bluuebunny/crossref_metadata_2025_split huggingface dataset:
RETROFIT: REFERENCE-FREE DECONVOLUTION OF CELL-TYPE MIXTURES IN SPATIAL TRANSCRIPTOMICS
Authors: Singh Roopali , He Xi , Park Adam Keebum , Hardison Ross Cameron , Zhu Xiang , Li Qunhua 
Published: June 2023

ABSTRACTSpatial transcriptomics (ST) profiles gene expression in intact tissues. However, ST data measured at each spatial location may represent gene expression of multiple cell types, making it difficult to identify cell-type-specific transcriptional variation across spatial contexts. Existing cell-type deconvolutions of ST data often require single-cell transcriptomic references, which can be limited by availability, completeness and platform effect of such references. We present RETROFIT, a reference-free Bayesian method that produces sparse and interpretable solutions to deconvolve cell types underlying each location independent of single-cell transcriptomic references. Results from synthetic and real ST datasets acquired by Slide-seq and Visium platforms demonstrate that RETROFIT outperforms existing reference-based and reference-free methods in estimating cell-type composition and reconstructing gene expression. Applying RETROFIT to human intestinal development ST data reveals spatiotemporal patterns of cellular composition and transcriptional specificity. RETROFIT is available athttps://bioconductor.org/packages/release/bioc/html/retrofit.html.
In Silico Transcriptome-based Screens Identify Epidermal Growth Factor Receptor Inhibitors as Therapeutics for Noise-induced Hearing Loss
Authors: Vijayakumar Sarath , DiGuiseppi Joe A. , Dabestani Jila , Ryan William G. , Vielman Quevedo Rene , Li Yuju , Diers Jack , Tu Shu , Fleegel Jonathan , Nguyen Cassidy , Rhoda Lauren M. , Imami Ali Sajid , Hamoud Ali Abdul-Rizaq , Lovas Sándor , McCullumsmith Robert , Zallocchi Marisa , Zuo Jian 
Published: June 2023

AbstractNoise-Induced Hearing Loss (NIHL) represents a widespread disease for which no therapeutics have been approved by the Food and Drug Administration (FDA). Addressing the conspicuous void of efficacious in vitro or animal models for high throughput pharmacological screening, we utilized an in silico transcriptome-oriented drug screening strategy, unveiling 22 biological pathways and 64 promising small molecule candidates for NIHL protection. Afatinib and zorifertinib, both inhibitors of the Epidermal Growth Factor Receptor (EGFR), were validated for their protective efficacy against NIHL in experimental zebrafish and murine models. This protective effect was further confirmed with EGFR conditional knockout mice and EGF knockdown zebrafish, both demonstrating protection against NIHL. Molecular analysis using Western blot and kinome signaling arrays on adult mouse cochlear lysates unveiled the intricate involvement of several signaling pathways, with particular emphasis on EGFR and its downstream pathways being modulated by noise exposure and Zorifertinib treatment. Administered orally, Zorifertinib was successfully detected in the perilymph fluid of the inner ear in mice with favorable pharmacokinetic attributes. Zorifertinib, in conjunction with AZD5438 – a potent inhibitor of cyclin dependent kinase 2 – produced synergistic protection against NIHL in the zebrafish model. Collectively, our findings underscore the potential application of in silico transcriptome-based drug screening for diseases bereft of efficient screening models and posit EGFR inhibitors as promising therapeutic agents warranting clinical exploration for combatting NIHL.HighlightsIn silico transcriptome-based drug screens identify pathways and drugs against NIHL.EGFR signaling is activated by noise but reduced by zorifertinib in mouse cochleae.Afatinib, zorifertinib and EGFR knockout protect against NIHL in mice and zebrafish.Orally delivered zorifertinib has inner ear PK and synergizes with a CDK2 inhibitor.
Speckle rheological spectroscopy reveals wideband viscoelastic spectra of biological tissues
Authors: Leartprapun Nichaluk , Zeng Ziqian , Hajjarian Zeinab , Bossuyt Veerle , Nadkarni Seemantini K. 
Published: June 2023

AbstractMechanical transformation of tissue is not merely a symptom but a decisive driver in pathological processes. Comprising intricate network of cells, fibrillar proteins, and interstitial fluid, tissues exhibit distinct solid- (elastic) and liquid-like (viscous) behaviours that span a wide band of frequencies. Yet, characterization of wideband viscoelastic behaviour in whole tissue has not been investigated, leaving a vast knowledge gap in the higher frequency range that is linked to fundamental intracellular processes and microstructural dynamics. Here, we present wideband Speckle rHEologicAl spectRoScopy (SHEARS) to address this need. We demonstrate, for the first time, analysis of frequency-dependent elastic and viscous moduli up to the sub-MHz regime in biomimetic scaffolds and tissue specimens of blood clots, breast tumours, and bone. By capturing previously inaccessible viscoelastic behaviour across the wide frequency spectrum, our approach provides distinct and comprehensive mechanical signatures of tissues that may provide new mechanobiological insights and inform novel disease prognostication.
Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets
Authors: Koldobskiy Michael A. , Camacho Oscar , Reddy Pradeep , Izpisua Belmonte Juan Carlos , Feinberg Andrew P. 
Published: June 2023

ABSTRACTRejuvenation of tissues in physiologically aging mice can be accomplished by long-term partial reprogramming via expression of reprogramming factors (Oct4, Sox2, Klf4 and c-Myc). To investigate the epigenetic determinants of partial reprogramming-mediated rejuvenation, we used whole genome bisulfite sequencing to carry out unbiased comprehensive profiling of DNA methylation changes in skin from mice subjected to partial reprogramming, as well as young and untreated old controls. We found a striking convergence of age- and rejuvenation-related epigenetic alterations on targets of the Polycomb repressive complex 2 (PRC2). These results are also supported by a likewise prominent enrichment of PRC2 targets in gene expression data, suggesting that PRC2 activity can modulate aging and mediate tissue rejuvenation.
Associating Transcription Factors to Single-Cell Trajectories with DREAMIT
Authors: Maulding Nathan D , Seninge Lucas , Stuart Joshua M. 
Published: June 2023

AbstractTrajectory methods have enabled the organization of cells into contiguous cellular changes from their transcriptional profiles measured by single cell RNA sequencing. Few methods enable investigating the implied gene regulatory network dynamics from the cell transitions between and along trajectory branches. In particular, there remains an opportunity to develop methods that leverage the predicted “pseudotime” orderings of cells to reveal transcription factor (TF) dynamics. Here we present DREAMIT (DynamicRegulation ofExpressionAcrossModules inInferredTrajectories), a novel framework developed to detect patterns of TF activity along single-cell trajectory branches. It detects significant TF-target associations using a relational enrichment approach. Using a benchmark representing several different tissues, the method was found to have increased tissue-specific sensitivity and specificity over competing approaches. To illustrate the utility of the approach, we apply it to the analysis of a peripheral blood mononucleocyte dataset and discuss several examples of TF networks associated with monocytes and erythrocytes that reveal potential causal relationships among TFs. In summary, DREAMIT provides a useful tool for uncovering potential TF-to-target gene regulatory mechanisms associated with the cell-to-cell transitions predicted by trajectory inference methods.
Cerebrospinal fluid reference proteins increase accuracy and interpretability of biomarkers for brain diseases
Authors: Karlsson Linda , Vogel Jacob , Arvidsson Ida , Åström Kalle , Janelidze Shorena , Blennow Kaj , Palmqvist Sebastian , Stomrud Erik , Mattsson-Carlgren Niklas , Hansson Oskar 
Published: June 2023

AbstractCerebrospinal fluid (CSF) biomarkers reflect brain pathophysiology and are used extensively in translational research as well as in clinical practice for diagnosis of neurological diseases, e.g., Alzheimer’s disease (AD). However, CSF biomarker concentrations may be influenced by non-disease related mechanisms which vary between individuals, such as CSF production and clearance rates. Here we use a data-driven approach to demonstrate the existence of inter-individual variability in mean CSF protein levels. We show that these non-disease related differences cause many commonly reported CSF biomarkers to be highly correlated, thereby producing misleading results if not accounted for. To adjust for this inter-individual variability, we identified and evaluated high-performing reference proteins which improved the diagnostic accuracy of key CSF AD biomarkers. Our novel reference protein method attenuates the risk for false positive findings, and improves the sensitivity and specificity of CSF biomarkers, with broad implications for both research and clinical practice.
Subpopulations of corticotropin-releasing factor containing neurons and internal circuits in the chicken central extended amygdala
Authors: Pross Alessandra , Metwalli Alek H. , Abellán Antonio , Desfilis Ester , Medina Loreta 
Published: June 2023

AbstractIn mammals, the central extended amygdala is critical for regulation of the stress response. This regulation is extremely complex, involving multiple subpopulations of GABAergic neurons and complex networks of internal and external connections. Two neuron subpopulations expressing corticotropin-releasing factor (CRF), located in the central amygdala and the lateral bed nucleus of the stria terminalis (BSTL), play key roles in the long-term components of fear learning and in sustained fear responses akin to anxiety. Very little is known on the regulation of stress by the amygdala in non-mammals, hindering efforts for trying to improve animal welfare. In birds, one of the major problems relates to the high evolutionary divergence of the telencephalon, where the amygdala is located. In the present study, we aimed to investigate the presence of CRF neurons of the central extended amygdala in chicken and the local connections within this region. We found two major subpopulations of CRF cells in BSTL and the medial capsular central amygdala of chicken. Based on multiple labeling of CRF mRNA with different developmental transcription factors, all CRF neurons seem to originate within the telencephalon since they express Foxg1, and there are two subtypes with different embryonic origins that express Islet1 or Pax6. In addition, we demonstrated direct projections from Pax6 cells of the capsular central amygdala to BSTL and the oval central amygdala. We also found projections from Islet1 cells of the oval central amygdala to BSTL, which may constitute an indirect pathway for regulation of BSTL output cells. Part of these projections may be mediated by CRF cells, in agreement with expression of CRF receptors in both Ceov and BSTL. Our results show a complex organization of the central extended amygdala in chicken, and open new venues for studying how different cells and circuits regulate stress in these animals.
De novo design of aβ-helix tau protein scaffold: An oligomer-selective vaccine immunogen candidate for Alzheimer’s disease
Authors: Aina Adekunle , Hsueh Shawn C.C. , Gibbs Ebrima , Peng Xubiao , Cashman Neil R. , Plotkin Steven S. 
Published: June 2023

AbstractTau pathology is associated with many neurodegenetive disorders, including Alzheimer’s disease (AD), where the spatio-temporal pattern of tau neurofibrillary tangles strongly correlates with disease progression, which motivates therapeutics selective for misfolded tau. Here, we introduce a new avidity-enhanced, multi-epitope approach for protein misfolding immunogen design, which is predicted to mimic the conformational state of an exposed epitope in toxic tau oligomers. A predicted oligomer-selective tau epitope343KLDFK347was scaffolded by designing aβ-helix structure that incorporated multiple instances of the 16-residue tau fragment339VKSEKLDFKDRVQSKI354. Largescale conformational ensemble analyses involving Jensen-Shannon Divergence and the embedding depth 𝒟 showed that the multi-epitope scaffolding approach, employed in designing theβ-helix scaffold, was predicted to better discriminate toxic tau oligomers than other “monovalent” strategies utilizing a single instance of an epitope for vaccine immunogen design. Using Rosetta, 10,000 sequences were designed and screened for the linker portions of theβ-helix scaffold, along with a C-terminal stabilizingα-helix that interacts with the linkers, to optimize the folded structure and stability of the scaffold. Structures were ranked by energy, and the lowest 1% (82 unique sequences) were verified using AlphaFold. Several selection criteria involving AlphaFold are implemented to obtain a lead designed sequence. The structure was further predicted to have free energetic stability by using Hamiltonian replica exchange molecular dynamics (MD) simulations. The synthesizedβ-helix scaffold showed direct binding in surface plasmon resonance (SPR) experiments to several antibodies that were raised to the structured epitope using a designed cyclic peptide. Moreover the strength of binding of these antibodies toin vitrotau oligomers correlated with the strength of binding to theβ-helix construct, suggesting that the construct presents an oligomer-like conformation and may thus constitute an effective oligomer-selective immunogen.
Overburdened Ferroptotic Stress Impairs Tooth Morphogenesis
Authors: Wang H.S. , Wang X.F. , Huang L.Y. , Wang C.L. , Yu F.Y. , Ye L. 
Published: June 2023

AbstractThe role of regulated cell death (RCD) in organ development, particularly the impact of non-apoptotic cell death, remains largely uncharted. Ferroptosis, a non-apoptotic cell death pathway known for its iron dependence and lethal lipid peroxidation, is currently being rigorously investigated for its pathological functions. The balance between ferroptotic stress (iron and iron-dependent lipid peroxidation) and ferroptosis supervising pathways (anti-lipid peroxidation systems) serves as the key mechanism regulating the activation of ferroptosis. Comparing to other forms of regulated necrotic cell death (RNCD), ferroptosis is critically related to the metabolism of lipid and iron which are also important in organ development. In our study, we examined the role of ferroptosis in organogenesis using anex vivotooth germ culture model, investigating the presence and impact of ferroptotic stress on tooth germ development. Our findings revealed that ferroptotic stress increased during tooth development, while the expression of Gpx4, a crucial anti-lipid peroxidation enzyme, also escalated in dental epithelium/mesenchyme cells. The inhibition of ferroptosis was found to partially rescue erastin-impaired tooth morphogenesis. Our results suggest that while ferroptotic stress is present during tooth organogenesis, its effects are efficaciously controlled by the subsequent upregulation of Gpx4. Notably, an overabundance of ferroptotic stress, as induced by erastin, suppresses tooth morphogenesis.
A novel sorting signal for RNA packaging into small extracellular vesicles
Authors: Oka Yuma , Tanaka Kosei , Kawasaki Yuki 
Published: June 2023

AbstractExtracellular vesicles (EVs) play a critical role in the transport of functional RNAs to target recipient cells in numerous physiological processes. The RNA profiles present in EVs differed significantly from those in the originating cells, suggesting selective and active loading of specific RNAs into EVs. Small EVs (sEVs) obtained by stepwise ultracentrifugation have been reported to contain non-sEV components. Analysis of sEVs separated from non-sEVs components revealed that microRNAs may not be released by sEVs. This has raised interest in other RNA types, such as mRNA, which may be functional molecules released by sEVs. However, the molecular mechanisms underlying selective loading of mRNA into sEVs remain unclear. Here, we show that the part of 3’ untranslated region (UTR) sequence ofRAB13selectively enriches RNA in sEVs and serves as an RNA signal for loading into sEVs. Our results demonstrate thatRAB13is the most enriched RNA in sEVs, and this enrichment is primarily driven by its 3’UTR sequence. These findings highlight the potential of theRAB133’UTR sequence as an RNA signal that enables the loading of target RNA into sEVs. This technology has the potential to improve EV-based drug delivery and other applications.
Innate immune responses yield tissue-specific bottlenecks that scale with pathogen dose
Authors: Hullahalli Karthik , Dailey Katherine G. , Waldor Matthew K. 
Published: June 2023

AbstractTo cause infection, pathogens must overcome bottlenecks imposed by the host immune system. These bottlenecks restrict the inoculum and largely determine whether pathogen exposure results in disease. Infection bottlenecks therefore quantify the effectiveness of immune barriers. Here, using a model ofEscherichia colisystemic infection, we identify bottlenecks that tighten or widen with higher inoculum sizes, revealing that the efficacy of innate immune responses can increase or decrease with pathogen dose. We term this concept “dose scaling”. DuringE. colisystemic infection, dose scaling is tissue specific, dependent on the LPS receptor TLR4, and can be recapitulated by mimicking high doses with killed bacteria. Scaling is therefore due to sensing of pathogen molecules rather than interactions between the host and live bacteria. We propose that dose scaling quantitatively links innate immunity with infection bottlenecks and is a valuable framework for understanding how the inoculum size governs the outcome of pathogen exposure.
Prediction of Heart Disease and Survivability using Support Vector Machine and Naive Bayes Algorithm
Authors: Patel Tanvi S. , Patel Daxesh P. , Sanyal Mallika , Shrivastav Pranav S. 
Published: June 2023

AbstractPurposeIn the present work, we examined the outcomes and accuracy of the Support vector machine (SVM) and the Naive Bayes algorithms on a dataset, to predict whether the patient has heart disease or not, and the patient’s survival prediction status.MethodThe machine learning procedures were developed using the clinically validated datasets with sixteen attributes from the University of California, Irvine’s Centre for Machine Learning, and Intelligent Systems. Confusion matrix was used to visualise the accuracy, recall, precision, and error of the models. Statistical analysis was done to prove the model accuracy using the receiver operating characteristic (ROC) curve and area under the curve (AUC).ResultsThe proposed method of heart disease prediction using Naïve Bayes had 87 % accuracy. The accuracy for heart survivability models using SVM and Naïve Bayes were 88 % and 93 %. The model efficiency for heart survivability using ROC curve with AUC 0.93 for Naïve Bayes and AUC 0.91 for SVM.ConclusionSuch prediction systems can help the medical sector to save energy, cost, and time by providing more efficient techniques to forecast decisions with high accuracy. This study will enable the statisticians and researchers to select more efficient and accurate machine learning algorithms to achieve better prediction of the “cardiovascular disease”.
Enhancing the antibacterial function of probioticEscherichia coliNissle: when less is more
Authors: Bartram Emma , Asai Masanori , Gabant Philippe , Wigneshweraraj Sivaramesh 
Published: June 2023

ABSTRACTProbiotic bacteria confer multiple health benefits, including preventing the growth, colonisation, or carriage of harmful bacteria in the gut. Bacteriocins are antibacterial peptides produced by diverse bacteria and their production is tightly regulated and coordinated at the transcriptional level. A popular strategy for enhancing the antibacterial properties of probiotic bacteria is to retrofit them with the ability to overproduce heterologous bacteriocins. This is often achieved from non-native constitutive promoters or in response to host or pathogen signal from synthetic promoters. How the dysregulated overproduction of heterologous bacteriocins affects the fitness and antibacterial efficacy of the retrofitted probiotic bacteria is often overlooked. We have conferred the prototypical probioticEscherichia colistrain Nissle (EcN) the ability to produce McC from the wild-type promoter and two mutant promoters that allow, relative to the wild-type promoter, high and low amounts of McC production. This was done by introducing specific changes to the sequence of the wild-type promoter driving transcription of the McC operon, whilst ensuring that the modified promoters respond to native regulation. By studying the transcriptomic responses and antibacterial efficacy of the retrofitted EcN bacteria in aGalleria mellonellainfection model of enterohemorrhagicE. coli, we show that EcN bacteria that produce the lowest amount of McC display the highest antibacterial efficacy with little to none undesired collateral impact on their fitness. The results highlight considerations researchers may take into account when retrofitting probiotic bacteria with heterogenous gene products for therapeutic, prophylactic or diagnostic applications.IMPORTRANCEBacteria that resist killing by antibiotics are a major risk to modern medicine. The use of beneficial ‘probiotic’ bacteria as chassis to make antibiotic-like compounds at the site of infection in the body is emerging as a popular alternative to the use of conventional antibiotics. A potential drawback of engineering probiotic bacteria in this way is that producing antibiotic-like compounds could impart undesired side-effects on the performance of such bacteria and thereby compromise their intended use. This study highlights considerations researchers may take into account when engineering probiotic bacteria for therapeutic, prophylactic or diagnostic applications.