bluuebunny/crossref_metadata_2025_split huggingface dataset:
AutoCumulus: an Automated Mammographic Density Measure Created Using Artificial Intelligence
Authors: Al-qershi Osamah , Nguyen Tuong L , Elliott Michael S , Schmidt Daniel F , Makalic Enes , Li Shuai , Fox Samantha K , Dowty James G , Peña-Solorzano Carlos A , Kwok Chun Fung , Chen Yuanhong , Wang Chong , Lippey Jocelyn , Brotchie Peter , Carneiro Gustavo , McCarthy Davis J , Jeong Yeojin , Sung Joohon , Frazer Helen ML , Hopper John L 
Published: February 2024

AbstractBackgroundMammographic (or breast) density is an established risk factor for breast cancer. There are a variety of approaches to measurement including quantitative, semi-automated and automated approaches. We present a new automated measure, AutoCumulus, learnt from applying deep learning to semi-automated measures.MethodsWe used mammograms of 9,057 population-screened women in the BRAIx study for which semi-automated measurements of mammographic density had been made by experienced readers using the CUMULUS software. The dataset was split into training, testing, and validation sets (80%, 10%, 10%, respectively). We applied a deep learning regression model (fine-tuned ConvNeXtSmall) to estimate percentage density and assessed performance by the correlation between estimated and measured percent density and a Bland-Altman plot. The automated measure was tested on an independent CSAW-CC dataset in which density had been measured using the LIBRA software, comparing measures for left and right breasts, sensitivity for high sensitivity, and areas under the receiver operating characteristic curve (AUCs).ResultsBased on the testing dataset, the correlation in percent density between the automated and human measures was 0.95, and the differences were only slightly larger for women with higher density. Based on the CSAW-CC dataset, AltoCumulus outperformed LIBRA in correlation between left and right breast (0.95 versus 0.79; P<0.001), specificity for 95% sensitivity (13% versus 10% (P<0.001)), and AUC (0.638 cf. 0.597; P<0.001).ConclusionWe have created an automated measure of mammographic density that is accurate and gives superior performance on repeatability within a woman, and for prediction of interval cancers, than another well-established automated measure.
Dietary Sodium and Potassium Patterns in Adults with Food Insecurity in the Context of Hypertension Risk
Authors: Onugha Elizabeth A. , Banerjee Ankona , Vimalajeewa Horahenage D. , Nobleza Kenneth J. , Nguyen Duc T. , Racette Susan B. , Dave Jayna M. 
Published: February 2024

AbstractBackgroundFood insecurity (FIS), characterized by the lack of consistent access to nutritious food, is associated with hypertension and adverse health outcomes. Despite evidence of a higher prevalence of hypertension (HTN) in patients living with FIS, there is limited data exploring the underlying mechanism.MethodsWe conducted a cross-sectional analysis of 17,015 adults aged 18-65 years, using dietary recall data from the National Health and Nutrition Examination Survey (2011-2018). Univariate and multivariable analyses were used to examine the association between FIS, HTN, and dietary sodium and potassium levels.ResultsIndividuals reporting FIS had a significantly lower mean intake of potassium (2.5±0.03 gm) compared to those in food-secure households (2.74±0.02 gm). No significant difference was found in the mean dietary sodium intake based on food security status. Non-Hispanic Black participants showed a high prevalence of HTN and FIS. While Non-Hispanic White and Hispanic participants had a high prevalence of FIS, it did not appear to influence their risk of HTN.ConclusionsAdults with FIS and HTN were more likely to report a lower dietary potassium intake. Increasing access to healthy foods, particularly potassium-rich foods, for individuals facing FIS, may contribute to reducing the HTN prevalence and improving cardiovascular outcomes.
Scalable single-cell pooled CRISPR screens with conventional knockout vector libraries
Authors: Islam Mirazul , Yang Yilin , Simmons Alan J. , Xu Yanwen , Fisher Emilie L. , Deng Wentao , Grieb Brian C , Molina Paola , de Caestecker Christian , Ramirez-Solano Marisol A. , Liu Qi , Tansey William P. , Macara Ian G. , Rathmell Jeffrey C. , Coffey Robert J. , Lau Ken S. 
Published: February 2024

AbstractCurrent methods for single-cell RNA profiling of pooled CRISPR screens are limited, either by indirect capture of single guide RNAs (sgRNAs) or by custom modification of plasmid libraries. Here, we present a direct sgRNA capture platform called Native sgRNA Capture and sequencing (NSC-seq) that enables single-cell CRISPR screens using common knockout plasmid libraries, facilitating genotype-phenotype mapping at multiple scalesin vitroandin vivo. Additionally, we characterize sgRNA expression in three whole-genome knockout libraries, revealing a substantial subset of truncated (isoform) spacer reads. We provide this dataset as a reference of expressed sgRNA isoforms that may potentially have compromised CRISPR gene editing efficacy and precision.
A hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data
Authors: Cheng Youshu , Cai Biao , Li Hongyu , Zhang Xinyu , D’Souza Gypsyamber , Shrestha Sadeep , Edmonds Andrew , Meyers Jacquelyn , Fischl Margaret , Kassaye Seble , Anastos Kathryn , Cohen Mardge , Aouizerat Bradley E , Xu Ke , Zhao Hongyu 
Published: February 2024

AbstractBackgroundMethylation Quantitative Trait Loci (meQTLs) are chromosomal regions that harbor genetic variants affecting DNA methylation levels. The identification of meQTLs can be accomplished through quantifying the effects of single nucleotide polymorphisms (SNPs) on DNA methylation levels, and these inferred meQTLs can shed light on the complex interplay between the genome and methylome. However, most meQTL studies to date utilize bulk methylation datasets composed of different cell types that may have distinct methylation patterns in each cell type. Current technological challenges hinder the comprehensive collection of large-scale, cell-type-specific (CTS) methylation data, which limits our understanding of CTS methylation regulation. To address this challenge, we propose a hierarchical Bayesian interaction model (HBI) to infer CTS meQTLs from bulk methylation data.ResultsOur HBI method integrates bulk methylations data from a large number of samples and CTS methylation data from a small number of samples to estimate CTS meQTLs. Through simulations, we show that HBI improves the estimation (accuracy and power) of CTS genetic effects on DNA methylation. To systematically characterize genome-wide SNP-methylation level associations in multiple cell types, we apply HBI to bulk methylation data measured in peripheral blood mononuclear cells (PBMC) from a cohort of 431 individuals together with flow-sorted cell-derived methylation sequencing (MC-seq) data measured in isolated white blood cells (CD4+ T-cells, CD8+ T-cells, CD16+ monocytes) for 47 individuals. We demonstrate that HBI can identify CTS meQTLs and improve the functional annotation of SNPs.ConclusionsHBI can incorporate strong and robust signals from MC-seq data to improve the estimation of CTS meQTLs. Applying HBI to link the methylome and genome data helps to identify biologically relevant cell types for complex traits.
The long noncoding RNA lnc-FANCI-2 intrinsically restricts RAS signaling and phosphorylation of Akt and Erk in HPV16-infected cervical cancer
Authors: Liu Haibin , Yu Lulu , Majerciak Vladimir , Meyer Thomas , Yi Ming , Johnson Peter F. , Cam Maggie , Lowy Douglas R. , Zheng Zhi-Ming 
Published: February 2024

ABSTRACTWe recently discovered increased expression of a long noncoding RNA, lnc-FANCI-2, coinciding with cervical lesion progression from CIN1, CIN2-3 to cervical cancer. Viral E7 of high-risk HPVs and host transcription factor YY1 are two major factors promoting lnc-FANCI-2 expression. To explore possible roles of lnc-FANCI-2 in HPV-induced cervical carcinogenesis, we ablated the expression oflnc-FANCI-2in the HPV16-positive cervical cancer cell line, CaSki. Knock-out (KO) single cell clones expressed HPV16 oncogenes normally but displayed altered cell morphology when compared with the parental cells. Proteomic profiling of cytosolic and secreted proteins from the parental and KO cells showed that lnc-FANCI-2 regulates expression of a subset of cell surface and adhesion-related proteins, including inhibition of MCAM, PODXL2 and ECM1 and increased levels of ADAM8 and TIMP2. RNA-seq analyses revealed that, relative to the parental cells, KO cells exhibited significantly increased RAS signaling but decreased IFN pathways. In KO cells, phosphorylated Akt and Erk1/2, two important RAS pathway effectors, were increased more than 3-fold, accompanied by increase of IGFBP3, MCAM, VIM, and CCND2 (cyclin D2) and decrease of RAC3. Accordingly, high levels of lnc-FANCI-2 and lower levels of MCAM in cervical cancer patients are associated with improved survival. We found that lnc-FANCI-2 in CaSki cells interacts specifically with 32 host proteins, including H13, HNRH1, K1H1, MAP4K4, and RNPS1, and knockdown of MAP4K4 led to increase phosphorylation of Akt and Erk1/2. In summary, a key function of lnc-FANCI-2 is to intrinsically regulate RAS signaling, thereby affecting cervical cancer outcome.SignificanceExpression of lnc-FANCI-2 is related to cervical lesion progression. Knock-out (KO) or knock-down (KD) of lnc-FANCI-2 expression in HPV16-positive cervical cancer cells CaSki significantly increases RAS signaling, phosphorylation of Akt and Erk1/2, and increase of epithelial mesenchymal transition factors. lnc-FANCI-2 KO also regulates the expression of a subset of cell surface and adhesion-related proteins IGFBP3 and MCAM. A high level of lnc-FANCI-2 and lower level of MCAM in cervical cancer patients are associated with improved survival. lnc-FANCI-2 in CaSki cells interacts specifically with 32 host proteins, including MAP4K4. KD of MAP4K4 expression in CaSki cells led to increase phosphorylation of Akt and Erk1/2. Thus, one lnc-FANCI-2 function is to intrinsically regulate RAS signaling to impact cervical lesion progression.
Genomic and phenotypic studies amongClostridioides difficileisolates show a high prevalence of clade 2 and great diversity in clinical isolates from Mexican adults and children with healthcare-associated diarrhea
Authors: Meléndez Sánchez D , Hernández Laura , Ares Miguel , Méndez Tenorio A , Flores-Luna Lourdes , Torres Javier , Camorlinga-Ponce M 
Published: February 2024

AbstractClostridioides difficileis the most common cause of healthcare-associated infection worldwide. Its pathogenesis is mainly due to the production of toxins A, B, and CDT, whose genetic variants may be associated with disease severity. We studied genetic diversity inC. difficileisolates from hospitalized adults and children using different gene and genome typing methods and investigated their association with in vitro expression of toxins.Whole-genome was sequenced in 39 toxigenicC. difficileisolates and used for multilocus sequence typing (MLST),tcdA, andtcdBtyping sequence type, and for phylogenetic analysis. Strains were grown in broth media, and expression of toxin genes was measured by real-time PCR and cytotoxicity was determined in culture assays.We found that clustering after genome-wide phylogeny followed clade classification, although different clusters were identified within each clade. The toxin profiletcdA+/tcdB+/cdtA+/cdtB+ and clade 2/ST1 were the most prevalent among isolates from children and adults. Isolates presented two TcdA and three TcdB subtypes, of which A2 and B2 were dominant. Toxin gene expression or cytotoxicity were not associated with genotyping or toxin subtypes. In conclusion, genomic and phenotypic analysis shows high diversity amongC. difficileisolates from patients with healthcare-associated-diarrhea.ImportanceClostridioides difficileis a toxin-producing bacterial pathogen associated with healthcare, and different genetic or phenotypic typing have been proposed for classification. We extensively studied cytotoxicity, expression of toxins, whole genome phylogeny, and toxin typing in clinicalC. difficileisolates. Most isolates presented atcdA+ tcdB+cdtA+ cdtB+pattern, with high diversity in cytotoxicity, and clade 2/ST1 was the most prevalent. However, they all had the same TcdA2/TcdB2 toxin subtype. Advances in genomics and bioinformatics tools offer the opportunity to understand the virulence ofC. difficilebetter and find markers with better clinical use.
Antagonizing the SAMD9 pathway is key to myxoma virus host shut-off and immune evasion
Authors: Raza Tahseen , Perterson Erich , Liem Jason , Liu Jia 
Published: February 2024

AbstractPoxviruses have life cycles exclusively in the cytoplasm. However, these viruses can have profound impact to host transcription. One possible mechanism is through viral manipulation of host protein synthesis and such ability is critical for viral immune evasion. Many mammalian poxviruses encode more than one viral protein to interact with the host SAMD9 protein. In myxoma virus (MYXV), a rabbit specific poxvirus and non-pathogenic for other species, viral M062 protein is the lone inhibitor to SAMD9 with broad species specificity and loss ofM062Rin viral genome (ΔM062Rmutant) leads to profound infection defect. We previously found ΔM062Rremodeled transcriptomic landscape in monocytes/macrophages that is associated with the crosstalk between the SAMD9 pathway and cGAS/STING/IRF3 DNA sensing pathway. In this study we completed the characterization of ΔM062Rinfection. We observed that although this replication-defective virus preserved intact early protein synthesis, it failed to conduct host shutoff. Despite a defect in viral DNA replication, ΔM062Rinfection retained intact intermediate protein synthesis comparable to the wildtype virus. Using time course dual RNAseq analyses we found that the overall viral gene transcription profile was mostly indistinguishable from that of the wildtype MYXV. However, the slightly attenuated late RNA synthesis along with the block at viral protein synthesis led to its infection defect. Infection by ΔM062Rin macrophages potentiated the antiviral responses to new danger signals. We provided an initial characterization of such a state in which host antiviral protein synthesis may be promoted leading to the immunological consequence.ImportancePoxviruses utilize multi-faceted strategies to evade and manipulate host immunity. Through targeted gene deletion, we generated useful tools of mutant poxviruses to investigate specific crosstalk between host defense mechanisms. Through studying MYXV M062 protein function, we previously identified SAMD9 as one host target of poxvirusC7Lsuperfamily, in which familyM062Ris one member. However, what kind of cellular outcome caused by ΔM062Rinfection remained unknown. The infection defect of ΔM062Rcaused the induction of host inflammation program is likely due to the activation of the host pathway governed by SAMD9. Because little is known about SAMD9 cellular function and the pathways it regulates, which are important for cellular homeostasis and immune regulation, this study on ΔM062Rinduced effect in host cells will provide new insight on how SAMD9 affects cellular protein synthesis and immunological responses.
αMI-domain of Integrin Mac-1 Binds the Cytokine Pleiotrophin Using Multiple Mechanisms
Authors: Nguyen Hoa , Podolnikova Nataly P. , Ugarova Tatiana P. , Wang Xu 
Published: February 2024

SUMMARYThe integrin Mac-1 (αMβ2, CD11b/CD18, CR3) is an important adhesion receptor expressed on macrophages and neutrophils. Mac-1 is also the most promiscuous member of the integrin family that binds a diverse set of ligands through its αMI-domain. However, the binding mechanism of most ligands is not clear. We have determined the interaction of αMI-domain with the cytokine pleiotrophin (PTN), a cationic protein known to bind αMI-domain and induce Mac-1-mediated cell adhesion and migration. Our data show that PTN’s N-terminal domain binds a unique site near the N- and C-termini of the αMI-domain using a metal-independent mechanism. However, stronger interaction is achieved when an acidic amino acid in a zwitterionic motif in PTN’s C-terminal domain chelates the divalent cation in the metal ion-dependent adhesion site of the active αMI-domain. These results indicate that αMI-domain can bind ligands using multiple mechanisms, and suggest that active αMI-domain prefers acidic amino acids in zwitterionic motifs.HIGHLIGHTSαMI-domain’s interaction with the cytokine pleiotrophin (PTN) was investigated with solution NMR.αMI-domain binds PTN using multiple mechanisms.PTN’s N-terminal domain binds both active and inactive αMI-domains using a unique site near αMI-domain’s termini.PTN’s C-terminal domain binds only active αMI-domain through a metal-dependent interaction.
GSDMD pore formation regulates caspase-4 cleavage to limit IL-18 production in the intestinal epithelium
Authors: Bruce J.K. , Li L. , Tang Y. , Winsor N. , Krustev C. , Keely S. , Philpott D.J. , Girardin S.E. 
Published: February 2024

AbstractEpithelial inflammasomes induce pyroptosis and release cytokines to defend against cytosolic pathogens. However, pyroptosis in epithelial barriers must be carefully regulated to facilitate elimination of infected cells while limiting widespread pyroptosis to preserve the single cell barrier. How epithelial cells achieve this is unknown. In this study, we describe a novel epithelial caspase regulation mechanism. By examining caspase-4 activation in human epithelial cells, we discovered that GSDMD pore formation serves as a signal to terminate caspase-4 activity thus facilitating epithelial cell expulsion while controlling cytokine secretion. Inhibition of epithelial pyroptosis led to IL-18 hyperproduction, likely as a mechanism to combat increased pathogen burden and initiate a wider immune response. Moreover, we demonstrate that full-length, rather than cleaved caspase-4 is active against IL-18 and propose that GSDMD pore formation facilitates cleavage of caspase-4 to terminate its catalytic activity. By comparing human cells and murine epithelial organoids to immune cells, we show that GSDMD pore mediated inhibition of caspase activity is largely specific to epithelial cells. Overall, these studies characterise a novel, epithelial-specific negative feedback loop that modulates inflammasome activity and challenge the dogma that autocatalytic caspase cleavage is required for caspase activity against substrates.Graphical AbstractIn intestinal epithelial cells, caspase activation simultaneously leads to GSDMD pore formation and IL-18 release. GSDMD pore formation provides a signal to terminate caspase activity and limit cytokine production. In GSDMD deficient cells, lack of an inhibition signal leads to caspase mediated IL-18 hyperproduction. Upon cell death this leads to release of massive amounts of IL-18. Created with BioRender.com
A combination of two-enzyme system and enzyme engineering improved the activity of a new PET hydrolase identified from soil bacterial genome
Authors: Mabashi-Asazuma Hideaki , Hirai Makoto , Sakurai Shigeru , Ide Keigo , Kogawa Masato , Matsushita Ai , Hosokawa Masahito , Tsuda Soichiro 
Published: February 2024

AbstractWe here report a novel PET hydrolase originating from a soil microbial genome sequence. This enzyme, bbPET0069, exhibits characteristics resembling a cutinase-like Type I PET-degrading enzyme but lacks disulfide bonds. Notably, bbPET0069 displayed remarkable synergy withCandida antarcticalipase B (CALB), demonstrating rapid and efficient PET degradation. To improve the PET degradation activity of bbPET0069, we employed a three-dimensional (3D) structural modeling to identify mutation sites around its substrate binding domain combined with a protein language model for effective mutation prediction. Through three initial rounds of directed evolution, we achieved a significant enhancement in PET degradation with CALB, resulting in a 12.6-fold increase compared to wild-type bbPET0069 without CALB. We confirmed its PET degradation activity in PET nanoparticles and films, and our proposed approach enabled efficient PET degradation to terephthalic acid monomers up to 95.5%. Our approach, which integrates a two-enzyme system with protein engineering, demonstrates the potential for enhancing the activity of emerging PET-degradation enzymes, which may possess unique attributes.Graphical AbstractA novel PET hydrolase, bbPET0069, was identified from a soil microbial genome. bbPET0069 and CALB showed remarkable synergy in PET degradation. Using surface feature analysis, PET degradation activity of bbPET0069 was significantly improved. This combination of a two-enzyme system and surface feature analysis holds promise for enhancing emerging PET-degradation enzymes.
Characterization of severe fever with thrombocytopenia syndrome virus Japanese isolate YG1 strain quasispecies using reverse genetics approaches
Authors: Lokupathirage Sithumini M.W. , Muthusinghe Devinda S. , Sarii Rakiiya S. , Akanbi Olusola A. , Shimizu Kenta , Tsuda Yoshimi , Yoshimatsu Kumiko 
Published: February 2024

AbstractThree amino acid mutations have been identified in the isolated YG1 strain of severe fever thrombocytopenia syndrome virus (SFTSV), Gn (Y328H) accounts for 26.9% of the virus in patients’ blood, Gc (R624W) and L (N1891K) those are minor. To investigate viral properties caused by each mutation, we rescued viruses with one–three mutations. Mutations Y328H and R624W in GP increased the cell fusion activity and plaque size. Theses enhancement was more pronounced for both Y328H and R624W. The pseudotyped vesicular stomatitis virus coated with the SFTSV GP Y328H mutant showed lower infectivity in Vero E6 cells, which was compensated for by the additional R624W mutation. In the process of adaptation for virus with Y328H, the R624W mutation may be acquired. Moreover, only the viruses with the N1891K mutation in L showed significant CPE and the CPE was inhibited by the pan-caspase inhibitor, suggesting that caspase-dependent cell death occurred. Programmed cell death associated molecules caspase-1 and caspase-3 were induced in both CPE inducing and wild-type virus-infected cells. Furthermore, infection with the wild-type virus suppressed actinomycin D-induced cell death. These results suggest that SFTSV infected cells initiate programmed cell death, whereas wildt-ype virus may inhibit cell death. Furthermore, the N1891K mutation in L virus was outcompeted by a 10-fold less wild-type virus in Vero E6 cells indicating that it was not advantageous for viral survival in Vero E6 cells. Thus the quasispecies composition of SFTSV appeared to be influenced by propagative environment.ImportanceThis study shows information on viral pathogenesis by analyzing quasispecies derived from one fatal case of severe fever with thrombocytopenia syndrome virus (SFTSV) infection. Observation with recombinant SFTSV altered Gn and Gc suggests that combining mutations may increase the viability of mutant viruses, selecting viruses to create a suitable population for propagation. The N1891K mutation in L protein of SFTSV was related to CPE appearance. On the other hand, wild-type virus which is major population in patient infection was suppressive for cell death. It was suggested that SFTSV has a mechanism to escape cell death for the prolonged viral propagation in infected cells. Although the mechanism is still unknown, it has been suggested that RNA virus polymerase might be involved in the regulation of cell death. This study proposed the mechanism underlying the adaptation to the environment and survival of virus as quasispecies.