 5 mm2with a high spatial resolution down to 700 nm, enabling the capture of information-rich images with detailed sub-cellular features. We demonstrate such capability in delineating molecular characteristics underlying rare dynamic cellular phenomena, such as cancer cell responses to chemotherapy and the emergence of polyploidy in drug-resistant cells. Moreover, the cost-effectiveness and the simplicity of our Omni-Mesoscope democratizes mesoscopic imaging, making it accessible across diverse biomedical research fields. To further demonstrate its versatility, we integrate expansion microscopy to enhance 3D volumetric super-resolution imaging of thicker tissues, opening new avenues for biological exploration at unprecedented scales and resolutions.
Systematic Analysis of Human Colorectal Cancer scRNA-seq Revealed Limited Pro-tumoral IL-17 Production Potential in Gamma Delta T Cells
Authors: Ran Ran , Trapecar Martin , Brubaker Douglas K.
Published: July 2024

Gamma delta (γδ) T cells play a crucial role in anti-tumor immunity due to their cytotoxic properties. However, the role and extent of γδ T cells in production of pro-tumorigenic interleukin-17 (IL-17) within the tumor microenvironment (TME) of colorectal cancer (CRC) remains controversial. In this study, we re-analyzed nine published human CRC whole-tissue single-cell RNA sequencing (scRNA-seq) datasets, identifying 18,483 γδ T cells out of 951,785 total cells, in the neoplastic or adjacent normal tissue of 165 human CRC patients. Our results confirm that tumor-infiltrating γδ T cells exhibit high cytotoxicity-related transcription in both tumor and adjacent normal tissues, but critically, none of the γδ T cell clusters showed IL-17 production potential. We also identified various γδ T cell subsets, including Teff, TRM, Tpex, and Tex, and noted an increased expression of cytotoxic molecules in tumor-infiltrating γδ T cells compared to their normal area counterparts. Our work demonstrates that γδ T cells in CRC primarily function as cytotoxic effector cells rather than IL-17 producers, mitigating the concerns about their potential pro-tumorigenic roles in CRC, highlighting the importance of accurately characterizing these cells for cancer immunotherapy research and the unneglectable cross-species discrepancy between the mouse and human immune system in the study of cancer immunology.
Auditory-motor entrainment and listening experience shape the perceptual learning of concurrent speech
Authors: MacLean Jessica , Stirn Jack , Bidelman Gavin M.
Published: July 2024

Background

Plasticity from auditory experience shapes the brain’s encoding and perception of sound. Though prior research demonstrates that neural entrainment (i.e., brain-to-acoustic synchronization) aids speech perception, how long- and short-term plasticity influence entrainment to concurrent speech has not been investigated. Here, we explored neural entrainment mechanisms and the interplay between short- and long-term neuroplasticity for rapid auditory perceptual learning of concurrent speech sounds in young, normal-hearing musicians and nonmusicians.

Method

Participants learned to identify double-vowel mixtures during ∼45 min training sessions with concurrent high-density EEG recordings. We examined the degree to which brain responses entrained to the speech-stimulus train (∼9 Hz) to investigate whether entrainment to speech prior to behavioral decision predicted task performance. Source and directed functional connectivity analyses of the EEG probed whether behavior was driven by group differences auditory-motor coupling.

Results

Both musicians and nonmusicians showed rapid perceptual learning in accuracy with training. Interestingly, listeners’ neural entrainment strength prior to target speech mixtures predicted behavioral identification performance; stronger neural synchronization was observed preceding incorrect compared to correct trial responses. We also found stark hemispheric biases in auditory-motor coupling during speech entrainment, with greater auditory-motor connectivity in the right compared to left hemisphere for musicians (R>L) but not in nonmusicians (R=L).

Conclusions

Our findings confirm stronger neuroacoustic synchronization and auditory-motor coupling during speech processing in musicians. Stronger neural entrainment to rapid stimulus trains preceding incorrect behavioral responses supports the notion that alpha-band (∼10 Hz) arousal/suppression in brain activity is an important modulator of trial-by-trial success in perceptual processing.
Cerebrospinal Fluid and Plasma Metabolites with Parkinson’s Disease: A Mendelian Randomization Study
Authors: Wang Jia-Li , Zheng Ran , Fang Yi , Cao Jin , Zhang Bao-Rong
Published: July 2024

Background and Objective

Previous studies have identified associations between metabolites and Parkinson’s disease (PD), but the causal relationships remain unclear. This study aims to identify causal relationships between specific cerebrospinal fluid (CSF) and plasma metabolites and the PD risk using Mendelian Randomization (MR).

Methods

We utilized data on 338 CSF metabolites from the Wisconsin Alzheimer’s Disease Research Center and the Wisconsin Registry for Alzheimer’s Prevention, and 1,400 plasma metabolites from the Canadian Longitudinal Study on Aging. PD outcome data were obtained from a GWAS meta-analysis by the International Parkinson’s Disease Genomics Consortium. MR analysis was conducted using the TwoSampleMR package in R.

Results

MR analysis identified 49 plasma metabolites with suggestive causal relationships with PD risk, including 21 positively associated metabolites, 23 negatively associated metabolites, and 5 unknown compounds. In the CSF, six metabolites showed suggestive causal relationships with PD, including positively associated dimethylglycine, gluconate, oxalate (ethanedioate), and the unknown metabolite X-12015, while (1-enyl-palmitoyl)-2-arachidonoyl-GPC (P-16:0/20:4) and the unknown metabolite X-23587 were negatively associated. Among the plasma metabolites, those with a positive association with PD risk include hydroxy-3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (hydroxy-CMPF), carnitine C14, 1-linoleoyl-GPG (18:2), glucose to maltose ratio, and cis-3,4-methyleneheptanoate. Conversely, metabolites with a negative association with PD risk include tryptophan, succinate to acetoacetate ratio, N,N,N-trimethyl-alanylproline betaine (TMAP), glucuronide of piperine metabolite C17H21NO3, and linoleoylcholine.

Conclusion

Our study underscores the correlation between CSF and plasma metabolites and PD risk, highlighting specific metabolites as potential biomarkers for diagnosis and therapeutic targets.
Eyes on VR: Unpacking the Causal Chain Between Exposure, Reception, and Retention for Emotional Billboard Messages
Authors: Cho Hee Jung , Lim Sue , Turner Monique Mitchell , Bente Gary , Schmälzle Ralf
Published: July 2024

The causal chain from message exposure to reception to effects is widely accepted as the basic explanatory model for communication outcomes. Problematically, the chain’s links are often studied in isolation, leaving measurement gaps that compromise the ecological validity and practical utility of experimental research. Here we introduce a VR-based paradigm that encompasses a realistic message reception context, i.e., a simulated car ride on a highway flanked by billboards. We varied attentional message factors (emotional content) as well as contextual task distractions (trash-counting). VR-integrated eye trackers were used to capture participants’ incidental message exposure dependent on their actual gaze behavior. Consistent with our predictions, results show that 1. exposure gates all subsequent effects; 2. distraction impacts likelihood of exposure; 3. both the manipulation of emotional content and distraction affect retention. This comprehensive analysis of the exposure-reception-retention chain can be broadly applied to a variety of message reception contexts that will be discussed.
Quasinormal modes and their excitation beyond general relativity
Authors: Silva Hector O. , Tambalo Giovanni , Glampedakis Kostas , Yagi Kent , Steinhoff Jan
Published: July 2024

The response of black holes to small perturbations is known to be partially described by a superposition of quasinormal modes. Despite their importance to enable strong-field tests of gravity, little to nothing is known about what overtones and quasinormal-mode amplitudes are like for black holes in extensions to general relativity. We take a first step in this direction and study what is arguably the simplest model that allows first-principle calculations to be made: a nonrotating black hole in an effective-field-theory extension of general relativity with cubic-in-curvature terms. Using a phase-amplitude scheme that uses analytical continuation and the Prüfer transformation, we numerically compute, for the first time, the quasinormal overtone frequencies (in this theory) and quasinormal-mode excitation factors (in any theory beyond general relativity). We find that the overtone quasinormal frequencies and their excitation factors are more sensitive than the fundamental mode to the length scale l introduced by the higher-derivative terms in the effective field theory. We argue that a description of all overtones cannot be made within the regime of validity of the effective field theory, and we conjecture that this is a general feature of any extension to general relativity that introduces a new length scale. We also find that a parametrization of the modifications to the general-relativistic quasinormal frequencies in terms of the ratio between l and the black hole’s mass is somewhat inadequate, and we propose a better alternative. As an application, we perform a preliminary study of the implications of the breakdown, in the effective field theory, of the equivalence between the quasinormal mode spectra associated to metric perturbations of polar and axial parity of the Schwarzschild black hole in general relativity. We also present a simple justification for the loss of isospectrality.

Published by the American Physical Society
2024