bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determinants of epidemic size and the impacts of lulls in seasonal influenza virus circulation
Authors: de Jong Simon P. J. , Felix Garza Zandra C. , Gibson Joseph C. , van Leeuwen Sarah , de Vries Robert P. , Boons Geert-Jan , van Hoesel Marliek , de Haan Karen , van Groeningen Laura E. , Hulme Katina D. , van Willigen Hugo D. G. , Wynberg Elke , de Bree Godelieve J. , Matser Amy , Bakker Margreet , van der Hoek Lia , Prins Maria , Kootstra Neeltje A. , Eggink Dirk , Nichols Brooke E. , Han Alvin X. , de Jong Menno D. , Russell Colin A. 
Published: January 2024

AbstractDuring the COVID-19 pandemic, levels of seasonal influenza virus circulation were unprecedentedly low, leading to concerns that a lack of exposure to influenza viruses, combined with waning antibody titres, could result in larger and/or more severe post-pandemic seasonal influenza epidemics. However, in most countries the first post-pandemic influenza season was not unusually large and/or severe. Here, based on an analysis of historical influenza virus epidemic patterns from 2002 to 2019, we show that historic lulls in influenza virus circulation had relatively minor impacts on subsequent epidemic size and that epidemic size was more substantially impacted by season-specific effects unrelated to the magnitude of circulation in prior seasons. From measurements of antibody levels from serum samples collected each year from 2017 to 2021, we show that the rate of waning of antibody titres against influenza virus during the pandemic was smaller than assumed in predictive models. Taken together, these results partially explain why the re-emergence of seasonal influenza virus epidemics was less dramatic than anticipated and suggest that influenza virus epidemic dynamics are not currently amenable to multi-season prediction.
Nanoparticle-based DNA vaccine protects against SARS-CoV-2 variants in female preclinical models
Authors: Guimaraes Lays Cordeiro , Costa Pedro Augusto Carvalho , Scalzo Júnior Sérgio Ricardo Aluotto , Ferreira Heloísa Athaydes Seabra , Braga Ana Carolina Soares , de Oliveira Leonardo Camilo , Figueiredo Maria Marta , Shepherd Sarah , Hamilton Alex , Queiroz-Junior Celso Martins , da Silva Walison Nunes , da Silva Natália Jordana Alves , Rodrigues Alves Marco Túllio , Santos Anderson Kenedy , de Faria Kevin Kelton Santos , Marim Fernanda Martins , Fukumasu Heidge , Birbrair Alexander , Teixeira-Carvalho Andréa , de Aguiar Renato Santana , Mitchell Michael J. , Teixeira Mauro Martins , Vasconcelos Costa Vivian , Frezard Frederic , Guimaraes Pedro Pires Goulart 
Published: January 2024

AbstractA safe and effective vaccine with long-term protection against SARS-CoV-2 variants of concern (VOCs) is a global health priority. Here, we develop lipid nanoparticles (LNPs) to provide safe and effective delivery of plasmid DNA (pDNA) and show protection against VOCs in female small animal models. Using a library of LNPs encapsulating unique barcoded DNA (b-DNA), we screen for b-DNA delivery after intramuscular administration. The top-performing LNPs are further tested for their capacity of pDNA uptake in antigen-presenting cells in vitro. The lead LNP is used to encapsulate pDNA encoding the HexaPro version of SARS-CoV-2 spike (LNP-HPS) and immunogenicity and protection is tested in vivo. LNP-HPS elicit a robust protective effect against SARS-CoV-2 Gamma (P.1), correlating with reduced lethality, decreased viral load in the lungs and reduced lung damage. LNP-HPS induce potent humoral and T cell responses against P.1, and generate high levels of neutralizing antibodies against P.1 and Omicron (B.1.1.529). Our findings indicate that the protective efficacy and immunogenicity elicited by LNP-HPS are comparable to those achieved by the approved COVID-19 vaccine from Biontech/Pfizer in animal models. Together, these findings suggest that LNP-HPS hold great promise as a vaccine candidate against VOCs.
Acetylcholine receptor based chemogenetics engineered for neuronal inhibition and seizure control assessed in mice
Authors: Nguyen Quynh-Anh , Klein Peter M. , Xie Cheng , Benthall Katelyn N. , Iafrati Jillian , Homidan Jesslyn , Bendor Jacob T. , Dudok Barna , Farrell Jordan S. , Gschwind Tilo , Porter Charlotte L. , Keravala Annahita , Dodson G. Steven , Soltesz Ivan 
Published: January 2024

AbstractEpilepsy is a prevalent disorder involving neuronal network hyperexcitability, yet existing therapeutic strategies often fail to provide optimal patient outcomes. Chemogenetic approaches, where exogenous receptors are expressed in defined brain areas and specifically activated by selective agonists, are appealing methods to constrain overactive neuronal activity. We developed BARNI (Bradanicline- and Acetylcholine-activated Receptor for Neuronal Inhibition), an engineered channel comprised of the α7 nicotinic acetylcholine receptor ligand-binding domain coupled to an α1 glycine receptor anion pore domain. Here we demonstrate that BARNI activation by the clinical stage α7 nicotinic acetylcholine receptor-selective agonist bradanicline effectively suppressed targeted neuronal activity, and controlled both acute and chronic seizures in male mice. Our results provide evidence for the use of an inhibitory acetylcholine-based engineered channel activatable by both exogenous and endogenous agonists as a potential therapeutic approach to treating epilepsy.
Mobility networks in Greater Mexico City
Authors: Flores-Garrido Marisol , de Anda-Jáuregui Guillermo , Guzmán Plinio , Meneses-Viveros Amilcar , Hernández-Álvarez Alfredo , Cruz-Bonilla Erika , Hernández-Rosales Maribel 
Published: January 2024

AbstractBased on more than 11 billion geolocated cell phone records from 33 million different devices, daily mobility networks were constructed over a 15-month period for Greater Mexico City, one of the largest and most diverse metropolitan areas globally. The time frame considered spans the entire year of 2020 and the first three months of 2021, enabling the analysis of population movement dynamics before, during, and after the COVID-19 health contingency. The nodes within the 456 networks represent the basic statistical geographic areas (AGEBs) established by the National Institute of Statistics, Geography, and Informatics (INEGI) in Mexico. This framework facilitates the integration of mobility data with numerous indicators provided by INEGI. Edges connecting these nodes represent movement between AGEBs, with edge weights indicating the volume of trips from one AGEB to another. This extensive dataset allows researchers to uncover travel patterns, cross-reference data with socio-economic indicators, and conduct segregation studies, among other potential analyses.
A chromosome-level genome assembly of the Echiura Urechis unicinctus
Authors: Cheng Yunying , Chen Ruanni , Chen Jinlin , Huang Wanlong , Chen Jianming 
Published: January 2024

AbstractEchiura is a distinctive family of unsegmented sausage-shaped marine worms whose phylogenetic relationship still needs strong evidence from the phylogenomic analysis. In this family, Urechis unicinctus is known for its high nutritional and medicinal value and adaptation to harsh intertidal conditions. Herein, we combined PacBio long-read, short-read Illumina and Hi-C sequencing, generating a high-quality chromosome-level genome assembly of U. unicinctus. The assembled genome spans ~1,138.6 Mb with a scaffold N50 of 68.3 Mb, of which 1,113.8 Mb (97.82%) were anchored into 17 pseudo-chromosomes. The BUSCO analysis demonstrated the completeness of the genome assembly and gene model prediction are 93.5% and 91.5%, respectively. A total of 482.1 Mb repetitive sequences, 21,524 protein-coding genes, 1,535 miRNAs, 3,431 tRNAs, 124 rRNAs, and 348 snRNAs were annotated. This study significantly improves the quality of U. unicinctus genome assembly, sets the footsteps for molecular breeding and further study in genome evolution, genetic and molecular biology of U. unicinctus.
A dataset of oracle characters for benchmarking machine learning algorithms
Authors: Wang Mei , Deng Weihong 
Published: January 2024

AbstractOracle bone script is an ancient Chinese writing system engraved on turtle shells and animal bones, serving as a valuable resource for interpreting ancient culture, history, and language. We introduce the Oracle-MNIST dataset, comprising of 28 × 28 grayscale images of 30,222 ancient characters from 10 categories, designed for benchmarking pattern classification, with particular challenges related to image noise and distortion. The training set totally consists of 27,222 images, and the test set contains 300 images per class. Oracle-MNIST follows the same data format with the original MNIST dataset, enabling direct compatibility with all existing classifiers and systems, but it constitutes a more challenging classification task than MNIST. The images of ancient characters suffer from (1) extremely serious and unique noises caused by three-thousand years of burial and aging and (2) dramatically variant writing styles by ancient Chinese, which all make them realistic for machine learning research.
Geospatial data on the sediments of Lake Balaton
Authors: Kocsis Mihály , Pásztor László , Makó András , Kassai Piroska , Csermák Kálmán , Csermák Alice , Aradvári-Tóth Erzsébet , Szatmári Gábor 
Published: January 2024

AbstractFreshwater lakes in most inhabited areas of the world are threatened by water quality issues. Standard water conservation measures have shown efficiency in the past; however, polluted lakes have only partially recovered from eutrophication. Our knowledge is still incomplete about the sensitivity of these lakes to different anthropogenic sources and to the changes in their internal processes due to global warming. In this article, we present a database comprising sediment data from Lake Balaton (Hungary), which can facilitate further analysis helping to better understand the internal processes and changes occurring in the lake. The published dataset includes the following parameters measured in 4211 lake bed sediment samples: pHKCl, calcium carbonate (CaCO3), organic carbon (Corg), total nitrogen (Ntotal), soluble phosphorus (AL-P2O5) and soluble potassium (AL-K2O), magnesium (Mg2+), zinc (Zn2+), copper (Cu2+) and manganese (Mn2+). We are confident that our database serves as a strong basis for further research relating to freshwater lakes influenced by human activities.
Depth-dependent microbial metagenomes sampled in the northeastern Indian Ocean
Authors: Wang Xiaomeng , Zain Ul Arifeen Muhammad , Hou Shengwei , Zheng Qiang 
Published: January 2024

AbstractThe northeastern Indian Ocean exhibits distinct hydrographic characteristics influenced by various local and remote forces. Variations in these driving factors may alter the physiochemical properties of seawater, such as dissolved oxygen levels, and affect the diversity and function of microbial communities. How the microbial communities change across water depths spanning a dissolved oxygen gradient has not been well understood. Here we employed both 16S rDNA amplicon and metagenomic sequencing approaches to study the microbial communities collected from different water depths along the E87 transect in the northeastern Indian Ocean. Samples were collected from the surface, Deep Chlorophyll Maximum (DCM), Oxygen Minimum Zone (OMZ), and bathypelagic layers. Proteobacteria were prevalent throughout the water columns, while Thermoproteota were found to be abundant in the aphotic layers. A total of 675 non-redundant metagenome-assembled genomes (MAGs) were constructed, spanning 21 bacterial and 5 archaeal phyla. The community structure and genomic information provided by this dataset offer valuable resources for the analysis of microbial biogeography and metabolism in the northeastern Indian Ocean.
Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals
Authors: Kırdök Emrah , Kashuba Natalija , Damlien Hege , Manninen Mikael A. , Nordqvist Bengt , Kjellström Anna , Jakobsson Mattias , Lindberg A. Michael , Storå Jan , Persson Per , Andersson Björn , Aravena Andrés , Götherström Anders 
Published: January 2024

AbstractPrehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890–9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70–80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.
A new (T-X$$^\theta$$) family of distributions: properties, discretization and estimation with applications
Authors: Mandouh Rasha M. , Mahmoud Mahmoud R. , Abdelatty Rasha E. 
Published: January 2024

AbstractIn this paper, a new class of distributions called the T-X$$^\theta$$

θ

family of distributions for bounded—(0,1)—and unbounded—$$(0,\infty )$$

(
0
,
∞
)

—supported random variables is suggested. Some special sub-models of the proposed family are utilized. A new sub-model is selected to be studied in details. The statistical properties of the suggested family including quantile function, moments, moment generating function, order statistics and Rényi entropy are discussed. The maximum likelihood method is provided to estimate the parameters of the distribution and a Monte Carlo simulation study is used. The discretized T-X$$^\theta$$

θ

family provided many sub-families and sub-models. In addition, eight real data sets are utilized to demonstrate the flexibility of the proposed continuous and discrete family’s multiple sub models.
Rapid detection method of bacterial pathogens in surface waters and a new risk indicator for water pathogenic pollution
Authors: Gao Min , Tan Feiyang , Shen Yuan , Peng Yao 
Published: January 2024

AbstractIn this study, a accurate, rapid quantitative PCR method for the simultaneous detection of 4 kinds of pathogenic bacteria in water was established, and the distribution of pathogenic bacteria in surface waters with different levels of pollution (Yulin region, China) was detected. The results showed that the detection accuracy was 94%; the detection limit was 2.7 in bacterial cells. Salmonella enterica subsp. enterica serovar typhimurium and Salmonella dysenteria were always present in water when the universal primer for pathogenic bacteria abundance detection was greater than 104 copies 100 mL−1. When the detection value is lower than 104 copy 100 mL−1, the bacteria in the water are rarely pathogenic bacteria, so the detection value of 104 copy 100 mL−1 can be used as a new indicator of waterborne pathogen pollution.
Potassium humate and cobalt enhance peanut tolerance to water stress through regulation of proline, antioxidants, and maintenance of nutrient homeostasis
Authors: Elshamly Ayman M. S. , Parrey Zubair Ahmad , Gaafar Abdel-Rhman Z. , Siddiqui Manzer H. , Hussain Sadam 
Published: January 2024

AbstractWater stress is an important factor that substantially impacts crop production. As a result, there is a need for various strategies that can mitigate these negative effects. One such strategy is the application of potassium humate (Kh) and cobalt (Co), which have been reported to enhance the resistance of crop plants. Therefore, the present experiment was designed to investigate whether the application of Kh and Co could positively affect proline, chlorophyll and mineral elements contents, and antioxidant defense systems which in turn will mitigate the negative impact of water stress under different irrigation strategies. In 2021 and 2022, an open-field experiments were conducted by using a split-plot design. The main plots were divided to represent different irrigation strategies (ST), with additional control of full irrigation requirements (ST1). Four STs were implemented, with ST1, followed by the application of 75%, 50%, and 25% irrigation strategies in ST2, ST3, and ST4 respectively, in the next irrigation, followed by the full requirements, and so on. In the subplots, peanut plants were treated with tap water (Control), Kh at 2 g l−1 and 3 g l−1, Co, Co + Kh 2 g l−1 and Co + Kh 3 g l−1. The yield was negatively affected by the implementation of ST4, despite the increase in proline contents. Furthermore, there was a decrease in relative water content, chlorophyll content, antioxidant enzymes, protein, and mineral nutrient elements. However, the application of Kh or Co showed better improvements in most of the studied parameters. It is worth noting that there was an antagonistic relationship between Co and iron/manganese, and the intensity of this relationship was found to depend on the STs implemented. The highest mineral nutrient accumulation, chlorophyll content, relative water content, protein content, oil content, seed yield, and water productivity were observed when peanut plants were treated with Kh 3 g l−1 + Co under the ST2 water strategy.
Development and validation of a prognostic nomogram for predicting in-hospital mortality of patients with acute paraquat poisoning
Authors: Tang Guo , Jiang Zhen , Xu Lingjie , Yang Ying , Yang Sha , Yao Rong 
Published: January 2024

AbstractThis study aimed to develop and validate a predictive model to determine the risk of in-hospital mortality in patients with acute paraquat poisoning. This retrospective observational cohort study included 724 patients with acute paraquat poisoning whose clinical data were collected within 24 h of admission. The primary outcome was in-hospital mortality. Patients were randomly divided into training and validation cohorts (7/3 ratio). In the training cohort, the least absolute shrinkage and selection operator regression models were used for data dimension reduction and feature selection. Multivariate logistic regression was used to generate a predictive nomogram for in-hospital mortality. The prediction model was assessed for both the training and validation cohorts. In the training cohort, decreased level of consciousness (Glasgow Coma Scale score < 15), neutrophil-to-lymphocyte ratio, alanine aminotransferase, creatinine, carbon dioxide combining power, and paraquat plasma concentrations at admission were identified as independent predictors of in-hospital mortality in patients with acute paraquat poisoning. The calibration curves, decision curve analysis, and clinical impact curves indicated that the model had a good predictive performance. It can be used on admission to the emergency department to predict mortality and facilitate early risk stratification and actionable measures in clinical practice after further external validation.
b map evaluation and on-fault stress state for the Antakya 2023 earthquakes
Authors: Convertito V. , Tramelli A. , Godano C. 
Published: January 2024

AbstractThe analysis of on-fault seismicity can enlighten the current stress state on the fault itself. Its definition is relevant to individuate fault patches that have not released all the accumulated stress even after the occurrence of a high magnitude earthquake. We use the b value to characterize the stress state on the fault of the Antakya 2023 main events, being b inversely proportional to the stress. The small magnitude seismicity occurring on the maximum slip fault-patches does not allow the b value estimation. This represents a strong indication that the maximum slip zone released most of the stress previously accumulated. Conversely, the lowest b values are located at the bends of the faults and close to the nucleation zone suggesting that, there, still exists not released stress implying that it could be reactivated in the future.
Mechanisms of rainfall-induced landslides and interception dynamic response: a case study of the Ni changgou landslide in Shimian, China
Authors: Li Yu , Yang Xuezhi , Hu Xiao , Wan Liyan , Ma Erlong 
Published: January 2024

AbstractGeological hazards, especially landslides and mudslides, are frequent in Caoke County, Sichuan Province, China. In September 2022, the mechanical parameters of the soil were obtained through a basic investigation of the landslide characteristics of Ni changgou. Upon that, the finite element-discrete element method was used to reconstruct the three-dimensional numerical model of the landslide on the right bank of Ni changgou, and the initiation mechanism of rainfall on landslide and the formation of debris flow impact dam process were simulated. Furthermore, the pore pressure, stability coefficient as well as displacement of the landslide body were analyzed. It turned out that with the increase of rainfall intensity, the pore water pressure value also increases, where pore water pressure rises rapidly. the slope is close to the unstable edge, Eventually, it tends to one under rainfall conditions, and due to gravity, the slide of the landslide is induced. The duration of landslide movement is about 200 s, the maximum average velocity of the landslide reaches 4.85 m/s, and the average movement distance is close to 500 m. In addition, this method is applied to the Chutougou debris flow, and the corresponding hazard analysis is added which could better show the treatment and application of debris flow in actual engineering.
Construction of a near infrared fluorescence system for imaging of biological tissues
Authors: Zhao Xu , Li Shilin , Song Yue , Fan Lianhui 
Published: January 2024

AbstractSurgical procedures often rely on unaided visual observation or endoscopic assistance, which may pose challenges in cases involving intricate anatomical relationships. Real-time imaging technologies capable of intraoperative visualization of target organs have the potential to enhance the precision of surgical procedures by facilitating accurate identification, separation, and protection of vital tissues or organs. Despite these advantages, the widespread adoption of such technologies has been hindered by factors such as the prohibitive cost of equipment. This study aims to optimize and develop a device based on Indocyanine Green (ICG) for fluorescence imaging. The objective is to monitor changes in the average fluorescence intensity of ICG in the bladder, offering valuable guidance for surgeries involving the bladder. 1. Male rabbits were administered 0.01 mg/ml ICG via the renal pelvis and ear vein to obtain fluorescence images of the ureter, bladder, and small intestine. 2. After ligating the bilateral ureters of male rabbits, a retrograde bladder perfusion of 5 ml 0.01 mg/ml ICG was conducted to capture fluorescence images of the bladder over time. The average fluorescence intensity was computed using Image Pro Plus 6.0, and the corresponding curve was generated using Prism 8.0. Using a similar methodology, the average fluorescence intensity of male rabbits without ureteral ligation was measured and plotted over time. 1. The developed device facilitated imaging of the ureter, bladder, and small intestine. 2. The bladder's average fluorescence intensity exhibited changes over time in response to urine production and ureteral ligation, contrasting with observations without ureteral ligation. We have successfully constructed and optimized a modular fluorescence imaging system for organs and tissues. This system proves effective in imaging experiments involving hollow organs in animals and offers valuable insights for relevant surgical procedures.