bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct prediction of intrinsically disordered protein conformational properties from sequence
Authors: Lotthammer Jeffrey M. , Ginell Garrett M. , Griffith Daniel , Emenecker Ryan J. , Holehouse Alex S. 
Published: January 2024

AbstractIntrinsically disordered regions (IDRs) are ubiquitous across all domains of life and play a range of functional roles. While folded domains are generally well described by a stable three-dimensional structure, IDRs exist in a collection of interconverting states known as an ensemble. This structural heterogeneity means that IDRs are largely absent from the Protein Data Bank, contributing to a lack of computational approaches to predict ensemble conformational properties from sequence. Here we combine rational sequence design, large-scale molecular simulations and deep learning to develop ALBATROSS, a deep-learning model for predicting ensemble dimensions of IDRs, including the radius of gyration, end-to-end distance, polymer-scaling exponent and ensemble asphericity, directly from sequences at a proteome-wide scale. ALBATROSS is lightweight, easy to use and accessible as both a locally installable software package and a point-and-click-style interface via Google Colab notebooks. We first demonstrate the applicability of our predictors by examining the generalizability of sequence–ensemble relationships in IDRs. Then, we leverage the high-throughput nature of ALBATROSS to characterize the sequence-specific biophysical behavior of IDRs within and between proteomes.
Tropomyosin 1-I/C coordinates kinesin-1 and dynein motors during oskar mRNA transport
Authors: Heber Simone , McClintock Mark A. , Simon Bernd , Mehtab Eve , Lapouge Karine , Hennig Janosch , Bullock Simon L. , Ephrussi Anne 
Published: January 2024

AbstractDynein and kinesin motors mediate long-range intracellular transport, translocating towards microtubule minus and plus ends, respectively. Cargoes often undergo bidirectional transport by binding to both motors simultaneously. However, it is not known how motor activities are coordinated in such circumstances. In theDrosophilafemale germline, sequential activities of the dynein–dynactin–BicD–Egalitarian (DDBE) complex and of kinesin-1 deliveroskarmessenger RNA from nurse cells to the oocyte, and within the oocyte to the posterior pole. We show through in vitro reconstitution that Tm1-I/C, a tropomyosin-1 isoform, links kinesin-1 in a strongly inhibited state to DDBE-associatedoskarmRNA. Nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and structural modeling indicate that Tm1-I/C suppresses kinesin-1 activity by stabilizing its autoinhibited conformation, thus preventing competition with dynein until kinesin-1 is activated in the oocyte. Our work reveals a new strategy for ensuring sequential activity of microtubule motors.
MALDI-TOF as a powerful tool for identifying and differentiating closely related microorganisms: the strange case of three reference strains of Paenibacillus polymyxa
Authors: Lebano Ilaria , Fracchetti Fabio , Vigni Mario Li , Mejia Juan Fernando , Felis Giovanna , Lampis Silvia 
Published: January 2024

AbstractAccurate identification and typing of microbes are crucial steps in gaining an awareness of the biological heterogeneity and reliability of microbial material within any proprietary or public collection.Paenibacillus polymyxais a bacterial species of great agricultural and industrial importance due to its plant growth-promoting activities and production of several relevant secondary metabolites. In recent years, matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used as an alternative rapid tool for identifying, typing, and differentiating closely related strains. In this study, we investigated the diversity of threeP. polymyxastrains. The mass spectra of ATCC 842T, DSM 292, and DSM 365 were obtained, analysed, and compared to select discriminant peaks using ClinProTools software and generate classification models. MALDI-TOF MS analysis showed inconsistent results in identifying DSM 292 and DSM 365 as belonging toP. polimixaspecies, and comparative analysis of mass spectra revealed the presence of highly discriminatory biomarkers among the three strains. 16S rRNA sequencing and Average Nucleotide Identity (ANI) confirmed the discrepancies found in the proteomic analysis. The case study presented here suggests the enormous potential of the proteomic-based approach, combined with statistical tools, to predict and explore differences between closely related strains in large microbial datasets.
Research on improved black widow algorithm for medical image denoising
Authors: Qu Hepeng , Liu Kun , Zhang Lina 
Published: January 2024

AbstractImproving the quality of medical images is crucial for accurate clinical diagnosis; however, medical images are often disrupted by various types of noise, posing challenges to the reliability and diagnostic accuracy of the images. This study aims to enhance the Black Widow optimization algorithm and apply it to the task of denoising medical images to improve both the quality of medical images and the accuracy of diagnostic results. By introducing Tent mapping, we refined the Black Widow optimization algorithm to better adapt to the complex features of medical images. The algorithm's denoising capabilities for various types of noise were enhanced through the combination of multiple filters, all without the need for training each time to achieve preset goals. Simulation results, based on processing a dataset containing 1588 images with Gaussian, salt-and-pepper, Poisson, and speckle noise, demonstrated a reduction in Mean Squared Error (MSE) by 0.439, an increase in Peak Signal-to-Noise Ratio (PSNR) by 4.315, an improvement in Structural Similarity Index (SSIM) by 0.132, an enhancement in Edge-to-Noise Ratio (ENL) by 0.402, and an increase in Edge Preservation Index (EPI) by 0.614. Simulation experiments verified that the proposed algorithm has a certain advantage in terms of computational efficiency. The improvement, incorporating Tent mapping and a combination of multiple filters, successfully elevated the performance of the Black Widow algorithm in medical image denoising, providing an effective solution for enhancing medical image quality and diagnostic accuracy.
National prevalence and trends in food labeling awareness, comprehension, usage, and COVID-19 pandemic-related factors in South Korea, 2014–2022
Authors: Choi Yujin , Kim Hyeon Jin , Park Jaeyu , Lee Seung Won , Rahmati Masoud , Koyanagi Ai , Smith Lee , Kim Min Seo , López Sánchez Guillermo F. , Dragioti Elena , Lee Jinseok , Rhee Sang Youl , Kim Sunyoung , Lim Hyunjung , Yon Dong Keon 
Published: January 2024

AbstractAlthough food labeling on food packages is crucial for promoting a healthy diet, limited research has been conducted on how the COVID-19 pandemic (hereinafter “the pandemic”) has affected food labeling awareness. Therefore, this study aims to analyze the changes in trends in food labeling awareness, comprehension, and usage in South Korea during the pandemic. We utilized a nationwide, large-scale, and long-term dataset provided by the Korea Community Health Survey (KCHS) from 2014 to 2022 (total = 1,756,847 participants). This allowed the researchers to assess the long-term trends in the prevalence of food labeling awareness, comprehension, and usage. Furthermore, we investigated the factors associated with awareness specifically related to the pandemic. In total, 1,756,847 adults (54.19% women) participated in this study. The upward slope in overall food labeling awareness became less pronounced and even exhibited a downward slope during the pandemic (βdiff − 1.759; 95% CI − 1.874 to − 1.644). The upward slope in food labeling comprehension and usage became more pronounced during the pandemic (comprehension: βdiff 0.535; 95% CI 0.436–0.634; usage: βdiff 0.693; 95% CI 0.601–0.785). The vulnerability factors associated with lower food labeling awareness during the pandemic included older age, male, obesity, residing in rural areas, lower household income, lower educational level, smoking, and increased alcohol consumption. This study analyzed the 9-year trend in the prevalence of food labeling awareness, comprehension, and usage based on nationally representative data of adults in South Korea from 2014 to 2022. Our findings suggest that personalized nutrition strategies are needed to recognize vulnerable groups with risk factors and improve food labeling awareness among Korean adults during the pandemic.
Investigation of the emergency water supply schemes for youkou groundwater source field in Nanchang using a simulation–optimization model
Authors: Ma Qingshan , Wu Huijie , Ge Weiya , Zhang Jia 
Published: January 2024

AbstractTo enhance the resilience of Nanchang’s water supply system and ensure a dependable emergency water supply. Taking youkou emergency groundwater source field as an example, a flow simulation model was developed through an analysis of the hydrogeological conditions in the study area. Additionally, an optimization model based on the genetic algorithm (GA) technique was constructed and integrated into the flow simulation model. Subsequently, various water supply schemes were simulated with the minimum cost of groundwater extraction as the objective function. The results show that the values of the objective function were reduced by 4.92%, 15.67%, and 42.35% for the three different optimization schemes, namely pumping rates, joint pumping rates and the number of wells, and joint pumping rates, number of wells and well location. Ultimately, the optimal emergency water supply scheme was determined by considering a comprehensive range of factors. These factors encompassed considerations such as the area of the water level depression funnel, the dewatering thickness of the aquifer and the recovery of the groundwater level. The practice shows that the simulation–optimization model could effectively simulate complex groundwater flow systems, meeting the objective function and constraints toachieve the optimal exploitation scheme.
Temporal dynamics of the early immune response following Mycobacterium bovis infection of cattle
Authors: Holder Thomas , Srinivasan Sreenidhi , McGoldrick Adrian , Williams Gareth A. , Palmer Simonette , Clarke John , O’Brien Amanda , Conlan Andrew J. K. , Juleff Nick , Vordermeier H. Martin , Jones Gareth J. , Kapur Vivek 
Published: January 2024

AbstractBovine tuberculosis is an infectious disease of global significance that remains endemic in many countries. Mycobacterium bovis infection in cattle is characterized by a cell-mediated immune response (CMI) that precedes humoral responses, however the timing and trajectories of CMI and antibody responses determined by newer generation assays remain undefined. Here we used defined-antigen interferon-gamma release assays (IGRA) and an eleven-antigen multiplex ELISA (Enferplex TB test) alongside traditional tuberculin-based IGRA and IDEXX M. bovis antibody tests to assess immune trajectories following experimental M. bovis infection of cattle. The results show CMI responses developed as early as two-weeks post-infection, with all infected cattle testing positive three weeks post-infection. Interestingly, 6 of 8 infected animals were serologically positive with the Enferplex TB assay as early as 4 weeks post-infection. As expected, application of the tuberculin skin test enhanced subsequent serological reactivity. Infrequent M. bovis faecal shedding was observed but was uncorrelated with observed immune trajectories. Together, the results show that early antibody responses to M. bovis infection are detectable in some individuals and highlight an urgent need to identify biomarkers that better predict infection outcomes, particularly for application in low-and-middle income countries where test-and-slaughter based control methods are largely unfeasible.
Facial and genital color ornamentation, testosterone, and reproductive output in high-ranking male rhesus macaques
Authors: Sobral Gisela , Dubuc Constance , Winters Sandra , Ruiz‑Lambides Angelina , Emery Thompson Melissa , Maestripieri Dario , Milich Krista M. 
Published: January 2024

AbstractMales in many vertebrate species have colorful ornaments that evolved by sexual selection. The role of androgens in the genesis and maintenance of these signals is unclear. We studied 21 adult high-ranking male rhesus macaques from nine social groups in the free-ranging population on Cayo Santiago, Puerto Rico, and analyzed facial and genital skin luminance and redness, fecal androgens, rates of mating behaviors, and offspring sired. Facial and genital coloration varied in relation to age, mating behavior, reproductive success, and testosterone concentration. Our results indicate that skin coloration in high-ranking male rhesus macaques is a sexually-selected trait mediated by androgens. These results add to the growing literature on the proximate and ultimate causes of male sexual signals and highlight the need to examine how these characteristics change with age in other species.
Automated deep learning model for estimating intraoperative blood loss using gauze images
Authors: Yoon Dan , Yoo Mira , Kim Byeong Soo , Kim Young Gyun , Lee Jong Hyeon , Lee Eunju , Min Guan Hong , Hwang Du-Yeong , Baek Changhoon , Cho Minwoo , Suh Yun-Suhk , Kim Sungwan 
Published: January 2024

AbstractThe intraoperative estimated blood loss (EBL), an essential parameter for perioperative management, has been evaluated by manually weighing blood in gauze and suction bottles, a process both time-consuming and labor-intensive. As the novel EBL prediction platform, we developed an automated deep learning EBL prediction model, utilizing the patch-wise crumpled state (P-W CS) of gauze images with texture analysis. The proposed algorithm was developed using animal data obtained from a porcine experiment and validated on human intraoperative data prospectively collected from 102 laparoscopic gastric cancer surgeries. The EBL prediction model involves gauze area detection and subsequent EBL regression based on the detected areas, with each stage optimized through comparative model performance evaluations. The selected gauze detection model demonstrated a sensitivity of 96.5% and a specificity of 98.0%. Based on this detection model, the performance of EBL regression stage models was compared. Comparative evaluations revealed that our P-W CS-based model outperforms others, including one reliant on convolutional neural networks and another analyzing the gauze’s overall crumpled state. The P-W CS-based model achieved a mean absolute error (MAE) of 0.25 g and a mean absolute percentage error (MAPE) of 7.26% in EBL regression. Additionally, per-patient assessment yielded an MAE of 0.58 g, indicating errors < 1 g/patient. In conclusion, our algorithm provides an objective standard and streamlined approach for EBL estimation during surgery without the need for perioperative approximation and additional tasks by humans. The robust performance of the model across varied surgical conditions emphasizes its clinical potential for real-world application.
Analysis of related factors of plasma antibody levels in patients with severe and critical COVID-19
Authors: Xie Yudi , Xia Yang , Xu Haixia , Wang Jue , Zhang Wei , Li Ling , Liu Zhong 
Published: January 2024

AbstractCoronavirus disease 2019 (COVID-19) continues to impact global public health. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become less virulent as it mutates, prompting China to ease restrictions at the end of 2022. With the complete reopening, a surge in COVID-19 cases has ensued. Therefore, we conducted a study to explore the correlation between plasma antibody levels and baseline conditions or clinical outcomes in severe and critical patients. We collected the basic information of 79 included patients. Enzyme-linked immunosorbent assay (ELISA) tests were performed on plasma samples. The receptor-binding domain (RBD) IgG antibody level of the mild group was significantly higher than that of the severe/critical group (P = 0.00049). And in the severe/critical group, there existed an association between plasma antibody levels and age (P < 0.001, r = − 0.471), as well as plasma antibody levels and vaccination status (P = 0.00147, eta2 = 0.211). Besides, the level of plasma antibody seemed to be moderately correlated with the age, indicating the need for heightened attention to infections in the elderly. And plasma antibody levels were strongly associated with vaccination status in the severe/critical patients.
Evidence that recent climatic changes have expanded the potential geographical range of the Mediterranean fruit fly
Authors: Szyniszewska Anna M. , Bieszczak Hanna , Kozyra Karol , Papadopoulos Nikos T. , De Meyer Marc , Nowosad Jakub , Ota Noboru , Kriticos Darren J. 
Published: January 2024

AbstractThe species distributions migration poleward and into higher altitudes in a warming climate is especially concerning for economically important insect pest species, as their introduction can potentially occur in places previously considered unsuitable for year-round survival. We explore the expansion of the climatically suitable areas for a horticultural pest, the Mediterranean fruit fly (medfly) Ceratitis capitata (Diptera, Tephritidae), with an emphasis on Europe and California. We reviewed and refined a published CLIMEX model for C. capitata, taking into consideration new records in marginal locations, with a particular focus on Europe. To assess the model fit and to aid in interpreting the meaning of the new European distribution records, we used a time series climate dataset to explore the temporal patterns of climate suitability for C. capitata from 1970 to 2019. At selected bellwether sites in Europe, we found statistically significant trends in increasing climate suitability, as well as a substantial northward expansion in the modelled potential range. In California, we also found a significant trend of northward and altitudinal expansion of areas suitable for C. capitata establishment. These results provide further evidence of climate change impacts on species distributions and the need for innovative responses to increased invasion threats.
Modeling mutation-specific arrhythmogenic phenotypes in isogenic human iPSC-derived cardiac tissues
Authors: Maurissen Thomas L. , Kawatou Masahide , López-Dávila Víctor , Minatoya Kenji , Yamashita Jun K. , Woltjen Knut 
Published: January 2024

AbstractDisease modeling using human induced pluripotent stem cells (hiPSCs) from patients with genetic disease is a powerful approach for dissecting pathophysiology and drug discovery. Nevertheless, isogenic controls are required to precisely compare phenotypic outcomes from presumed causative mutations rather than differences in genetic backgrounds. Moreover, 2D cellular models often fail to exhibit authentic disease phenotypes resulting in poor validation in vitro. Here we show that a combination of precision gene editing and bioengineered 3D tissue models can establish advanced isogenic hiPSC-derived cardiac disease models, overcoming these drawbacks. To model inherited cardiac arrhythmias we selected representative N588D and N588K missense mutations affecting the same codon in the hERG potassium channel gene KCNH2, which are reported to cause long (LQTS) and short (SQTS) QT syndromes, respectively. We generated compound heterozygous variants in normal hiPSCs, and differentiated cardiomyocytes (CMs) and mesenchymal cells (MCs) to form 3D cardiac tissue sheets (CTSs). In hiPSC-derived CM monolayers and 3D CTSs, electrophysiological analysis with multielectrode arrays showed prolonged and shortened repolarization, respectively, compared to the isogenic controls. When pharmacologically inhibiting the hERG channels, mutant 3D CTSs were differentially susceptible to arrhythmic events than the isogenic controls. Thus, this strategy offers advanced disease models that can reproduce clinically relevant phenotypes and provide solid validation of gene mutations in vitro.
Olfactory system structure and function in newly hatched and adult locusts
Authors: Sun Kui , Ray Subhasis , Gupta Nitin , Aldworth Zane , Stopfer Mark 
Published: January 2024

AbstractAn important question in neuroscience is how sensory systems change as animals grow and interact with the environment. Exploring sensory systems in animals as they develop can reveal how networks of neurons process information as the neurons themselves grow and the needs of the animal change. Here we compared the structure and function of peripheral parts of the olfactory pathway in newly hatched and adult locusts. We found that populations of olfactory sensory neurons (OSNs) in hatchlings and adults responded with similar tunings to a panel of odors. The morphologies of local neurons (LNs) and projection neurons (PNs) in the antennal lobes (ALs) were very similar in both age groups, though they were smaller in hatchlings, they were proportional to overall brain size. The odor evoked responses of LNs and PNs were also very similar in both age groups, characterized by complex patterns of activity including oscillatory synchronization. Notably, in hatchlings, spontaneous and odor-evoked firing rates of PNs were lower, and LFP oscillations were lower in frequency, than in the adult. Hatchlings have smaller antennae with fewer OSNs; removing antennal segments from adults also reduced LFP oscillation frequency. Thus, consistent with earlier computational models, the developmental increase in frequency is due to increasing intensity of input to the oscillation circuitry. Overall, our results show that locusts hatch with a fully formed olfactory system that structurally and functionally matches that of the adult, despite its small size and lack of prior experience with olfactory stimuli.
Aerosolized delivery of ESKAPE pathogens for murine pneumonia models
Authors: Rox Katharina , Medina Eva 
Published: January 2024

AbstractMurine pneumonia models for ESKAPE pathogens serve to evaluate novel antibacterials or to investigate immunological responses. The majority of published models uses intranasal or to a limited extent the intratracheal instillation to challenge animals. In this study, we propose the aerosol delivery of pathogens using a nebulizer. Aerosol delivery typically results in homogeneous distribution of the inoculum in the lungs because of lower particle size. This is of particular importance when compounds are assessed for their pharmacokinetic and pharmacodynamic (PK/PD) relationships as it allows to conduct several analysis with the same sample material. Moreover, aerosol delivery has the advantage that it mimics the ‘natural route’ of respiratory infection. In this short and concise study, we show that aerosol delivery of pathogens resulted in a sustained bacterial burden in the neutropenic lung infection model for five pathogens tested, whereas it gave a similar result in immunocompetent mice for three out of five pathogens. Moreover, a substantial bacterial burden in the lungs was already achieved 2 h post inhalation. Hence, this study constitutes a viable alternative for intranasal administration and a refinement of murine pneumonia models for PK/PD assessments of novel antibacterial compounds allowing to study multiple readouts with the same sample material.