bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spatial sequencing atlas of age-induced changes in the lung during influenza infection
Authors: Kasmani Moujtaba Y. , Topchyan Paytsar , Brown Ashley K. , Brown Ryan J. , Wu Xiaopeng , Chen Yao , Khatun Achia , Alson Donia , Wu Yue , Burns Robert , Lin Chien-Wei , Kudek Matthew R. , Sun Jie , Cui Weiguo 
Published: October 2023

AbstractInfluenza virus infection causes increased morbidity and mortality in the elderly. Aging impairs the immune response to influenza, both intrinsically and because of altered interactions with endothelial and pulmonary epithelial cells. To characterize these changes, we performed single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and bulk RNA sequencing (bulk RNA-seq) on lung tissue from young and aged female mice at days 0, 3, and 9 post-influenza infection. Our analyses identified dozens of key genes differentially expressed in kinetic, age-dependent, and cell type-specific manners. Aged immune cells exhibited altered inflammatory, memory, and chemotactic profiles. Aged endothelial cells demonstrated characteristics of reduced vascular wound healing and a prothrombotic state. Spatial transcriptomics identified novel profibrotic and antifibrotic markers expressed by epithelial and non-epithelial cells, highlighting the complex networks that promote fibrosis in aged lungs. Bulk RNA-seq generated a timeline of global transcriptional activity, showing increased expression of genes involved in inflammation and coagulation in aged lungs. Our work provides an atlas of high-throughput sequencing methodologies that can be used to investigate age-related changes in the response to influenza virus, identify novel cell-cell interactions for further study, and ultimately uncover potential therapeutic targets to improve health outcomes in the elderly following influenza infection.
Sonogenetic control of multiplexed genome regulation and base editing
Authors: Liu Pei , Foiret Josquin , Situ Yinglin , Zhang Nisi , Kare Aris J. , Wu Bo , Raie Marina N. , Ferrara Katherine W. , Qi Lei S. 
Published: October 2023

AbstractManipulating gene expression in the host genome with high precision is crucial for controlling cellular function and behavior. Here, we present a precise, non-invasive, and tunable strategy for controlling the expression of multiple endogenous genes both in vitro and in vivo, utilizing ultrasound as the stimulus. By engineering a hyper-efficient dCas12a and effector under a heat shock promoter, we demonstrate a system that can be inducibly activated through thermal energy produced by ultrasound absorption. This system allows versatile thermal induction of gene activation or base editing across cell types, including primary T cells, and enables multiplexed gene activation using a single guide RNA array. In mouse models, localized temperature elevation guided by high-intensity focused ultrasound effectively triggers reporter gene expression in implanted cells. Our work underscores the potential of ultrasound as a clinically viable approach to enhance cell and gene-based therapies via precision genome and epigenome engineering.
Subcycle surface electron emission driven by strong-field terahertz waveforms
Authors: Li Shaoxian , Sharma Ashutosh , Márton Zsuzsanna , Nugraha Priyo S. , Lombosi Csaba , Ollmann Zoltán , Márton István , Dombi Péter , Hebling János , Fülöp József A. 
Published: October 2023

AbstractThe advent of intense terahertz (THz) sources opened a new era when the demonstration of the acceleration and manipulation of free electrons by THz pulses became within reach. THz-field-driven electron emission was predicted to be confined to a single burst due to the single-cycle waveform. Here we demonstrate the confinement of single-cycle THz-waveform-driven electron emission to one of the two half cycles from a solid surface emitter. Either the leading or the trailing half cycle was active, controlled by reversing the field polarity. THz-driven single-burst surface electron emission sources, which do not rely on field-enhancement structures, will impact the development of THz-powered electron acceleration and manipulation devices, all-THz compact electron sources, THz waveguides and telecommunication, THz-field-based measurement techniques and solid-state devices.
The SMN complex drives structural changes in human snRNAs to enable snRNP assembly
Authors: Pánek Josef , Roithová Adriana , Radivojević Nenad , Sýkora Michal , Prusty Archana Bairavasundaram , Huston Nicholas , Wan Han , Pyle Anna Marie , Fischer Utz , Staněk David 
Published: October 2023

AbstractSpliceosomal snRNPs are multicomponent particles that undergo a complex maturation pathway. Human Sm-class snRNAs are generated as 3′-end extended precursors, which are exported to the cytoplasm and assembled together with Sm proteins into core RNPs by the SMN complex. Here, we provide evidence that these pre-snRNA substrates contain compact, evolutionarily conserved secondary structures that overlap with the Sm binding site. These structural motifs in pre-snRNAs are predicted to interfere with Sm core assembly. We model structural rearrangements that lead to an open pre-snRNA conformation compatible with Sm protein interaction. The predicted rearrangement pathway is conserved in Metazoa and requires an external factor that initiates snRNA remodeling. We show that the essential helicase Gemin3, which is a component of the SMN complex, is crucial for snRNA structural rearrangements during snRNP maturation. The SMN complex thus facilitates ATP-driven structural changes in snRNAs that expose the Sm site and enable Sm protein binding.
Infection- or AZD1222 vaccine-mediated immunity reduces SARS-CoV-2 transmission but increases Omicron competitiveness in hamsters
Authors: Port Julia R. , Yinda Claude Kwe , Riopelle Jade C. , Weishampel Zachary A. , Saturday Taylor A. , Avanzato Victoria A. , Schulz Jonathan E. , Holbrook Myndi G. , Barbian Kent , Perry-Gottschalk Rose , Haddock Elaine , Martens Craig , Shaia Carl. I. , Lambe Teresa , Gilbert Sarah C. , van Doremalen Neeltje , Munster Vincent J. 
Published: October 2023

AbstractLimited data is available on the effect of vaccination and previous virus exposure on the nature of SARS-CoV-2 transmission and immune-pressure on variants. To understand the impact of pre-existing immunity on SARS-CoV-2 airborne transmission efficiency, we perform a transmission chain experiment using naïve, intranasally or intramuscularly AZD1222 vaccinated, and previously infected hamsters. A clear gradient in transmission efficacy is observed: Transmission in hamsters vaccinated via the intramuscular route was reduced over three airborne chains (approx. 60%) compared to naïve animals, whereas transmission in previously infected hamsters and those vaccinated via the intranasal route was reduced by 80%. We also find that the Delta B.1.617.2 variant outcompeted Omicron B.1.1.529 after dual infection within and between hosts in naïve, vaccinated, and previously infected transmission chains, yet an increase in Omicron B.1.1.529 competitiveness is observed in groups with pre-existing immunity against Delta B.1.617.2. This correlates with an increase in the strength of the humoral response against Delta B.1.617.2, with the strongest response seen in previously infected animals. These data highlight the continuous need to improve vaccination strategies and address the additional evolutionary pressure pre-existing immunity may exert on SARS-CoV-2.
Arctic weather variability and connectivity
Authors: Meng Jun , Fan Jingfang , Bhatt Uma S. , Kurths Jürgen 
Published: October 2023

AbstractThe Arctic’s rapid sea ice decline may influence global weather patterns, making the understanding of Arctic weather variability (WV) vital for accurate weather forecasting and analyzing extreme weather events. Quantifying this WV and its impacts under human-induced climate change remains a challenge. Here we develop a complexity-based approach and discover a strong statistical correlation between intraseasonal WV in the Arctic and the Arctic Oscillation. Our findings highlight an increased variability in daily Arctic sea ice, attributed to its decline accelerated by global warming. This weather instability can influence broader regional patterns via atmospheric teleconnections, elevating risks to human activities and weather forecast predictability. Our analyses reveal these teleconnections and a positive feedback loop between Arctic and global weather instabilities, offering insights into how Arctic changes affect global weather. This framework bridges complexity science, Arctic WV, and its widespread implications.
Metabolic fingerprinting on retinal pigment epithelium thickness for individualized risk stratification of type 2 diabetes mellitus
Authors: Yang Shaopeng , Zhu Zhuoting , Chen Shida , Yuan Yixiong , He Mingguang , Wang Wei 
Published: October 2023

AbstractThe retina is an important target organ of diabetes mellitus, with increasing evidence from patients and animal models suggesting that retinal pigment epithelium (RPE) may serve as an early marker for diabetes-related damages. However, their longitudinal relationship and the biological underpinnings remain less well understood. Here, we demonstrate that reduced in vivo measurements of RPE thickness (RPET) represents a significant risk factor for future type 2 diabetes mellitus (T2DM) and its microvascular phenotypes. After performing systematic analyses of circulating plasma metabolites using two complementary approaches, we identify a wide range of RPET metabolic fingerprints that are independently associated with reduced RPET. These fingerprints hold their potential to improve predictability and clinical utility for stratifying future T2DM and related microvascular phenotypes beyond traditional clinical indicators, providing insights into the promising role of retinas as a window to systemic health.
The ClpX protease is essential for inactivating the CI master repressor and completing prophage induction in Staphylococcus aureus
Authors: Thabet Mohammed A. , Penadés José R. , Haag Andreas F. 
Published: October 2023

AbstractBacteriophages (phages) are the most abundant biological entities on Earth, exerting a significant influence on the dissemination of bacterial virulence, pathogenicity, and antimicrobial resistance. Temperate phages integrate into the bacterial chromosome in a dormant state through intricate regulatory mechanisms. These mechanisms repress lytic genes while facilitating the expression of integrase and the CI master repressor. Upon bacterial SOS response activation, the CI repressor undergoes auto-cleavage, producing two fragments with the N-terminal domain (NTD) retaining significant DNA-binding ability. The process of relieving CI NTD repression, essential for prophage induction, remains unknown. Here we show a specific interaction between the ClpX protease and CI NTD repressor fragment of phages Ф11 and 80α in Staphylococcus aureus. This interaction is necessary and sufficient for prophage activation after SOS-mediated CI auto-cleavage, defining the final stage in the prophage induction cascade. Our findings unveil unexpected roles of bacterial protease ClpX in phage biology.
Microgravity studies of solidification patterns in model transparent alloys onboard the International Space Station
Authors: Akamatsu S. , Bottin-Rousseau S. , Witusiewicz V. T. , Hecht U. , Plapp M. , Ludwig A. , Mogeritsch J. , Şerefoğlu M. , Bergeon N. , Mota F. L. , Sturz L. , Zimmermann G. , McFadden S. , Sillekens W. 
Published: October 2023

AbstractWe review recent in situ solidification experiments using nonfaceted model transparent alloys in science-in-microgravity facilities onboard the International Space Station (ISS), namely the Transparent Alloys (TA) apparatus and the Directional Solidification Insert of the DEvice for the study of Critical Liquids and Crystallization (DECLIC-DSI). These directional-solidification devices use innovative optical videomicroscopy imaging techniques to observe the spatiotemporal dynamics of solidification patterns in real time in large samples. In contrast to laboratory conditions on ground, microgravity guarantees the absence or a reduction of convective motion in the liquid, thus ensuring a purely diffusion-controlled growth of the crystalline solid(s). This makes it possible to perform a direct theoretical analysis of the formation process of solidification microstructures with comparisons to quantitative numerical simulations. Important questions that concern multiphase growth patterns in eutectic and peritectic alloys on the one hand and single-phased, cellular and dendritic structures on the other hand have been addressed, and unprecedented results have been obtained. Complex self-organizing phenomena during steady-state and transient coupled growth in eutectics and peritectics, interfacial-anisotropy effects in cellular arrays, and promising insights into the columnar-to-equiaxed transition are highlighted.
Mediation and longitudinal analysis to interpret the association between clozapine pharmacokinetics, pharmacogenomics, and absolute neutrophil count
Authors: Lock Siobhan K. , Legge Sophie E. , Kappel Djenifer B. , Willcocks Isabella R. , Helthuis Marinka , Jansen John , Walters James T. R. , Owen Michael J. , O’Donovan Michael C. , Pardiñas Antonio F. 
Published: October 2023

AbstractClozapine is effective at reducing symptoms of treatment-resistant schizophrenia, but it can also induce several adverse outcomes including neutropenia and agranulocytosis. We used linear mixed-effect models and structural equation modelling to determine whether pharmacokinetic and genetic variables influence absolute neutrophil count in a longitudinal UK-based sample of clozapine users not currently experiencing neutropenia (N = 811). Increased daily clozapine dose was associated with elevated neutrophil count, amounting to a 133 cells/mm3 rise per standard deviation increase in clozapine dose. One-third of the total effect of clozapine dose was mediated by plasma clozapine and norclozapine levels, which themselves demonstrated opposing, independent associations with absolute neutrophil count. Finally, CYP1A2 pharmacogenomic activity score was associated with absolute neutrophil count, supporting lower neutrophil levels in CYP1A2 poor metabolisers during clozapine use. This information may facilitate identifying at-risk patients and then introducing preventative interventions or individualised pharmacovigilance procedures to help mitigate these adverse haematological reactions.
A benchmark dataset for machine learning in ecotoxicology
Authors: Schür Christoph , Gasser Lilian , Perez-Cruz Fernando , Schirmer Kristin , Baity-Jesi Marco 
Published: October 2023

AbstractThe use of machine learning for predicting ecotoxicological outcomes is promising, but underutilized. The curation of data with informative features requires both expertise in machine learning as well as a strong biological and ecotoxicological background, which we consider a barrier of entry for this kind of research. Additionally, model performances can only be compared across studies when the same dataset, cleaning, and splittings were used. Therefore, we provide ADORE, an extensive and well-described dataset on acute aquatic toxicity in three relevant taxonomic groups (fish, crustaceans, and algae). The core dataset describes ecotoxicological experiments and is expanded with phylogenetic and species-specific data on the species as well as chemical properties and molecular representations. Apart from challenging other researchers to try and achieve the best model performances across the whole dataset, we propose specific relevant challenges on subsets of the data and include datasets and splittings corresponding to each of these challenge as well as in-depth characterization and discussion of train-test splitting approaches.
IRIDIA-AF, a large paroxysmal atrial fibrillation long-term electrocardiogram monitoring database
Authors: Gilon Cédric , Grégoire Jean-Marie , Mathieu Marianne , Carlier Stéphane , Bersini Hugues 
Published: October 2023

AbstractAtrial fibrillation (AF) is the most common sustained heart arrhythmia in adults. Holter monitoring, a long-term 2-lead electrocardiogram (ECG), is a key tool available to cardiologists for AF diagnosis. Machine learning (ML) and deep learning (DL) models have shown great capacity to automatically detect AF in ECG and their use as medical decision support tool is growing. Training these models rely on a few open and annotated databases. We present a new Holter monitoring database from patients with paroxysmal AF with 167 records from 152 patients, acquired from an outpatient cardiology clinic from 2006 to 2017 in Belgium. AF episodes were manually annotated and reviewed by an expert cardiologist and a specialist cardiac nurse. Records last from 19 hours up to 95 hours, divided into 24-hour files. In total, it represents 24 million seconds of annotated Holter monitoring, sampled at 200 Hz. This dataset aims at expanding the available options for researchers and offers a valuable resource for advancing ML and DL use in the field of cardiac arrhythmia diagnosis.
Optimal heat emissivity control of n population system based on individual size-distribution
Authors: Ba Zhenggang , Wang Ye 
Published: October 2023

AbstractThis paper generalizes a class of controllability problems based on the scale structure population system model. Based on the comparison principle of linear systems, the solution of the nonlinear system model is obtained by referring to the fixed point theorem. The non-negative, boundedness, existence, and uniqueness of the solution of the system model are established. The optimality condition is described in detail by means of a normal cone and conjugate system under the condition of proving the continuous dependence of the state environment on the solution to control variables.
Correlation analysis of obesity phenotypes with leptin and adiponectin
Authors: Aisike Guliqiekeran , Kuerbanjiang Maierheba , Muheyati Dina , Zaibibuli Kaibinuer , Lv Mei-Xia , Han Jia 
Published: October 2023

AbstractObesity can be categorized as metabolically healthy obesity (MHO) and metabolically unhealthy obesity (MUO). However, individuals with MHO are characterized by the absence of metabolic syndrome (MS) and appear to have lower inflammation levels compared to MUO. This study aimed to investigate the association of obesity phenotypes with leptin (LEP) and adiponectin (ADP). According to the inclusion and exclusion criteria, we selected 178 subjects from the previous cross-sectional survey. Based on the body mass index (BMI) and diagnostic criteria of MS, we divided the individuals into three groups, including healthy control group (HC group), metabolically healthy obesity group (MHO group) and metabolically unhealthy obesity group (MUO group). The concentrations of LEP and ADP in serum were measured, and the association of these two cytokines with different obesity phenotypes were subsequently analyzed. Compared to both the HC and MHO groups, the MUO group showed significantly higher BMI, waist circumference (WC), waist-hip ratio (WHR), triglyceride (TG), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), fasting plasma glucose (FPG), homeostasis model assessment of insulin resistance (Homa-IR) and blood pressure (P < 0.05). In contrast, serum high-density lipoprotein cholesterol (HDL-C) was notably lower in the MUO group (P < 0.05). ADP was found to have a positive correlation with systolic blood pressure (SBP) and a negative correlation with FPG in the MHO group. In the MUO group, LEP demonstrated a positive correlation with fasting insulin (FINS) and Homa-IR, while ADP showed a positive correlation with TC and SBP. Linear regression analysis further indicated that SBP (β = 0.234, P = 0.043), TG (β = − 0.292, P = 0.001) and LDL-C (β = 0.626, P = 0.000) were independently correlated with ADP, and BMI (β = 0.398, P = 0.002) was independently correlated with LEP in obese individuals. In conclusion, ADP and LEP were closely related with glucose and lipid metabolism in obese individuals, these two cytokines might play critical roles in obesity-associated metabolic disorders.
An empirical comparison of deep learning explainability approaches for EEG using simulated ground truth
Authors: Sujatha Ravindran Akshay , Contreras-Vidal Jose 
Published: October 2023

AbstractRecent advancements in machine learning and deep learning (DL) based neural decoders have significantly improved decoding capabilities using scalp electroencephalography (EEG). However, the interpretability of DL models remains an under-explored area. In this study, we compared multiple model explanation methods to identify the most suitable method for EEG and understand when some of these approaches might fail. A simulation framework was developed to evaluate the robustness and sensitivity of twelve back-propagation-based visualization methods by comparing to ground truth features. Multiple methods tested here showed reliability issues after randomizing either model weights or labels: e.g., the saliency approach, which is the most used visualization technique in EEG, was not class or model-specific. We found that DeepLift was consistently accurate as well as robust to detect the three key attributes tested here (temporal, spatial, and spectral precision). Overall, this study provides a review of model explanation methods for DL-based neural decoders and recommendations to understand when some of these methods fail and what they can capture in EEG.
Relative lateral wall thickness is an improved predictor for postoperative lateral wall fracture after trochanteric femoral fracture osteosynthesis
Authors: van Knegsel Kenneth P. , Hsu C.-E. , Huang K.-C. , Benca Emir , Pastor Torsten , Ganse Bergita , Varga Peter , Gueorguiev Boyko , Knobe Matthias 
Published: October 2023

AbstractLateral wall thickness is a known predictor for postoperative stability of trochanteric femoral fractures and occurrence of secondary lateral wall fractures. Currently, the AO/OTA classification relies on the absolute lateral wall thickness (aLWT) to distinguish between stable A1.3 and unstable A2.1 fractures that does not take interpersonal patient differences into account. Thus, a more individualized and accurate measure would be favorable. Therefore, we proposed and validated a new patient-specific measure—the relative lateral wall thickness (rLWT)—to consider individualized measures and hypothesized its higher sensitivity and specificity compared with aLWT. First, in 146 pelvic radiographs of patients without a trochanteric femoral fracture, the symmetry of both caput-collum-diaphyseal angle (CCD) and total trochanteric thickness (TTT) was assessed to determine whether the contralateral side can be used for rLWT determination. Then, data of 202 patients were re-evaluated to compare rLWT versus previously published aLWT. Bilateral symmetry was found for both CCD and TTT (p ≥ 0.827), implying that bone morphology and geometry of the contralateral intact side could be used to calculate rLWT. Validation revealed increased accuracy of the rLWT compared with the gold standard aLWT, with increased specificity by 3.5% (Number Needed to Treat = 64 patients) and sensitivity by 1% (Number Needed to Treat = 75 patients). The novel rLWT is a more accurate and individualized predictor of secondary lateral wall fractures compared with the standard aLWT. This study established the threshold of 50.5% rLWT as a reference value for predicting fracture stability in trochanteric femoral fractures.