bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors Limiting the Success of an All-Variant COVID-19 Vaccine: A Simulation Study
Authors: Kosinski Robert J. 
Published: April 2024

AbstractThis paper simulates a hypothetical pan-coronavirus vaccine that confers immediate sterilizing immunity against all SARS-CoV-2 variants. Simulations used a SEIIS spreadsheet model that ran two parallel subpopulations: one that accepted vaccination, and another that refused it. The two subpopulations could transmit infections to one another. Using data from the United States (US), the simulated vaccine was tested against limiting factors such as vaccine hesitancy, slow vaccination distribution, and the development of high-transmission variants. The vaccine was often successful at reducing cases, but high-transmission variants and discontinuation of non-pharaceutical interventsions (NPIs) such as masking greatly elevated cases. A puzzling outcome was that if NPIs are discontinued and high-transmission variants become common, the model predicted consistently higher rates of disease than are actually observed in the US in 2024. However, if cumulative exposure to virus antigens increases the duration of immunity or decreases the infectivity of the virus, the model predictions were brought back into a more realistic range. The major finding was that even when a COVID vaccine always produces sterilizing immunity against every SARS-CoV-2 variant, its ability to control the epidemic can be compromised by multiple common conditions.
Multiscale Detrended Cross-Correlation Coefficient: Estimating Coupling in Nonstationary Neurophysiological Signals
Authors: Stylianou Orestis , Susi Gianluca , Hoffmann Martin , Suárez-Méndez Isabel , López-Sanz David , Schirner Michael , Ritter Petra 
Published: April 2024

AbstractThe brain consists of a vastly interconnected network of regions, the connectome. By estimating the statistical interdependence of neurophysiological time series, we can measure the functional connectivity (FC) of this connectome. Pearson’s correlation (rP) is a common metric of coupling in FC studies. YetrPdoes not account properly for the non-stationarity of the signals recorded in neuroimaging. In this study, we introduced a novel estimator of coupled dynamics termed multiscale detrended cross-correlation coefficient (MDC3). Firstly, we showed that MDC3had higher accuracy compared torPusing simulated time series with known coupling, as well as simulated functional magnetic resonance imaging (fMRI) signals with known underlying structural connectivity. Next, we computed functional brain networks based on empirical magnetoencephalography (MEG) and fMRI. We found that by using MDC3we could construct networks of healthy populations with significantly different properties compared torPnetworks. Based on our results, we believe that MDC3is a valid alternative torPthat should be incorporated in future FC studies.Author SummaryThe brain consists of a vastly interconnected network of regions. To estimate the connection strength of such networks the coupling between different brain regions should be calculated. This can be achieved by using a series of statistical methods that capture the connection strength between signals originating across the brain, one of them being Pearson’s correlation (rP). Despite its benefits,rPis not suitable for realistic estimation of brain network architecture. In this study, we introduced a novel estimator called multiscale detrended cross-correlation coefficient (MDC3). Firstly, we showed that MDC3was more accurate thanrPusing simulated signals with known connection strength, as well as simulated brain activity emerging from realistic brain simulations. Next, we constructed brain networks based on real-life brain activity, recorded using two different methodologies. We found that by using MDC3we could construct networks of healthy populations with significantly different properties compared torPnetworks. Based on our results, we believe that MDC3is a valid alternative torPthat should be incorporated in future studies of brain networks.
Colonoscopy polyp classification via enhanced scattering wavelet convolutional neural network
Authors: Tan Jun , Yuan Jiamin , Fu Xiaoyong , Bai Yilin 
Published: April 2024

AbstractAmong the most common cancers, colorectal cancer (CRC) has a high death rate. The best way to screen for colorectal cancer (CRC) is with a colonoscopy, which has been shown to lower the risk of the disease. As a result, Computer-aided polyp classification technique is applied to identify colorectal cancer. But visually categorizing polyps is difficult since different polyps have different lighting conditions.Different from previous works, this article presents Enhanced Scattering Wavelet Convolutional Neural Network (ESWCNN), a polyp classification technique that combines Convolutional Neural Network (CNN) and Scattering Wavelet Transform (SWT) to improve polyp classification performance. This method concatenates simultaneously learnable image filters and wavelet filters on each input channel. The scattering wavelet filters can extract common spectral features with various scales and orientations, while the learnable filters can capture image spatial features that wavelet filters may miss.A network architecture for ESWCNN is designed based on these principles and trained and tested using colonoscopy datasets (two public datasets and one private dataset). An n-fold cross-validation experiment was conducted for three classes (adenoma, hyperplastic, serrated) achieving a classification accuracy of 96.4%, and 94.8% accuracy in two-class polyp classification (positive and negative). In the three-class classification, correct classification rates of 96.2% for adenomas, 98.71% for hyperplastic polyps, and 97.9% for serrated polyps were achieved. The proposed method in the two-class experiment reached an average sensitivity of 96.7% with 93.1% specificity.Furthermore, we compare the performance of our model with the state-of-the-art general classification models and commonly used CNNs. Six end-to-end models based on CNNs were trained using 2 dataset of video sequences. The experimental results demonstrate that the proposed ESWCNN method can effectively classify polyps with higher accuracy and efficacy compared to the state-of-the-art CNN models. These findings can provide guidance for future research in polyp classification.
Masseter Muscle Volume and Its Association with Sarcopenia and Muscle Determinants with Insights from ACTN3 Polymorphism in Older Japanese Adults: the Bunkyo Health Study
Authors: Abudurezake Abulaiti , Kakehi Saori , Umemura Futaba , Kaga Hideyoshi , Someya Yuki , Tabata Hiroki , Yoshizawa Yasuyo , Naito Hitoshi , Tajima Tsubasa , Ito Naoaki , Otsuka Hikaru , Shi Huicong , Sugimoto Mari , Sakamoto Shota , Muroga Yukiko , Wakabayashi Hidetaka , Kawamori Ryuzo , Watada Hirotaka , Tamura Yoshifumi 
Published: April 2024

AbstractAimSarcopenia has been associated with a decrease in masseter muscle (MM) thickness in high-risk older populations. However, the relationship to sarcopenia and determinants of MM volume (MMV) in the general older population remain unclear.MabethodIn a cross-sectional study of 1484 older adults of Tokyo, we evaluated MMV using 3D MRI scanning, appendicular skeletal muscle mass (ASMM), handgrip strength, dietary intake, smoking, insulin-like growth factor 1 (IGF-1) levels, and the ACTN3 R577X polymorphism. Participants were divided into quintiles based on MMV (Q1-5).ResultsOur study of participants with a mean age of 73.0 ± 5.3 years, MMV (Men:35.3 ± 7.8 ml, Women: 25.0 ± 5.1 ml) was significantly larger in men than in women. A significant association between MMV and sarcopenia was observed, with the lowest quintile (Q1) showing a higher risk compared to the highest quintile (Q5) in both sexes. Body mass index (BMI) and age were independent determinants of ASMM in both sexes, while BMI, but interestingly not age, was a determinant of MMV. Moreover, IGF-1 was positively correlated with MMV in both sexes; smoking negatively correlated with MMV in women. The ACTN3 577X polymorphism was associated with only smaller MMV in men.ConclusionLow MMV increased the risk of sarcopenia, particularly in men. BMI and age strongly influenced ASMM, while MMV was only weakly associated with BMI and not with age. Notably, the IGF-1 level was positively correlated to only MMV, and the ACTN3 genotype was linked to reduced only MMV in men.
Accurate prediction of neurologic changes in critically ill infants using pose AI
Authors: Gleason Alec , Richter Florian , Beller Nathalia , Arivazhagan Naveen , Feng Rui , Holmes Emma , Glicksberg Benjamin S , Morton Sarah U , La Vega-Talbott Maite , Fields Madeline , Guttmann Katherine , Nadkarni Girish N , Richter Felix 
Published: April 2024

ABSTRACTInfant alertness and neurologic changes can reflect life-threatening pathology but are assessed by exam, which can be intermittent and subjective. Reliable, continuous methods are needed. We hypothesized that our computer vision method to track movement, pose AI, could predict neurologic changes in the neonatal intensive care unit (NICU). We collected 4,705 hours of video linked to electroencephalograms (EEG) from 115 infants. We trained a deep learning pose algorithm that accurately predicted anatomic landmarks in three evaluation sets (ROC-AUCs 0.83–0.94), showing feasibility of applying pose AI in an ICU. We then trained classifiers on landmarks from pose AI and observed high performance for sedation (ROC-AUCs 0.87–0.91) and cerebral dysfunction (ROC-AUCs 0.76–0.91), demonstrating that an EEG diagnosis can be predicted from video data alone. Taken together, deep learning with pose AI may offer a scalable, minimally invasive method for neuro-telemetry in the NICU.
Incorporating Real-World Clinico-Genomic Insights to Inform Diversity Enrollment Targets in Oncology Trials
Authors: De La Vega Francisco M. , Pouliot Yannick , Rhead Brooke 
Published: April 2024

AbstractThe passage of the US Food and Drug Administration (FDA) Omnibus Reform Act of 2022 underscores a national commitment to enhancing diversity in clinical trials. This commitment recognizes not only the ethical imperative of inclusivity but also the practical necessity to ensure the safety and efficacy of medications across all demographic groups. Particularly for Phase 3 and pivotal clinical trials, the FDA has issued draft guidance that recommends sponsors to develop diversity plans with race and ethnicity (R/E) enrollment targets informed by the epidemiological landscape of the disease in the therapy’s target population. For biomarker-driven oncology trials, real-world data (RWD), especially when enriched with multimodal clinico-genomic information, holds immense promise for informing these R/E enrollment goals.However, leveraging RWD comes with hurdles, including the overrepresentation of insured patients, significant non-random missingness in R/E data, and disparities between R/E distributions in RWD and disease incidence databases—often attributed to healthcare access and socioeconomic disparities. Here, we propose a robust methodology to harness clinico-genomic RWD, addressing these challenges through strategies that include accurate R/E imputation and incidence adjustment factors. Our approach then utilizes clinical data and biomarker prevalence in RWD to derive a data-driven R/E distribution for clinical trial enrollment targets.Through a case study on a hypothetical biomarker-driven clinical trial targeting prostate adenocarcinoma and leveraging a cohort from the Tempus clinco-genomic database, we demonstrate the application of our methodology. This example illustrates the potential of RWD to offer enrollment target scenarios, grounded in disease epidemiology and empirical R/E distributions adjusted for biomarker prevalence. Such data-driven targets are pivotal for the development of informed and equitable diversity plans in oncology clinical trials, paving the way for more representative and generalizable research outcomes.
Barley powdery mildew invasion coincides with the dynamic accumulation of leaf apoplastic extracellular vesicles that are associated with host stress response proteins
Authors: Thieron Hannah , Spanu Pietro , Buhl Miriam , Hülsmann Charlotte , Kummer Charlotte , Demir Fatih , Huesgen Pitter , Panstruga Ralph 
Published: April 2024

AbstractThe mutual exchange of extracellular vesicles across kingdom borders is a feature of many plant-microbe interactions. The occurrence and cargos of extracellular vesicles has been studied in several instances, but their dynamics in the course of infection have remained elusive. Here we used two different procedures, differential high-speed centrifugation and polymer-based enrichment, to collect extracellular vesicles from the apoplastic wash fluid of barley (Hordeum vulgare) leaves challenged by its fungal powdery mildew pathogen,Blumeria hordei. Both methods yielded extracellular vesicles of similar quality and morphological characteristics, though the polymer approach was associated with higher reproducibility. We noted that extracellular vesicles derived from the apoplastic wash fluid constitute polydisperse populations that are selectively responsive to leaf infection byB. hordei. Extracellular vesicles of ∼100 nm – 300 nm diameter became progressively more abundant, in particular from 72 hours post inoculation onwards, resulting in a major peak late during fungal infection. Vesicles of ∼300 nm – 500 nm showed similar accumulation dynamics but reached much lower levels, suggesting they might constitute a separate population. Proteome analysis uncovered an enrichment of biotic stress response proteins associated with the extracellular vesicles. The barley t-SNARE protein Ror2, the ortholog of the PEN1 marker protein of extracellular vesicles inArabidopsis thaliana, accumulates in extracellular vesicles during powdery mildew infection, hence also qualifying as a potential marker protein. Our study serves as a starting point for investigating the role of extracellular vesicles at different stages of plant-microbe interactions.
Meiotic DNA break resection and recombination rely on chromatin remodeler Fun30
Authors: Huang Pei-Ching , Hong Soogil , Mimitou Eleni P. , Kim Keun P. , Murakami Hajime , Keeney Scott 
Published: April 2024

AbstractDNA double-strand breaks (DSBs) are nucleolytically processed to generate single-stranded DNA tails for homologous recombination. InSaccharomyces cerevisiaemeiosis, this 5’-to-3’ resection involves initial nicking by the Mre11–Rad50–Xrs2 complex (MRX) plus Sae2, then exonucleolytic digestion by Exo1. Chromatin remodeling adjacent to meiotic DSBs is thought to be necessary for resection, but the relevant remodeling activity was unknown. Here we show that the SWI/SNF-like ATPase Fun30 plays a major, non-redundant role in resecting meiotic DSBs. Afun30null mutation shortened resection tract lengths almost as severely as anexo1-nd(nuclease-dead) mutation, and resection was further shortened in thefun30 exo1-nddouble mutant. Fun30 associates with chromatin in response to meiotic DSBs, and the constitutive positioning of nucleosomes governs resection endpoint locations in the absence of Fun30. We infer that Fun30 directly promotes both the MRX- and Exo1-dependent steps in resection, possibly by removing nucleosomes from broken chromatids. Moreover, we found that the extremely short resection in thefun30 exo1-nddouble mutant is accompanied by compromised interhomolog recombination bias, leading to defects in recombination and chromosome segregation. Thus, this study also provides insight about the minimal resection lengths needed for robust recombination.
MePHD1.2 affects the synthesis of cyanogenic glycosides by regulating the transcription ofMeCYP79D2in cassava
Authors: Li Mengtao , Zhao Xiao , Li Yuanchao , Zhao Xiaoye , Mai Weitao , Li Yajun , Liang Qibing , Yin Qingchun , Wang Wenquan , Liu Jinping , Chen Xin 
Published: April 2024

SummaryThe high content of cyanogenic glycosides (CG) in cassava storage tubers seriously affects human food safety. CG play crucial roles in plant growth and development and can protect cassava leaves from being masticated by herbivorous predators.Nevertheless, the regulatory mechanism of CG biosynthesis, which results in a low CG content in storage tubers and high CG content in leaves, remains poorly understood.Here, yeast one-hybrid assay was performed using a mixed cDNA library of cassava storage roots and leaves as prey and the promoter ofMeCYP79D2as bait. MeCYP79D2, a cytochrome P450 protein, is the rate-limiting enzyme for CG synthesis in cassava. From this information, a candidate regulator ofMeCYP79D2, that is, transcription factor MePHD1.2, was selected.MePHD1.2, which is located in the nucleus and exhibits a transcription inhibitory activity, can directly bind to PD2 segment in the promoter ofMeCYP79D2, which results in its repressed expression. In cassava, the transcriptional activity ofMeCYP79D2was considerably enhanced inmephd1.2lines, which caused an increase in the contents of linamarin and lotaustralin.Our findings unveil a novel regulatory module governing CG biosynthesis, wherein mutation ofMePHD1.2attenuates its transcription inhibition onMeCYP79D2and boosts CGs biosynthesis in cassava.
Rapid mortality in captive bush dogs (Speothos venaticus) caused by influenza A of avian origin (H5N1) at a wildlife collection in the United Kingdom
Authors: Falchieri Marco , Reid Scott M. , Dastderji Akbar , Cracknell Jonathan , Warren Caroline J. , Mollett Benjamin C. , Peers-Dent Jacob , Schlachter Audra-Lynne D , Mcginn Natalie , Hepple Richard , Thomas Saumya , Ridout Susan , Quayle Jen , Pizzi Romain , Núñez Alejandro , Byrne Alexander M. P. , James Joe , Banyard Ashley C. 
Published: April 2024

AbstractEurope has suffered unprecedented epizootics of high pathogenicity avian influenza (HPAI) clade 2.3.4.4b H5N1 since Autumn 2021. As well as impacting upon commercial and wild avian species, the virus has also infected mammalian species more than ever observed previously. Mammalian species involved in spill over events have primarily been scavenging terrestrial carnivores and farmed mammalian species although marine mammals have also been affected. Alongside reports of detections in mammalian species found dead through different surveillance schemes, several mass mortality events have been reported in farmed and wild animals. During November 2022, an unusual mortality event was reported in captive bush dogs (Speothos venaticus) with clade 2.3.4.4b H5N1 HPAIV of avian origin being the causative agent. The event involved an enclosure of fifteen bush dogs, ten of which succumbed during a nine-day period with some dogs exhibiting neurological disease. Ingestion of infected meat is proposed as the most likely infection route.
Resolving theEuphorbia neriifolia(Euphorbiaceae) complex: a taxonomy with two new succulent species from Western India
Authors: Malpure Nilesh V. , De Jong Bruce E. , Raut Prashant S. , Sardesai Milind M. 
Published: April 2024

AbstractLinnaeus appears to have clubbed three distinct species underEuphorbia neriifolia, a species from China and Indonesia that is the originalE. neriifolia, a species from India and Sri Lanka which is now recognized asE. nivulia, and a species from West Africa which is now calledE. drupifera. After conducting field studies and examining the applicable protologues, original type material, world literature, and world herbaria, we conclude that for hundreds of years, workers have erroneously clubbed various species from India underE. neriifolia. These species includeE. ligulariafrom Northeast India and two common succulents from Western India described here as new species viz.E. yadaviiandE. paschimia. An epitype forE. neriifoliafrom Indonesia is designated to stabilize the species,E. ligulariais reinstated as a species, a neotype is designated forE. drupifera.E. complanatais synonymized underE. neriifolia, andE. undulatifoliais synonymized underE. ligularia. We present amended descriptions ofE. neriifolia,E. nivulia,E. drupiferaandE. ligularia.
Factors Associated with Non-and Incomplete Vaccination Among Children Aged 12-23 Months in Gindhir Rural District, Southeast Ethiopia: A Multinomial Analysis
Authors: Mulugeta Geremew Tsegaye , Gemeda Desta Hiko , Dimore Abraham Lomboro , Getu Tihitian Yohannes , Gelaw Adamu Zerihun , Doyamo Adane Woldeab 
Published: April 2024

AbstractBackgroundChildhood immunization is one of the most successful public health interventions that prevent children’s morbidity and mortality from Vaccine Preventable Diseases (VPDs). Despite this, achieving high vaccination coverage is still one of the pressing public health problems globally, particularly in low-and middle-income countries.ObjectiveThis study aims to identify factors associated with non- and incomplete vaccination status among children aged 12-23 months in Gindhir rural district, East Bale zone, Southeast Ethiopia.MethodsA cross-sectional study supplemented with a qualitative study was conducted in the Gindhir district from April 25-June10/ 2021. A total of 563 mothers of children 12-23 months participated. Study participants were selected using computer-generated random numbers. The sample was proportionally allocated to the size of children 12-23 months in each kebele. An administered structured questionnaire was used to collect data using face-to-face interviews. Epi– data version 3.1 was used for data entry and SPSS version 25 software was used for data analysis. Bivariate and Multinomial logistic regression analysis was used to identify the determinants of vaccination status at a P value of less than 0.05. Seven in-depth interviews and two focused group discussions were conducted and analyzed manually by coding.Results-Totally 563 mothers/caregivers with children aged 12-23 months participated with a 96.6% response rate. Of the 563 children included in the study, 307 (54.5% [95%CI: 50.1-58.8]) were fully vaccinated, 142(25.5% [95%CI:21.7-29.1]) were incompletely vaccinated and 114 (20.2% [95%CI: 16.7-23.8]) were not vaccinated at all. Home delivery [3.46 (95%CI: 1.27-9.40)], absence of nearby health facility[4.84(95% CI: 1.75-13.39)], lack of transportation incur cost [2.75(95%CI:1.06-7.14)], mothers/caregivers negative perceived benefits of child vaccination [2.69(95%CI: 1.35-5.37)], mothers/caregivers poor knowledge about VPDs [2.78(95%CI: 1.14-5.30)] and vaccination schedule [5.54(95%CI: 2.74-11.22)], and negative attitude towards vaccination[2.01(95%CI: 1.01-3.98)] were identified as independent predictors of non-vaccination. While home delivery [6.85 (95%CI: 1.69-27.79)], lack of provision of counselling by health workers [2.19(95%CI: 1.13-4.27)], mothers/caregivers’ poor knowledge about VPDs [2.71(95%CI: 1.60-4.58)] and vaccination schedule [3.30(95%CI: 1.90-5.74)], and attitude towards vaccination [2.53(95%CI: 1.47-3.38)] were significantly associated with incomplete vaccination status.ConclusionDesigning and implementing public health interventions tailored to locally identified problems is vital to narrow the observed variation in childhood vaccination status.