bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Validation of a Simulation Model for Ureteral Stent Placement
Authors: Wood Nicole J. , Cheng Laura J. , Buller Dylan , Volkin Dmitry , O'Sullivan David M. , Tunitsky-Bitton Elena 
Published: November 2024

Importance
Currently, there are no validated training models for cystoscopy with ureteral stent placement.

Objectives
The objectives of this study were to develop and validate a novel endoscopic simulation model for training in ureteral stent placement.

Study Design
A low-cost, low-fidelity training model was developed to simulate ureteral stent placement. Recruited participants were divided into 3 groups: novices (postgraduate year 3/4 gynecology residents), advanced learners (urogynecology and reconstructive pelvic surgery fellows), and experts (urology residents, urogynecology faculty, and urology faculty). Construct validity was measured using de-identified video-recorded performances on the model, which were evaluated by 2 expert reviewers using validated scales (Global Operative Assessment of Laparoscopic Skills [GOALS], Global Rating Scale [GRS]) and procedure-specific metrics.

Results
The model was created using a hollow Styrofoam sphere, plastic tubing from a retropubic sling, and a silicone pacifier. Thirty-six surgeons were assessed performing the procedure using the model with cystoscopic equipment. The experts (n = 12) performed significantly better than the advanced learners (n = 17) and novices (n = 7) in total scores (max 75, median [IQR]: 75 [75–75], 61 [56.5–68.5], 45 [43–46], respectively; P < 0.001) and within each individual scale domain. Increasing experience with ureteral stent placement had a significant correlation (P < 0.001) with better performance on the model. A minimum total passing score of 63 was established. On post simulation assessment, most participants “agreed” or “strongly agreed” that the model closely approximates the feel of ureteral stent placement.

Conclusion
This ureteral stenting simulation model is easy to construct, affordable, and reproducible. The model is valid and reliable for practicing the procedure in preparation for live surgery.
Roseovarius phycicola sp. nov. and Roseovarius rhodophyticola sp. nov., isolated from marine red algae
Authors: Lee Min Woo , Baek Ju Hye , Kim Jeong Min , Bayburt Hülya , Choi Byeong Jun , Jia Baolei , Jeon Che Ok 
Published: November 2024

Two Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacteria, designated as strains S88T and W115T, exhibiting catalase- and oxidase-positive reactions, were isolated from marine red algae in South Korea. Strain S88T exhibited growth at 20–30 °C, pH 6.0–9.0 and 2.0–5.0% (w/v) NaCl, while strain W115T grew at 20–30 °C, pH 7.0–9.0 and 2.0–5.0% (w/v) NaCl. Strain S88T contained summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c), C16 : 0 and C16 : 0 2-OH as major fatty acids (>5%), with major polar lipids being phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid and two unidentified lipids. Strain W115T contained summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) and C16 : 0 as major fatty acids (>5%), with major polar lipids including phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid and unidentified lipids. Ubiquinone-10 was the sole respiratory quinone in both strains, and the genomic DNA G+C contents were 57.0% for strain S88T and 56.5% for strain W115T. Despite 99.86% 16S rRNA gene sequence similarity, strains S88T and W115T shared 88.8% average nucleotide identity (ANI) and 36.8% digital DNA–DNA hybridization (dDDH) value, indicating different species. Phylogenetic and phylogenomic analyses based on 16S rRNA gene and genome sequences, respectively, revealed that strains S88T and W115T formed a phylogenetic lineage within the genus Roseovarius. ANI and dDDH values of both strains with other type strains were less than 73.7 and 20.3%, respectively, confirming that they represent novel species. Based on phenotypic, chemotaxonomic and molecular characteristics, strains S88T and W115T represent two novel species of the genus Roseovarius, for which the names Roseovarius phycicola sp. nov. (S88T =KACC 23423T =JCM 36647T) and Roseovarius rhodophyticola sp. nov. (W115T =KACC 23690T =JCM 36651T) are proposed, respectively.
Entomopoxvirus-like long DNA sequences in human centromeric and peri-centromeric regions
Authors: Hondo Eiichi , Mizutani Tetsuya , Shimoda Hiroshi , Iida Atsuo 
Published: November 2024

AbstractMammalian genomes harbor a range of endogenous virus-like sequences, although these sequences are typically affected by mutations and deletions, and no examples have been reported of long, conserved regions extending tens of kilobases or more. In this study, a comprehensive similarity search against the complete human T2T genome (hT2T) using high-quality viral genome data was performed. Among nearly continuous viral sequences, the longest identified was entomopoxvirus, spanning 140 kb with a similarity of over 57%. Notably, entomopoxvirus-like sequences stood out within the human genome, with a total of 2.42 Mb exhibiting similarity to human sequences. Seven entomopoxvirus species were fragmented into regions less than 37 kb each, with nearly all of these segments scattered throughout the human genome. Surprisingly, nearly all of these sequences were localized within the hsat1A regions of human centromeric and pericentromeric areas. On chromosome 3, for example, all sequences were confined within the centromere, and extensive transcription was observed across these regions. While the lack of fully sequenced genomes for other eukaryotic species limits our ability to infer the phylogenetic significance of these regions, our findings reveal remarkably long virus-like sequences within centromeric and related regions—as integral components of eukaryotic chromosomes. This discovery opens new avenues in the study of co-evolution between viruses and eukaryotes, offering intriguing insights into the genomic landscape at the core of eukaryotic biology.
Comparative Evaluation of Behavioral-Epidemic Models Using COVID-19 Data
Authors: Gozzi Nicolò , Perra Nicola , Vespignani Alessandro 
Published: November 2024

AbstractCharacterizing the feedback linking human behavior and the transmission of infectious diseases (i.e., behavioral changes) remains a significant challenge in computational and mathematical Epidemiology. Existing Behavioral Feedback Models often lack real-world data calibration and cross-model performance evaluation in both retrospective analysis and forecasting. In this study, we systematically compare the performance of three mechanistic behavioral models across nine geographies and two modeling tasks during the first wave of COVID-19, using various metrics. The first model, a Data-Driven Behavioral Feedback Model, incorporates behavioral changes by leveraging mobility data to capture variations in contact patterns. The second and third models are Analytical Behavioral Feedback Models, which simulate the feedback loop either through the explicit representation of different behavioral compartments within the population or by utilizing an effective non-linear force of infection. Our results do not identify a single best model overall, as performance varies based on factors such as data availability, data quality, and the choice of performance metrics. While the data-driven model incorporates substantial real-time behavioral information, the Analytical Compartmental Behavioral Feedback Model often demonstrates superior or equivalent performance in both retrospective fitting and out-of-sample forecasts. Overall, our work offers guidance for future approaches and methodologies to better integrate behavioral changes into the modeling and projection of epidemic dynamics.
Systematic identification and characterization of virus lncRNAs suggests extensive structural mimicry of host lncRNAs
Authors: Fu Ping , Cai Zena , You Ruina , Deng Lei , Li Zhaoyong , Miao Zhichao , Peng Yousong 
Published: November 2024

AbstractVirus long non-coding RNAs (vlncRNAs) play crucial roles in viral infections, yet their identification and characterization remain limited. This study identified 5,053 novel vlncRNAs across 25 viral species using third-generation sequencing, with two from Influenza A virus and Vesicular stomatitis virus validated by RT-qPCR. Most vlncRNAs originated from dsDNA viruses. Only 1% having annotated RNA families, suggesting many novel RNA structures. Although only seven vlncRNAs shared sequence similarities with human lncRNAs (hlncRNAs), 772 vlncRNAs from 15 human viruses structurally mimicked hlncRNAs. These vlncRNA and hlncRNAs bound to similar miRNAs, potentially acting as miRNA sponges to promote essential life process. Splicing analysis showed vlncRNAs had a prevalence of alternative first exon. Finally, we developed vlncRNAbase (http://computationalbiology.cn/vlncRNAbase/#/) to store and organize the newly identified and known vlncRNAs. Overall, the study provides a valuable resource for further investigation into vlncRNAs and deepens our understanding of the diversity, structure and function of the molecule.
The safety and efficacy of Ultrasound Histotripsy and human pluripotent stem cell-derived hepatic spheroid implantation as a potential therapy for treatment of congenital metabolic liver disease: assessment in an immunocompetent rodent model
Authors: Rashidi Hassan , Khalil Amjad , Froghi Saied , Hall Andrew , Gelat Pierre , Davidson Brian , Quaglia Alberto , Saffari Nader 
Published: November 2024

AbstractBackgroundLiver disease secondary to an inborn or genetic error of metabolism is a rare group of conditions often associated with chronic ill health and reduced survival. Curative treatment is mainly limited to liver transplantation with major long-term risks. Cell therapy is a promising alternative, but current approaches are ineffective.AimTo develop histotripsy, a non-invasive high intensity ultrasound procedure for liver tissue mechanical ablation, combined with hepatocyte stem cell implantation as a novel method of reversing liver failure from genetic disease. This study assessed the safety and feasibility of this approach in healthy rodents.MethodsUnder general anaesthesia, adult rats (n=12) underwent laparotomy and ultrasound histotripsy to the exposed liver. Around 1 million cells were injected into a single histotripsy cavity in each animal under direct vision (n=10) with two receiving only histotripsy without cell injection. On completion of cell implant haemostasis was secured, laparotomy incision closed, and the animals recovered. Groups of animals were terminated immediately and after 4 hrs, 8 hrs, 24hrs, 4 days and 7 days. Liver and vital organs were assessed for procedure related injuries and evidence of viable implanted cells by histology and immunohistochemistry.ResultsAll animals successfully recovered, and no complication was observed throughout the study. Created cavities were successfully identified in histological analysis of rat. The presence of human cells was verified using anti-human nuclei antibody confirming successful implantation of liver organoids into decellularized cavities.ConclusionsIn this feasibility study, we demonstrated suitability of histotripsy to create decellularized cavities in liver parenchyma. In addition, feasibility of direct transplantation of undissociated liver organoids into the created cavities was demonstrated as a potential approach to treat inborn liver disease by creating nodules of healthy cells capable of performing loss metabolic function. Therapeutic efficacy of this approach will be evaluated in an upcoming study.
Uncovering hidden gene-trait patterns through biclustering analysis of the UK Biobank
Authors: Pividori Milton , Sadeeq Suraju , Krishnan Arjun , Stranger Barbara E. , Gignoux Christopher R. 
Published: November 2024

AbstractThe growing availability of genome-wide association studies (GWAS) and large-scale biobanks provides an unprecedented opportunity to explore the genetic basis of complex traits and diseases. However, with this vast amount of data comes the challenge of interpreting numerous associations across thousands of traits, especially given the high polygenicity and pleiotropy underlying complex phenotypes. Traditional clustering methods, which identify global patterns in data, lack the resolution to capture overlapping associations relevant to subsets of traits or genes. Consequently, there is a critical need for innovative analytic approaches capable of revealing local, biologically meaningful patterns that could advance our understanding of trait comorbidities and gene-trait interactions. Here, we applied BiBit, a biclustering algorithm, to transcriptome-wide association study (TWAS) results from PhenomeXcan, a large resource of gene-trait associations derived from the UK Biobank. BiBit allows simultaneous grouping of traits and genes, identifying biclusters that represent local, overlapping associations. Our analyses uncovered biologically interpretable patterns, including asthma-related biclusters enriched for immune-related gene sets, connections between eye traits and blood pressure, and associations between dietary traits, high cholesterol, and specific loci on chromosome 19. These biclusters highlight gene-trait relationships and patterns of trait co-occurrence that may otherwise be obscured by traditional methods. Our findings demonstrate that biclustering can provide a nuanced view of the genetic architecture of complex traits, offering insights into pleiotropy and disease mechanisms. By enabling the exploration of complex, overlapping patterns within biobank-scale datasets, this approach provides a valuable framework for advancing research on genetic associations, comorbidities, and polygenic traits.
Enhanced lentiviral gene delivery to mammalian cells via paired cell surface and viral envelope engineering
Authors: Tannir Ryan , Chan Letitia , Grzywa Tomasz M. , Arevalo Orlando , Neeser Alexandra , Kahn Sara , Cozzone Austin , Olenick Lauren , Mason Nicola J , Ma Leyuan 
Published: November 2024

ABSTRACTLentiviral vectors that facilitate gene delivery to desired cell types have been widely used in routine laboratory research and therapeutic cell engineering. However, the lack of proper entry receptors on many cell types often results in poor gene delivery. Here, we present a simple paired virus-cell engineering approach that promotes lentiviral gene delivery into mammalian cells. Lentiviruses are dual-pseudotyped with VSV-G and a chimeric envelope protein specifically recognizing a small molecule fluorescein (αFITC-Env), and target cells are transiently labelled with FITC to create surrogate receptors for lentivirus attachment. The synthetic interaction between FITC-labeled cells and FITC-binding LVs enables efficient LV docking, viral entry and stable transgene expression in a range of mammalian cell lines and primary T cells. We showed that this approach enabled efficient delivery of a CD19-targeted chimeric antigen receptor (CAR) into naïve human T cells that are naturally refractory to conventional VSV-G LVs, which upon activation rapidly eradicated CD19+leukemic cells. This paired cell surface and virus envelope engineering approach may serve as a universal method for engineering synthetic virus-cell interactions to improve lentiviral gene delivery to mammalian cells.
Aggregation of Transthyretin by Fluid Agitation
Authors: Ritsch Irina , Dyson H. Jane , Wright Peter E. 
Published: November 2024

AbstractThe transthyretin (TTR) tetramer, assembled as a dimer of dimers, transports thyroxine and retinol binding protein in blood plasma and cerebrospinal fluid. Aggregation of wild type or pathogenic variant TTR leads to transthyretin amyloidosis (ATTR), which is associated with neurodegenerative and cardiac disease. The trigger for TTR aggregation under physiological conditions is unknown. The tetramer is extremely stable at neutral pH, but aggregation via tetramer dissociation and monomer misfolding can be inducedin vitroby lowering the pH. To elucidate factors that may cause TTR aggregation at neutral pH, we examined the effect of shear forces such as arise from fluid flow in the vascular system. Fluid shear forces were generated by rapidly stirring TTR solutions in conical microcentrifuge tubes. Under agitation, TTR formed β-rich aggregates and fibrils at a rate that was dependent upon protein concentration. The lag time before the onset of agitation-induced aggregation increases as the total TTR concentration is increased, consistent with a mechanism in which the tetramer first dissociates to form monomer that either partially unfolds to enter the aggregation pathway or reassociates to form tetramer. NMR spectra recorded at various time points during the lag phase revealed growth of an aggregation-prone intermediate trapped as a dynamically perturbed tetramer. Enhanced conformational fluctuations in the weak dimer-dimer interface suggests loosening of critical inter-subunit contacts which likely destabilizes the agitated tetramer and predisposes it towards dissociation. These studies provide new insights into the mechanism of aggregation of wild type human TTR under near physiological conditions.
WITHDRAWN: Neutralizing Activity and Viral Escape of Pemivibart by SARS-CoV-2 JN.1 sublineages
Authors: Yao Tianjiao , Ma Zhenghai , Lan Ke , Guo Yicheng , Liu Lihong 
Published: November 2024

Withdrawal StatementThe authors have withdrawn this manuscript because of a conflict of interest. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Fifteen-year Alcohol Consumption Trajectories and Their Association with Cardiovascular Events and Mortality: the Framingham Heart Study
Authors: Leng Yuanming , Ding Huitong , Li Yi , Liu Xue , Wang Mengyao , Lyu Chenglin , Levy Daniel , Ma Jiantao , Liu Chunyu 
Published: November 2024

AbstractBackgroundLong-term alcohol consumption patterns play a critical role in human health.ObjectivesWe aimed to identify alcohol consumption trajectories and analyze their associations with coronary heart disease (CHD) and all-cause mortality in the Framingham Heart Study (FHS).MethodsWe used a growth mixture model to identify sex-specific alcohol consumption trajectories over 15 years and Cox regression to examine associations of these trajectories with incident events that occurred during an additional 10-year follow-up, adjusting for covariates.ResultsWe identified four distinct trajectory groups among 6,570 participants (mean age 52; 55% women): Group 1 (n=2,713, reference) consisted of low-level drinkers; Group 2 (n=1,818) mainly included abstainers; Groups 3 (n=805) and 4 (n=1,234) comprised drinkers with varying patterns, with Group 4 consuming the most. Over 10 years of follow-up, women in Groups 2 to 4 had hazard ratios (HR) for CHD of 1.57 (95% CI = 1.11-2.22), 1.57 (95% CI = 1.08-2.29), and 1.27 (95% CI = 1.05-1.55) compared to Group 1. Women inGroups 2 (HR = 1.26, 95% CI = 1.05-1.50) and 3 (HR = 1.27, 95% CI = 1.05-1.55) also had higher all-cause mortality risks. Men in Group 2 had higher mortality (HR = 1.18, 95% CI = 1.02-1.37, P = 0.030) and CHD (HR = 1.56, 95% CI = 1.07-1.52, P = 0.001) risks compared to Group 1, while men in Group 4 had the highest mortality risk (HR = 1.27, 95% CI = 1.02-1.37).ConclusionThis study identified four distinct alcohol consumption trajectories and demonstrated that maintaining low to moderate levels of alcohol drinking over time is likely associated with a lower risk of CHD and mortality in both women and men.
AlphaFold-Metainference: Prediction of Structural Ensembles of Disordered Proteins
Authors: Brotzakis Z. Faidon , Zhang Shengyu , Murtada Mhd Hussein , Vendruscolo Michele 
Published: November 2024

AbstractDeep learning methods of predicting protein structures have reached an accuracy comparable to that of high-resolution experimental methods. It is thus possible to generate accurate models of the native states of hundreds of millions of proteins. An open question, however, concerns whether these advances can be translated to disordered proteins, which should be represented as structural ensembles because of their heterogeneous and dynamical nature. To address this problem, we introduce the AlphaFold-Metainference method to use AlphaFold-derived distances as structural restraints in molecular dynamics simulations to construct structural ensembles of ordered and disordered proteins. The results obtained using AlphaFold-Metainference illustrate the possibility of making predictions of the conformational properties of disordered proteins using deep learning methods trained on the large structural databases available for folded proteins.
Improved precision, sensitivity, and adaptability of Ordered Two-Template Relay cDNA library preparation for RNA sequencing
Authors: Ferguson Lucas , Upton Heather E. , Pimentel Sydney C. , Jeans Chris , Ingolia Nicholas T. , Collins Kathleen 
Published: November 2024

AbstractSequencing RNAs that are biologically processed or degraded to less than ∼100 nucleotides typically involves multi-step, low-yield protocols with bias and information loss inherent to ligation and/or polynucleotide tailing. We recently introduced Ordered Two-Template Relay (OTTR), a method that captures obligatorily end-to-end sequences of input molecules and, in the same reverse transcription step, also appends 5′ and 3′ sequencing adapters of choice. OTTR has been thoroughly benchmarked for optimal production of microRNA, tRNA and tRNA fragments, and ribosome-protected mRNA footprint libraries. Here we sought to characterize, quantify, and ameliorate any remaining bias or imprecision in the end-to-end capture of RNA sequences. We introduce new metrics for the evaluation of sequence capture and use them to optimize reaction buffers, reverse transcriptase sequence, adapter oligonucleotides, and overall workflow. Modifications of the reverse transcriptase and adapter oligonucleotides increased the 3′ and 5′ end-precision of sequence capture and minimized overall library bias. Improvements in recombinant expression and purification of the truncatedBombyx moriR2 reverse transcriptase used in OTTR reduced non-productive sequencing reads by minimizing bacterial nucleic acids that compete with low-input RNA molecules for cDNA synthesis, such that with miRNA input of 3 picograms (less than 1 fmol), fewer than 10% of sequencing reads are bacterial nucleic acid contaminants. We also introduce a rapid, automation-compatible OTTR protocol that enables gel-free, length-agnostic enrichment of cDNA duplexes from unwanted adapter-only side products. Overall, this work informs considerations for unbiased end-to-end capture and annotation of RNAs independent of their sequence, structure, or post-transcriptional modifications.