bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and validation of artificial intelligence-based algorithms for predicting the segments debulked by rotational atherectomy using intravascular ultrasound
Authors: Hashimoto Kenta , Fujii Kenichi , Ueda Daiju , Sumiyoshi Akinori , Hasegawa Katsuyuki , Fukuhara Rei , Otagaki Munemitsu , Okamura Atsunori , Yamamoto Wataru , Kawano Naoki , Yamamoto Akira , Miki Yukio , Shiojima Iichiro 
Published: November 2023

AbstractBackgroundAlthough rotation atherectomy (RA) is a useful technique for severely calcified lesions, patients undergoing RA show a greater incidence of catastrophic complications, such as coronary perforation. Therefore, prior to the RA procedure, it is important to predict which regions of the coronary plaque will be debulked by RA.ObjectivesWe develop and evaluate an artificial intelligence–based algorithm that uses pre-RA intravascular ultrasound (IVUS) images to automatically predict regions debulked by RAMethodsA total of 2106 IVUS cross-sections from 60 patients with de novo severely calcified coronary lesions who underwent IVUS-guided RA were consecutively collected. The two identical IVUS images of pre-and post-RA were merged, and the orientations of the debulked segments identified in the merged images are marked on the outer circle of each IVUS image. The artificial intelligence model was developed based on ResNet (deep residual learning for image recognition). The architecture connected 36 fully connected layers, each corresponding to one of the 36 orientations segmented every 10°, to a single feature extractor.ResultsIn each cross-sectional analysis, our artificial intelligence model achieved an average sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of 81%, 72%, 46%, 90%, and 75%, respectively.ConclusionsThe artificial intelligence–based algorithm can use information from pre-RA IVUS images to accurately predict regions debulked by RA. The proposed method will assist interventional cardiologists in determining the treatment strategies for severely calcified coronary lesions.
A CRISPR interference system for the nitrogen-fixing bacteriumAzotobacter vinelandii
Authors: Russell Steven J. , Garcia Amanda K. , Kaçar Betül 
Published: November 2023

ABSTRACTA grand challenge for the next century can be found in mitigating the effects of changing climate through bioengineering solutions. Biological nitrogen fixation, the globally consequential, nitrogenase-catalyzed reduction of atmospheric nitrogen to bioavailable ammonia, is a particularly vital area of focus. Nitrogen fixation engineering relies upon extensive understanding of underlying genetics in microbial models, including the broadly utilized gammaproteobacterium,Azotobacter vinelandii(A. vinelandii). Here we report the first CRISPR interference (CRISPRi) system for targeted gene silencing inA. vinelandiithat integrates genomically via site-specific transposon insertion. We demonstrate that CRISPRi can repress transcription of an essential nitrogen fixation gene by ∼60%. Further, we show that nitrogenase genes are suitably expressed from the transposon insertion site, indicating that CRISPRi and engineered nitrogen fixation genes can be co-integrated for combinatorial studies of gene expression and engineering. Our established CRISPRi system extends the utility ofA. vinelandiiand will aid efforts to engineer microbial nitrogen fixation for desired purposes.For Table of Contents Only
The five homologous CiaR-controlled Ccn sRNAs ofStreptococcus pneumoniaemodulate Zn-resistance
Authors: De Lay Nicholas R. , Verma Nidhi , Sinha Dhriti , Garrett Abigail , Osterberg Maximillian K. , Reiling Spencer , Porter Daisy , Giedroc David P. , Winkler Malcolm E. 
Published: November 2023

ABSTRACTZinc is a vital transition metal forStreptococcus pneumoniae, but is deadly at high concentrations. InS. pneumoniae, elevated intracellular free Zn levels result in mis-metallation of key Mn-dependent metabolic and superoxide detoxifying enzymes resulting in Zn intoxication. Here, we report our identification and characterization of the function of the five homologous, CiaRH-regulated Ccn sRNAs in controllingS. pneumoniaevirulence and metal homeostasis. We show that deletion of all fiveccngenes (ccnA,ccnB,ccnC,ccnD, andccnE) fromS. pneumoniaestrains D39 (serotype 2) and TIGR4 (serotype 4) causes Zn hypersensitivity and an attenuation of virulence in a murine invasive pneumonia model. We provide evidence that bioavailable Zn disproportionately increases inS. pneumoniaestrains lacking the fiveccngenes. Consistent with a response to Zn intoxication or relatively high intracellular free Zn levels, expression of genes encoding the CzcD Zn exporter and the Mn-independent ribonucleotide reductase, NrdD-NrdG, were increased in the ΔccnABCDEmutant relative to its isogenicccn+parent strain. The growth inhibition by Zn that occurs as the result of loss of theccngenes is rescued by supplementation with Mn or OxyraseTM, a reagent that removes dissolved oxygen. Lastly, we found that the Zn-dependent growth inhibition of the ΔccnABCDEstrain was not altered by deletion ofsodA, whereas theccn+ΔsodAstrain phenocopied the ΔccnABCDEstrain. Overall, our results indicate that the Ccn sRNAs have a crucial role in preventing Zn intoxication inS. pneumoniae.AUTHOR SUMMARYZn and Mn are essential micronutrients for many bacteria, includingStreptococcus pneumoniae. While Zn performs vital structural or catalytic roles in certain proteins, in excess, Zn can inhibit Mn uptake byS. pneumoniaeand displace, but not functionally replace Mn from key enzymes including superoxide dismutase A (SodA). Here, we show that the Ccn small regulatory RNAs promoteS. pneumoniaeresistance to Zn intoxication. Furthermore, we demonstrate that these small regulatory RNAs modulate the ability ofS. pneumoniaeto cause invasive pneumonia. Altogether, these findings reveal a new layer of regulation ofS. pneumoniaeZn homeostasis and suggest that there are factors in addition to known transporters that modulate intracellular, bioavailable Zn levels.
Craniofacial studies in chicken embryos confirm the pathogenicity of Frizzled2 variants associated with Robinow syndrome
Authors: Tophkhane Shruti S. , Fu Katherine , Verheyen Esther M. , Richman Joy M. 
Published: November 2023

ABSTRACTRobinow syndrome (RS) is a rare disease caused by mutations in seven WNT pathway genes. Features include craniofacial widening and jaw hypoplasia. We used the chicken embryo to test two autosomal dominant RS (ADRS) missenseFZD2variants on the frontonasal mass, the affected region in RS. The wild-type (wt) and variant hFZD2inhibited beak ossification. The bone hypoplasia was possibly mediated by decreased levels of WNT and BMP pathway genes. In primary cultures, hFZD2variants inhibited chondrogenesis, increased nuclear shuttling of β-catenin and increased expression of TWIST1, both known to suppress chondrogenesis. In luciferase reporter assays, proteins coding for1301G>Tand425C>TFZD2 variants weakly activated canonical WNT reporter and dominantly interfered with wtFZD2. In the JNK-PCP WNT pathway luciferase assay, only the425C>Tshowed a loss-of-function. The 1301G>T variant presumably acts through a JNK-independent pathway. This is the first study to demonstrate that the ADRS-FZD2missense variants cause craniofacial and WNT signaling defects. Frontonasal mass width is increased by both hFZD2variants which sheds light on the ontogeny of the broad facial features seen in individuals with RS.Summary StatementGain-of-function studies onFZD2missense variants associated with Robinow syndrome led to increased facial width, altered Wnt signaling and inhibition of beak skeletogenesis in chicken embryos.
Integrative learning of disentangled representations from single-cell RNA-sequencing datasets
Authors: Novella-Rausell Claudio , Peters D.J.M , Mahfouz Ahmed 
Published: November 2023

AbstractSingle-cell RNA-sequencing is instrumental in studying cellular diversity in biological systems. Using batch correction methods, cell identities are often jointly defined across multiple conditions, individuals, or modalities. These approaches overlook group-specific information and require either paired data or matching features across datasets. Here we present shared-private Variational Inference via Product of Experts with Supervision (spVIPES), a framework to analyze the shared and private components of unpaired groups of cells with non-matching features. spVIPES represents the cells from the different groups as a composite of private and shared factors of variation using a probabilistic latent variable model. We evaluate the performance of spVIPES with a simulated dataset and apply our model in three different scenarios: (i) cross-species comparisons, (ii) regeneration following long and short acute kidney injury, and (iii) IFN-βstimulation of PMBCs. In our study, we demonstrate that spVIPES accurately disentangles distinct sources of variation into private and shared representations while matching current state-of-the-art methods for batch correction. Furthermore, spVIPES’ shared space outperforms alternatives models at learning cell identities across datasets with non-matching features. We implemented spVIPES using thescvi-toolsframework and release it as an open-source software athttps://github.com/nrclaudio/spVIPES.
Bacteriophages from human skin infecting coagulase-negativeStaphylococcus:diversity, novel species and host resistance
Authors: Alsaadi Samah E. , Lu Hanshuo , Zhang Minxing , Dykes Gregory F. , Allison Heather E. , Horsburgh Malcolm J. 
Published: November 2023

AbstractThe human skin microbiome comprises diverse populations that differ temporally between body sites and individuals. The virome is a less studied component of the skin microbiome and the study of bacteriophages is required to increase knowledge of the modulation and stability of bacterial communities.Staphylococcusspecies are among the most abundant colonisers of skin and are associated with both health and disease yet the bacteriophages infecting the most abundant species on skin are less well studied. Here, we report the isolation and genome sequencing of 40 bacteriophages from human skin swabs that infect coagulase-negativeStaphylococcus(CoNS) species, which extends our knowledge of phage diversity. Six genetic clusters of phages were identified with two clusters representing novel phage species, one of which we characterise and name Alsa phage. We identified that Alsa phages have a greater ability to infect the speciesS. hoministhat was otherwise infected less than other CoNS species by the isolated phages, indicating an undescribed barrier to phage infection that could be in part due to numerous restriction-modification systems. The extended diversity ofStaphylococcusphages here enables further research to define their contribution to skin microbiome research and the mechanisms that limit phage infection.
Astrocyte-to-microglia communication via Sema4B-Plexin-B2 modulates injury-induced reactivity of microglia
Authors: Casden Natania , Belzer Vitali , Elkhayari Abdellatif , Elfatimy Rachid , Behar Oded 
Published: November 2023

AbstractAfter central nervous system injury, a rapid cellular and molecular response is induced. This response can be both beneficial and detrimental to neuronal survival in the first few days and increases the risk for neurodegeneration if persistent. Semaphorin4B (Sema4B), a transmembrane protein primarily expressed by cortical astrocytes, has been shown to play a role in neuronal cell death following injury. Our study shows that after cortical stab wound injury, cytokine expression is attenuated in Sema4B knockout mice and microglia/macrophage reactivity is altered.In vitro, Sema4B enhances the reactivity of microglia following injury, suggesting astrocytic Sema4B functions as a ligand. Moreover, injury-induced microglia reactivity is attenuated in the presence of Sema4B knockout astrocytes compared to heterozygous astrocytes.In vitro, experiments indicate Plexin-B2 is the Sema4B receptor on microglia. Consistent with this, in microglia/macrophage-specific Plexin-B2 knockout mice, similar to Sema4B knockout mice, microglial/macrophage reactivity and neuronal cell death are attenuated after cortical injury. Finally, in Sema4B/Plexin-B2 double heterozygous mice, microglial/macrophage reactivity is also reduced after injury, thus supporting the idea that both Sema4B and Plexin-B2 are part of the same signaling pathway. Taken together, we propose a model in which following injury, astrocytic Sema4B enhances the response of microglia/macrophages via Plexin-B2, leading to increased reactivity.Significance statementIn this study, we show that in the brain cortex, Sema4B, a protein mainly expressed by astrocytes, plays a crucial role in enhancing the reactivity of microglia/macrophages via Plexin-B2. These findings reveal new molecular signaling instigated by astrocytes toward microglia/macrophages in the context of central nervous system (CNS) injury, shedding new light on the complex interplay between astrocytes and microglia/macrophages. Taken together, our findings suggest that targeting the Sema4B/Plexin-B2 pathway could be a promising therapeutic approach for reducing microglia reactivity and improving the adaptive response in the context of CNS injury.
Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics
Authors: Waman Vaishali P. , Ashford Paul , Lam Su Datt , Sen Neeladri , Abbasian Mahnaz , Woodridge Laurel , Goldtzvik Yonathan , Bordin Nicola , Wu Jiaxin , Sillitoe Ian , Orengo Christine A 
Published: November 2023

AbstractThe COVID-19 disease is an ongoing global health concern. Although vaccination provides some protection, people are still susceptible to re-infection. Ostensibly, certain populations or clinical groups may be more vulnerable. Factors causing these differences are unclear and whilst socioeconomic and cultural differences are likely to be important, human genetic factors could influence susceptibility. Experimental studies indicate SARS-CoV-2 uses innate immune suppression as a strategy to speed-up entry and replication into the host cell. Therefore, it is necessary to understand the impact of variants in immunity-associated human proteins on susceptibility to COVID-19.In this work, we analysed missense coding variants in several SARS-CoV-2 proteins and its human protein interactors that could enhance binding affinity to SARS-CoV-2. We curated a dataset of 19 SARS-CoV-2: human protein 3D-complexes, from the experimentally determined structures in the Protein Data Bank and models built using AlphaFold2-multimer, and analysed impact of missense variants occurring in the protein-protein interface region. We analysed 468 missense variants from human proteins and 212 variants from SARS-CoV-2 proteins and computationally predicted their impacts on binding affinities to SARS-CoV-2 proteins, using 3D-complexes.We predicted a total of 26 affinity-enhancing variants from 14 human proteins implicated in increased binding affinity to SARS-CoV-2. These include key-immunity associated genes (TOMM70, ISG15, IFIH1, IFIT2, RPS3, PALS1, NUP98, RAE1, AXL, ARF6, TRIMM, TRIM25) as well as important spike receptors (KREMEN1, AXL and ACE2). We report both common (e.g., Y13N in IFIH1) and rare variants in these proteins and discuss their likely structural and functional impact, using information on known and predicted functional sites. Potential mechanisms associated with immune suppression implicated by these variants are discussed.Occurrence of certain predicted affinity-enhancing variants should be monitored as they could lead to increased susceptibility and reduced immune response to SARS-CoV-2 infection in individuals/populations carrying them. Our analyses aid in understanding the potential impact of genetic variation in immunity-associated proteins on COVID-19 susceptibility and help guide drug-repurposing strategies.
Unravelling the Role ofCandida albicansPrn1 in the Oxidative Stress Response Through a Proteomic Approach
Authors: Arribas Víctor , Monteoliva Lucía , Hernáez María Luisa , Gil Concha , Molero Gloria 
Published: November 2023

AbstractCandida albicansPrn1 is a protein that shares similarities with mammalian Pirin but with an unknown function in the yeast. Orthologues of Prn1 have been identified in other pathogenic fungi but not inSaccharomyces cerevisiae, suggesting a relationship with pathogenesis. Prn1 increase in abundance after H2O2treatment has been shown previously, thus, in the present work,C. albicans prn1Δmutant and the corresponding wild-type strain SN250 have been treated with H2O2and their response was studied by quantitative differential proteomics. These assays indicated a lower increase of proteins with oxidoreductase activity after treatment in theprn1Δstrain compared to the wild type, as well as an increase in proteasome-activating proteins and a decrease in translation-involved proteins. Accordingly, Prn1 absence, under H2O2treatment, led to a lower survival rate and a higher percentage of apoptosis, together with higher reactive oxygen species levels and higher proteasome activity. Besides, remarkable differences in the abundance of some transcription factors were observed between the two strains. Mnl1, involved in Prn1 expression, Bas1, Tiff33, and orf19.1150 presented an inverse pattern of expression under H2O2treatment respect to Nrg1, a Mnl1 antagonist. Interestingly, orf19.4850, a protein orthologue toS. cerevisiaeCub1, has shown to be involved in the response to H2O2presenting a conserved proteasome function. Under basal conditions, the proteomics results indicate a possible involvement of Prn1 in mitochondrial oxidative stress detoxication. Our experiments confirm Prn1 as a relevant actor in the oxidative response.ImportanceCandida albicansis a human opportunistic pathogen included in the WHO fungal priority pathogens list. The increase in resistant strains necessitates the discovery of new targets for antifungal therapies. Our research sheds light on the important role of the previously uncharacterizedC. albicansprotein Prn1 during the oxidative stress response. Study of the proteome remodelling under oxidative stress unveils the role of Prn1 in the decreased reactive oxygen species levels and the consequences, such as death by apoptosis and necrosis or cell growth delay. A proteomics approach allowed the identification of several proteins potentially involved in Prn1 activity, such as oxidoreductases and transcription factors. The lack of Prn1 orthologues inSaccharomyces cerevisiaebut the presence in otherCandidaandAspergillusspecies implicates this protein in pathogenesis and suggests that it may serve as a candidate for new drug targets.
Single-cell transcriptomic and genomic changes in the aging human brain
Authors: Jeffries Ailsa M. , Yu Tianxiong , Ziegenfuss Jennifer S. , Tolles Allie K. , Kim Yerin , Weng Zhiping , Lodato Michael A. 
Published: November 2023

AbstractAging brings dysregulation of various processes across organs and tissues, often stemming from stochastic damage to individual cells over time. Here, we used a combination of single-nucleus RNA-sequencing and single-cell whole-genome sequencing to identify transcriptomic and genomic changes in the prefrontal cortex of the human brain across life span, from infancy to centenarian. We identified infant-specific cell clusters enriched for the expression of neurodevelopmental genes, and a common down-regulation of cell-essential homeostatic genes that function in ribosomes, transport, and metabolism during aging across cell types. Conversely, expression of neuron-specific genes generally remains stable throughout life. We observed a decrease in specific DNA repair genes in aging, including genes implicated in generating brain somatic mutations as indicated by mutation signature analysis. Furthermore, we detected gene-length-specific somatic mutation rates that shape the transcriptomic landscape of the aged human brain. These findings elucidate critical aspects of human brain aging, shedding light on transcriptomic and genomics dynamics.
Kaposi’s sarcoma-associated herpesvirus (KSHV) gB dictates a low-pH endocytotic entry pathway as revealed by a dual-fluorescent virus system and a rhesus monkey rhadinovirus expressing KSHV gB
Authors: Schlagowski Sarah , Großkopf Anna K. , Liu Shanchuan , Khizanishvili Natalia , Scribano Stefano , Ensser Armin , Hahn Alexander S. 
Published: November 2023

ABSTRACTInteraction with host cell receptors initiates internalization of Kaposi’s sarcoma-associated herpesvirus (KSHV) particles via endocytosis or macropinocytosis. Fusion of viral and host cell membranes, which is followed by release of the viral capsid into the cytoplasm, is executed by the core fusion machinery composed of gH, gL, and gB, that is common to all herpesviruses. KSHV infection has been shown to be sensitive to inhibitors of vacuolar acidification, suggestive of low pH as a fusion trigger.To analyze KSHV entry at the single particle level we developed single- and dual-fluorescent recombinant KSHV strains that incorporate tagged glycoproteins, capsid proteins or a combination thereof. In addition, we generated a hybrid rhesus monkey rhadinovirus (RRV) that expresses KSHV gB in place of RRV gB to analyze gB-dependent differences in infection pathways.Our data demonstrate lytic reactivation and infectivity of dual-fluorescent KSHV and incorporation of fluorescently-tagged proteins into viral particles. Confocal microscopy was used to quantify co-localization of fluorescently-tagged glycoproteins and capsid proteins. By using the ratio of dual-positive KSHV particles to single-positive capsids as an indicator of fusion events we established the KSHV fusion kinetics upon infection of different target cells.We measured marked differences in the “time-to-fusion” between different cell types. Inhibition of vesicle acidification prevented virus-cell fusion, implicating low vesicle pH as a requirement for the KSHV fusion step. These findings were corroborated by comparison of RRV-YFP reporter virus with wildtype gB and RRV-YFP encoding KSHV gB in place of RRV gB. While RRV wt infection of receptor-overexpressing cells was unaffected by inhibition of vesicle acidification, RRV-YFP expressing KSHV gB was sensitive to Bafilomycin A1, an inhibitor of vacuolar acidification.Single- and dual-fluorescent KSHV strains eliminate the need for virus-specific antibodies and enable the tracking of single viral particles during entry and fusion. Together with a hybrid RRV expressing KSHV gB, these two novel tools identify low vesicle pH as an endocytotic trigger for KSHV membrane fusion.
New tools reveal PCP-dependent polarized mechanics in the cortex and cytoplasm of single cells during convergent extension
Authors: Weng Shinuo , Devitt Caitlin C. , Nyaoga Bill M. , Havnen Anna E. , Alvarado José , Wallingford John B. 
Published: November 2023

AbstractUnderstanding biomechanics of biological systems is crucial for unraveling complex processes like tissue morphogenesis. However, current methods for studying cellular mechanicsin vivoare limited by the need for specialized equipment and often provide limited spatiotemporal resolution. Here we introduce two new techniques, Tension by Transverse Fluctuation (TFlux) andin vivomicrorheology, that overcome these limitations. They both offer time-resolved, subcellular biomechanical analysis using only fluorescent reporters and widely available microscopes. Employing these two techniques, we have revealed a planar cell polarity (PCP)-dependent mechanical gradient both in the cell cortex and the cytoplasm of individual cells engaged in convergent extension. Importantly, the non-invasive nature of these methods holds great promise for its application for uncovering subcellular mechanical variations across a wide array of biological contexts.SummaryNon-invasive imaging-based techniques providing time-resolved biomechanical analysis at subcellular scales in developing vertebrate embryos.