bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversified, miniaturized and ancestral parts for mammalian genome engineering and molecular recording
Authors: McDiarmid Troy A. , Taylor Megan L. , Chen Wei , Chardon Florence M. , Choi Junhong , Liao Hanna , Li Xiaoyi , Kim Haedong , Lalanne Jean-Benoît , Li Tony , Nathans Jenny F. , Martin Beth K. , Knuth Jordan , Coradini Alessandro L.V. , Gray Jesse M. , Pinglay Sudarshan , Shendure Jay 
Published: October 2024

AbstractAs the synthetic biology and genome engineering fields mature and converge, there is a clear need for a “parts list” of components that are diversified with respect to both functional activity (to facilitate design) and primary sequence (to facilitate assembly). Here we designed libraries composed of extant, ancestral, mutagenized or miniaturized variants of Pol III promoters or guide RNA (gRNA) scaffolds and quantified their ability to mediate precise edits to the mammalian genome via multiplex prime editing. We identified thousands of parts that reproducibly drive a range of editing activities in human and mouse stem cells and cancer cell lines, including hundreds exhibiting similar or greater activity than the sequences used in conventional genome engineering constructs. We further conducted saturation mutagenesis screens of canonical Pol III promoters (U6p, 7SKp, H1p) and the prime editing guide RNA (pegRNA) scaffold, which identified tolerated variants that can be superimposed on baseline parts to further enhance sequence diversity. While characterizing thousands of orthologous promoters from hundreds of extant or ancestral genomes, we incidentally mapped the functional landscape of mammalian Pol III promoter evolution. Finally, to showcase the usefulness of these parts, we designed a “ten key” molecular recording array that lacks repetitive subsequences in order to facilitate its one-step assembly in yeast. Upon delivering this 15.8 kb tandem array of promoters and guides to mammalian cells, individual pegRNAs exhibited balanced activities as predicted by the activity of component parts, despite their relocation to a single locus. Looking forward, we anticipate that the diversified parts and variant effect maps reported here can be leveraged for the design, assembly and deployment of synthetic loci encoding arrays of gRNAs exhibiting predictable, differentiated levels of activity, which will be useful for multiplex perturbation, advanced biological recorders and complex genetic circuits.
Identification of Long Non-coding RNA Candidate Disease Genes Associated with Clinically Reported CNVs in Congenital Heart Disease
Authors: Penaloza Jacqueline S. , Moreland Blythe , Gaither Jeffrey B. , Landis Benjamin J. , Ware Stephanie M. , McBride Kim L. , White Peter ,   CCVM Consortium
Published: October 2024

AbstractBackgroundCopy Number Variants (CNVs) contribute to 3-10% of isolated Congenital Heart Disease (CHD) cases, but their roles in disease pathogenesis are often unclear. Traditionally, diagnostics have focused on protein-coding genes, overlooking the pathogenic potential of non-coding regions constituting 99% of the genome. Long non-coding RNAs (lncRNAs) are increasingly recognized for their roles in development and disease.MethodsIn this study, we systematically analyzed candidate lncRNAs overlapping with clinically validated CNVs in 1,363 CHD patients from the Cytogenomics of Cardiovascular Malformations (CCVM) Consortium. We identified heart-expressed lncRNAs, constructed a gene regulatory network using Weighted Gene Co-expression Network Analysis (WGCNA), and identified gene modules significantly associated with heart development. Functional enrichment analyses and network visualizations were conducted to elucidate the roles of these lncRNAs in cardiac development and disease. The code is stably archived athttps://doi.org/10.5281/zenodo.13799847.ResultsWe identified 18 lncRNA candidate genes within modules significantly correlated with heart tissue, highlighting their potential involvement in CHD pathogenesis. Notably, lncRNAs such aslnc-STK32C-3, lnc-TBX20-1, andCRMAdemonstrated strong associations with known CHD genes. Strikingly, while only 7.6% of known CHD genes were impacted by a CNV, 68.8% of the CNVs contained a lncRNA expressed in the heart.ConclusionsOur findings highlight the critical yet underexplored role of lncRNAs in the genomics of CHD. By investigating CNV-associated lncRNAs, this study paves the way for deeper insights into the genetic basis of CHD by incorporating non-coding genomic regions. The research underscores the need for advanced annotation techniques and broader genetic database inclusion to fully capture the potential of lncRNAs in disease mechanisms. Overall, this work emphasizes the importance of the non-coding genome as a pivotal factor in CHD pathogenesis, potentially uncovering novel contributors to disease risk.
In vitrodiscovery of a therapeutic lead for HFMD from a library screen of rocaglates/aglains
Authors: Oo Adrian , Borge Angel , Lee Regina Ching Hua , Salim Cyrill Kafi , Wang Wenyu , Ricca Michael , Fong Deborah Yuhui , Alonso Sylvie , Brown Lauren E. , Porco John A. , Chu Justin Jang Hann 
Published: October 2024

AbstractThe lack of an effective antiviral treatment for enteroviruses, including the human enterovirus A71 (EV-A71), has resulted in an immense global healthcare burden associated with hand-foot-and-mouth disease (HFMD). Rocaglates and aglains belong to a family of compounds produced byAglaiagenus plants. Since the initial discovery of rocaglates in 1982, various rocaglates and aglains have been synthesized and extensively studied as anticancer and antiviral agents. Here, we report our studies towards the discovery of a novel aglain derivative as an EV-A71 inhibitor and work to decipher its antiviral effect. From an immunofluorescence-based phenotypic screen of a library of 296 rocaglate and aglain derivatives, we identified a lead aglain derivative which effectively suppressed EV-A71 replication by 2.3 log fold at a non-cytotoxic concentration. Further validation revealed inhibition of EV-A71 across multiple cell types and a pan-enterovirus inhibitory spectrum against other enteroviruses. Subsequent mechanistic investigation revealed interference with EV-A71 intracellular post-entry events including viral RNA transcription and translation. Findings from this study have established a strong foundation for development of aglain scaffolds as much needed antiviral agents for HFMD, paving the way for future medicinal chemistry optimization andin vivostudies.
Concordance between Infectious Disease Society of America Criteria for Urinary Tract Infection Testing and Treating Vs. Actual Emergency Department Practice
Authors: Harhash Tarek , Chen Yi-Ru , Dokku Sahit , Menoudakos Demetra , Argueta Keyleen , Almiggaber Musa , Richman Mark 
Published: October 2024

AbstractIntroductionSymptomatic and asymptomatic urinary tract infections (UTIs) are common. The Infectious Disease Society of America (IDSA) discourages testing and treating ASB other than in pregnant women during routine obstetric visit screening and patients undergoing urologic procedures with expected mucosal bleeding. Unnecessary urinalysis (UA) and inappropriate antibiotic use persist in Emergency Departments (EDs). This study aims to evaluate UA testing and antibiotic treatment patterns for ASB in an urban ED, assessing adherence to IDSA guidelines and setting baseline rates for an educational intervention to align testing and treatment with IDSA guidelines.MethodsWe conducted a 15-month study to assess adherence to IDSA guidelines for proper UTI screenings and prescribing. We reviewed records of 50 adult patients who had a UA at the Long Island Jewish Medical Center ED to determine whether they met IDSA criteria for UA testing and appropriate antibiotic use. Patients with sepsis or other conditions requiring empiric antibiotics were excluded. We performed a univariate analysis to describe the population and factors associated with treating urinalysis findings. Statistical significance was set at p <0.05.ResultsSixty-four percent of patients were asymptomatic and 36% were symptomatic. None of the asymptomatic patients met IDSA criteria for UA testing. Symptomatic patients were nearly-statistically more likely than asymptomatic patients to have a positive UA (72.2% vs. 43.8%, p = 0.06), and were more-often prescribed antibiotics for a positive UA (61.5% vs. 14.3%; p = 0.0128). They were also more-often prescribed antibiotics for a negative UA (20.0% vs. 0%; p = 0.05).DiscussionThe study findings revealed significant discordance between IDSA guidelines and current ED practices, with 64% of UA tests deemed unnecessary for ASB patients. These results align with previous studies highlighting the prevalence of over-testing with UAs and over-treatment of ASB. Unnecessary testing and inappropriate antibiotic treatment lead to increased costs and risks of antibiotic resistance, adverse drug events, and Clostridium difficile infection. This study highlights the necessity for planned educational initiatives to reduce unnecessary UAs and treatment and improve adherence to evidence-based guidelines.
Brain-heart interactions are associated with mortality and acute encephalopathy in ICU patients with severe COVID-19
Authors: Hermann Bertrand , Benghanem Sarah , Pruvost-Robieux Estelle , Sharshar Tarek , Gavaret Martine , Cariou Alain , Diehl Jean-Luc , Candia-Rivera Diego 
Published: October 2024

AbstractObjectiveResearch in critical care has revealed the significance of autonomic dysfunctions, and more recently of brain-heart interactions, as valuable biomarkers for evaluating patients’ physiological status. These biomarkers provide insights into consciousness levels, severity, and outcomes. This study aims to determine the potential of these biomarkers in predicting the mortality and neurological outcome of severe COVID-19 patients.MethodsWe examined severe COVID-19 patients who required mechanical ventilation and observed them both during sedation and after sedation cessation. Standard EEG and ECG recordings were conducted at bedside, from which 5 minutes of continuous data were analyzed. Using a synthetic data generation model, we evaluated bidirectional brain-heart interactions from EEG power and heartbeat dynamics series.ResultsOur findings indicate that brain-heart interactions, especially involving cardiac parasympathetic activity, can provide information about patients’ severity. We observed correlations with acute encephalopathy duration (coma and delirium), particularly evident in top-down markers (from brain to heart) while bottom-up signaling (from heart to brain) correlated with ICU mortality. Additionally, we noted stronger modulation of brain-heart interactions in milder patients when comparing sedation versus non-sedation conditions, compared to those in more severe states.ConclusionsOur results imply that autonomic dysfunctions, as measured through brain-heart interactions, can track the pathophysiology of comatose states following COVID-19 infection.SignificanceThese findings highlight the potential of brain-heart interactions as an integrated marker for autonomic function in critical care, offering a more accurate assessment of patient severity and outcomes compared to isolated cardiac or brain measures.Highlights-Brain-heart interactions provide valuable insights into patient severity and neurological outcomes in severe COVID-19 pneumonia.-Brain-to-heart markers correlate with acute encephalopathy duration, while heart-to-brain signaling predicts ICU mortality.-Brain-heart interactions are modulated differently based on assessment timing and the presence of acute encephalopathy.
Percentile Scores for the Revised University of Pennsylvania Smell Identification Test for 16,972 Individuals 60 years of Age and Older
Authors: Pierz Kerri A. , Aamodt Whitley , Gochanour Caroline , Kurth Ryan , Brumm Michael C. , Coffey Christopher S. , Heathers Laura E. , Totten Michelle , Doty Richard L. , Marek Kenneth , Siderowf Andrew ,   the Parkinson’s Progression Markers Initiative
Published: October 2024

AbstractBackground and ObjectivesThe University of Pennsylvania Smell Identification Test (UPSIT) is a widely employed objective measure of smell function. A revised version of this test, termed the UPSIT-R, was developed in 2020 to update certain odorants and response options. The goal of this study was to establish normative age- and sex-specific data for the UPSIT-R in a large adult cohort and to compare the resultant percentiles to those of the original UPSIT. A second study was performed to compare the relative performance of these two tests in a small cohort of persons with and without Parkinson’s disease (PD).MethodsUPSIT-R percentiles were derived separately by age (60-64, 65-69, 70-74, 75-59, and ≥80 years) and sex (male, female) categories in 16,972 volunteers who were predominantly white and non-Hispanic. Percentiles were derived statistically using an empirical distribution averaging procedure. A Bland-Altman plot was employed to visualize the level of agreement between percentiles for the UPSIT-R and UPSIT. For the second study, non-parametric statistics were employed to compare the results of those with and without PD.ResultsUPSIT-R performance declined with increasing age; deficits were more pronounced in men than in women. The magnitude of the difference between the original and revised test percentile scores differed by age and sex; women had up to a 3-point improvement with the UPSIT-R whereas the oldest male age had up to a 3-point decline in percentile scores. Olfactory deficits in PD were confirmed on the UPSIT-R.DiscussionThis study provides normative data clinically useful for assessing the relative degree of dysfunction in persons 60 years of age and older using the UPSIT-R. Like the traditional version of the UPSIT, this version demonstrates that smell function declines with age and is generally better in women than in men, providing a solid clinical basis for physicians to accurately determine the degree of smell dysfunction in their patients.Trial Registration InformationClinicalTrials.govNCT05065060
Cell-type-informed genotyping of mosaic focal epilepsies reveals cell-autonomous and non-cell-autonomous disease-associated transcriptional programs
Authors: Bizzotto Sara , Stronge Edward A. , Talukdar Maya , Hu Qiwen , Zhou Zinan , Huang August Yue , Chhouk Brian H. , D’Gama Alissa M. , Yang Edward , Green Timothy E. , Reutens David C. , Mullen Saul A. , Hildebrand Michael S. , Buono Russell J , Poduri Annapurna H. , Khoshkhoo Sattar , Walsh Christopher A. 
Published: October 2024

AbstractRecent studies demonstrate growing roles for genetic mosaicism in neurodevelopmental and neuropsychiatric disorders, with the paradigm being drug-resistant pediatric focal epilepsy related to activating somatic variants in the PI3K-mTOR pathway. While identifying the genotype-associated changes at the single-cell level is fundamental to understanding disease pathophysiology, this remains technically challenging in human tissue samples with existing methods. Here, we performed single-nucleus RNA-sequencing (snRNA-seq) of 20 focal cortical dysplasia (FCD) samples removed surgically for treatment of drug-resistant epilepsy, and 10 non-FCD controls, and we developed a new approach, Genotyping Of Transcriptomes Enhanced with Nanopore sequencing (GO-TEN), that combines targeted complementary (c)DNA sequencing with snRNA-seq to perform concurrent single-nucleus genotyping and transcriptional analysis. We find that mosaic pathogenic variants in FCD do not produce a detectable novel cell identity, but instead we observe conserved cell types present both in FCD cases and non-FCD control specimens. Similarly, GO-TEN analysis shows that most pathogenic variant-carrying cells have well-differentiated neuronal or glial identities and are enriched for layer II-III excitatory neurons. We identify cell-intrinsic disruption of glutamate and GABA-A signaling pathways in variant-carrying neurons and altered intercellular signaling, making potential mechanisms for epileptogenesis in FCD. In summary, by addressing genotype-specific changes in mosaic epilepsy-associated lesions, our study highlights new potential disease mechanisms and therapeutic targets.
Enhanced bacterial chemotaxis in confined microchannels: Optimal performance in lane widths matching circular swimming radius
Authors: Yue Caijuan , Zhang Chi , Zhang Rongjing , Yuan Junhua 
Published: October 2024

AbstractUnderstanding bacterial behavior in confined environments is crucial for elucidating microbial ecology and developing strategies to manage bacterial infections. While extensive research has focused on bacterial motility on surfaces and in porous media, chemotaxis in confined spaces remains poorly understood. Here, we investigate the chemotaxis ofEscherichia coliwithin microfluidic lanes under a linear concentration gradient of L-aspartate. We demonstrate thatE. coliexhibits significantly enhanced chemotaxis in lanes with sidewalls compared to open surfaces, primarily due to cells aligning and swimming along the right sidewalls. By varying lane widths, we identify that an 8 μm width—approximating the radius of bacterial circular swimming on surfaces—maximizes chemotactic drift velocity. These results are supported by both experimental observations and stochastic simulations, establishing a clear proportional relationship between optimal lane width and the radius of bacterial circular swimming. Further geometric analysis provides an intuitive understanding of this phenomenon. Our results offer new insights into bacterial navigation in complex biological environments such as host tissues and biofilms, shedding light on microbial ecology in confined habitats and suggesting new avenues for controlling bacterial infections.
TheTrypanosoma cruzicell atlas; a single-cell resource for understanding parasite population heterogeneity and differentiation
Authors: Laidlaw Ross , Sanchez Marta Garcia , Pacheco Juliana Da Silva , Paradela Luciana De Sousa , Otto Thomas D , De Rycker Manu 
Published: October 2024

AbstractTrypanosoma cruzi, the causative agent of Chagas disease, exhibits a complex life cycle with multiple hosts, stages and differentiation steps. We present a complete cell atlas for theT. cruzilife cycle, based on single cell transcriptomes for over 31,000 cells and population-based transcriptomics. The atlas reveals many life cycle associated genes and can be utilised to accurately annotate life cycle stages. It provides detailed insights into cell heterogeneity, including cell-specific repertoires of surface antigens in trypomastigotes, with key implications for immune responses. Enabled by single-cell resolution, we define the transcriptomic changes that occur across the epimastigote to metacyclic trypomastigote differentiation axis. Furthermore, we provide comprehensive UTR annotation, identifying previously unannotated transcripts as well as revealing alternative poly-adenylation and an unanticipated complexity of reverse strand and antisense transcripts. ThisT. cruziatlas provides a comprehensive resource and unlocks a range of new avenues for research on this important human pathogen.
Longhorn Beetles Form Structural Colour Using Calcium Phosphate Biominerals
Authors: Chang Yin , Tseng Hsiang-Han , Tanahashi Masahiko , Pohl Darius , Rellinghaus Bernd , Bertinetti Luca , Politi Yael 
Published: October 2024

AbstractBrilliant structural colors originating from diverse photonic crystals are found across many phyla, including the striking iridescent colors of beetles and butterflies, produced by three-dimensional photonic crystal structures in the specialized cuticular scales. However, the precise composition of these structures remains largely unknown, although it is key to unravelling colour production mechanisms and morphogenesis. The longhorn beetleDoliops similisdisplays vibrant green patterns on its otherwise dark elytra. These patterns are formed by arrays of minute scales that encompass a three-dimensional photonic crystal made of orderly packed nanospheres. We found that these nanospheres are composed of carbonated amorphous calcium phosphate biomineral. By accurately parameterizing the structure and calculating the refractive index deduced from the relative fractions of the organic and inorganic phases, we derived reflection wavelengths that match the observed green hue, demonstrating the biomineral’s role in colour production. Our study further reveals that biomineralization is widespread in the Lamiinae subfamily, with colour diversity achieved through variations in nanosphere size, packing, and composition. This study opens new avenues for developing bioinspired mineral-based optical devices with high refractive indices and defect-resistance, overcoming the shortcomings of current polymer-based designs.
High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing
Authors: Shin David , Urbanek Madeleine E. , Larson H. Hanh , Moussa Anthony J. , Lee Kevin Y. , Baker Donovan L. , Standen-Bloom Elio , Ramachandran Sangeetha , Bogdanoff Derek , Cadwell Cathryn R. , Nowakowski Tomasz J. 
Published: October 2024

SUMMARYSingle cell genomics has revolutionized our understanding of neuronal cell types. However, scalable technologies for probing single-cell connectivity are lacking, and we are just beginning to understand how molecularly defined cell types are organized into functional circuits. Here, we describe a protocol to generate high-complexity barcoded rabies virus (RV) for scalable circuit mapping from tens of thousands of individual starter cells in parallel. In addition, we introduce a strategy for targeting RV-encoded barcode transcripts to the nucleus so that they can be read out using single-nucleus RNA sequencing (snRNA-seq). We apply this tool in organotypic slice cultures of the developing human cerebral cortex, which reveals the emergence of cell type– specific circuit motifs in midgestation. By leveraging the power and throughput of single cell genomics for mapping synaptic connectivity, we chart a path forward for scalable circuit mapping of molecularly-defined cell types in healthy and disease states.
Rotational migration in human pancreatic ductal organoids depends on actin and myosin activity
Authors: Xie Gengqiang , Wang Yue Julia , Thirumalai D. , Li Xin , Irianto Jerome 
Published: October 2024

AbstractRotational migration is one specific form of collective cell migration when epithelial cells are confined in a spherical geometry, such as in the epithelial acini. This tissue-level rotation motion is crucial for the morphogenesis of multiple epithelial systems. Here, we introduce a new primary human model for the study of rotational migration, pancreatic ductal organoids. Live imaging revealed the persistent rotation of the organoids over time. By tracking the nuclei, the three-dimensional trajectory of the cellular movement was reconstructed and the velocity of the rotation was quantified. The presence of focal adhesion clusters and prominent actin stress fibers were observed at the basal side of the organoids, suggesting the interactions between the cells and the surrounding extracellular matrix. Finally, our inhibition study showed the dependence of pancreatic ductal organoid rotational migration on myosin activity, actin polymerization, and actin branching. We hope that this model will enable future studies with human primary cells, which are more faithful to normal epithelial cells.