bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic epigenome editing captures the context-dependent instructive function of chromatin modifications
Authors: Policarpi Cristina , Munafò Marzia , Tsagkris Stylianos , Carlini Valentina , Hackett Jamie A. 
Published: May 2024

AbstractChromatin modifications are linked with regulating patterns of gene expression, but their causal role and context-dependent impact on transcription remains unresolved. Here we develop a modular epigenome editing platform that programs nine key chromatin modifications, or combinations thereof, to precise loci in living cells. We couple this with single-cell readouts to systematically quantitate the magnitude and heterogeneity of transcriptional responses elicited by each specific chromatin modification. Among these, we show that installing histone H3 lysine 4 trimethylation (H3K4me3) at promoters can causally instruct transcription by hierarchically remodeling the chromatin landscape. We further dissect how DNA sequence motifs influence the transcriptional impact of chromatin marks, identifying switch-like and attenuative effects within distinct cis contexts. Finally, we examine the interplay of combinatorial modifications, revealing that co-targeted H3K27 trimethylation (H3K27me3) and H2AK119 monoubiquitination (H2AK119ub) maximizes silencing penetrance across single cells. Our precision-perturbation strategy unveils the causal principles of how chromatin modification(s) influence transcription and dissects how quantitative responses are calibrated by contextual interactions.
q-Rung orthopair fuzzy 2-tuple linguistic WASPAS algorithm for patients’ prioritization based on prioritized Maclaurin symmetric mean aggregation operators
Authors: Abbas Fatima , Ali Jawad , Mashwani Wali Khan , Gündüz Necla , Syam Muhammad I. 
Published: May 2024

AbstractDue to the fuzziness of the medical field, q-rung orthopair fuzzy 2-tuple linguistic (q-RF2L) set is the privileged way to aid medical professionals in conveying their assessments in the patient prioritization problem. The theme of the present study is to put forward a novel approach centered around the merging of prioritized averaging (PA) and the Maclaurin symmetric mean (MSM) operator within q-RF2L context. According to the prioritization of the professionals and the correlation among the defined criteria, we apply both PA and MSM to assess priority degrees and relationships, respectively. Keeping the pluses of the PA and MSM operators in mind, we introduce two aggregation operators (AOs), namely q-RF2L prioritized Maclaurin symmetric mean and q-RF2L prioritized dual Maclaurin symmetric mean operators. Meanwhile, some essential features and remarks of the proposed AOs are discussed at length. Based on the formulated AOs, we extend the weighted aggregated sum product assessment methodology to cope with q-RF2L decision-making problems. Ultimately, to illustrate the practicality and effectiveness of the stated methodology, a real-world example of patients’ prioritization problem is addressed, and an in-depth analysis with prevailing methods is performed.
Towards optimal model evaluation: enhancing active testing with actively improved estimators
Authors: Lee JooChul , Kolla Likhitha , Chen Jinbo 
Published: May 2024

AbstractWith rapid advancements in machine learning and statistical models, ensuring the reliability of these models through accurate evaluation has become imperative. Traditional evaluation methods often rely on fully labeled test data, a requirement that is becoming increasingly impractical due to the growing size of datasets. In this work, we address this issue by extending existing work on active testing (AT) methods which are designed to sequentially sample and label data for evaluating pre-trained models. We propose two novel estimators: the Actively Improved Levelled Unbiased Risk (AILUR) and the Actively Improved Inverse Probability Weighting (AIIPW) estimators which are derived from nonparametric smoothing estimation. In addition, a model recalibration process is designed for the AIIPW estimator to optimize the sampling probability within the AT framework. We evaluate the proposed estimators on four real-world datasets and demonstrate that they consistently outperform existing AT methods. Our study also shows that the proposed methods are robust to changes in subsample sizes, and effective at reducing labeling costs.
Genomic characterization of Influenza A (H1N1)pdm09 and SARS-CoV-2 from Influenza Like Illness (ILI) and Severe Acute Respiratory Illness (SARI) cases reported between July–December, 2022
Authors: Singh Pushpendra , Sharma Kuldeep , Bhargava Anudita , Negi Sanjay Singh 
Published: May 2024

AbstractInfluenza Like Illness (ILI) and Severe Acute Respiratory Infection (SARI) cases are more prone to Influenza and SARS-CoV-2 infection. Accordingly, we genetically characterized Influenza and SARS-CoV-2 in 633 ILI and SARI cases by rRT-PCR and WGS. ILI and SARI cases showed H1N1pdm09 prevalence of 20.9% and 23.2% respectively. 135 (21.3%) H1N1pdm09 and 23 (3.6%) H3N2 and 5 coinfection (0.78%) of H1N1pdm09 and SARS-CoV-2 were detected. Phylogenetic analysis revealed H1N1pdm09 resemblance to clade 6B.1A.5a.2 and their genetic relatedness to InfA/Perth/34/2020, InfA/Victoria/88/2020 and InfA/Victoria/2570/2019. Pan 24 HA and 26 NA nonsynonymous mutations and novel HA (G6D, Y7F, Y78H, P212L, G339R, T508K and S523T) and NA (S229A) mutations were observed. S74R, N129D, N156K, S162N, K163Q and S164T alter HA Cb and Sa antibody recognizing site. Similarly, M19T, V13T substitution and multiple mutations in transmembrane and NA head domain drive antigenic drift. SARS-CoV-2 strains genetically characterized to Omicron BA.2.75 lineage containing thirty nonsynonymous spike mutations exhibited enhanced virulence and transmission rates. Coinfection although detected very minimal, the mutational changes in H1N1pdm09 and SARS-CoV-2 virus infected individuals could alter antibody receptor binding sites, allowing the viruses to escape immune response resulting in better adaptability and transmission. Thus continuous genomic surveillance is required to tackle any future outbreak.
Ultrasmall Fe3O4 nanoparticles self-assembly induced dual-mode T1/T2-weighted magnetic resonance imaging and enhanced tumor synergetic theranostics
Authors: Xie Qinghua , Wang Xuemei , Zhang Gaorui , Zhou Dawei , Zhao Yuxuan , Liu Hong , Duan Jiazhi , Yu Dexin , Sang Yuanhua 
Published: May 2024

AbstractIndividual theranostic agents with dual-mode MRI responses and therapeutic efficacy have attracted extensive interest due to the real-time monitor and high effective treatment, which endow the providential treatment and avoid the repeated medication with side effects. However, it is difficult to achieve the integrated strategy of MRI and therapeutic drug due to complicated synthesis route, low efficiency and potential biosafety issues. In this study, novel self-assembled ultrasmall Fe3O4 nanoclusters were developed for tumor-targeted dual-mode T1/T2-weighted magnetic resonance imaging (MRI) guided synergetic chemodynamic therapy (CDT) and chemotherapy. The self-assembled ultrasmall Fe3O4 nanoclusters synthesized by facilely modifying ultrasmall Fe3O4 nanoparticles with 2,3-dimercaptosuccinic acid (DMSA) molecule possess long-term stability and mass production ability. The proposed ultrasmall Fe3O4 nanoclusters shows excellent dual-mode T1 and T2 MRI capacities as well as favorable CDT ability due to the appropriate size effect and the abundant Fe ion on the surface of ultrasmall Fe3O4 nanoclusters. After conjugation with the tumor targeting ligand Arg-Gly-Asp (RGD) and chemotherapy drug doxorubicin (Dox), the functionalized Fe3O4 nanoclusters achieve enhanced tumor accumulation and retention effects and synergetic CDT and chemotherapy function, which serve as a powerful integrated theranostic platform for cancer treatment.
LRBA, a BEACH protein mutated in human immune deficiency, is widely expressed in epithelia, exocrine and endocrine glands, and neurons
Authors: Roussa Eleni , Juda Pavel , Laue Michael , Mai-Kolerus Oliver , Meyerhof Wolfgang , Sjöblom Markus , Nikolovska Katerina , Seidler Ursula , Kilimann Manfred W. 
Published: May 2024

AbstractMutations in LRBA, a BEACH domain protein, cause severe immune deficiency in humans. LRBA is expressed in many tissues and organs according to biochemical analysis, but little is known about its cellular and subcellular localization, and its deficiency phenotype outside the immune system. By LacZ histochemistry of Lrba gene-trap mice, we performed a comprehensive survey of LRBA expression in numerous tissues, detecting it in many if not all epithelia, in exocrine and endocrine cells, and in subpopulations of neurons. Immunofluorescence microscopy of the exocrine and endocrine pancreas, salivary glands, and intestinal segments, confirmed these patterns of cellular expression and provided information on the subcellular localizations of the LRBA protein. Immuno-electron microscopy demonstrated that in neurons and endocrine cells, which co-express LRBA and its closest relative, neurobeachin, both proteins display partial association with endomembranes in complementary, rather than overlapping, subcellular distributions. Prominent manifestations of human LRBA deficiency, such as inflammatory bowel disease or endocrinopathies, are believed to be primarily due to immune dysregulation. However, as essentially all affected tissues also express LRBA, it is possible that LRBA deficiency enhances their vulnerability and contributes to the pathogenesis.
Anti-fatigue activity of methyl dihydrojasmonate and linalool in a rat model evaluated by a novel index for neuro-immune and oxidative stress interactions
Authors: Nishimura Yasumitsu , Nomiyama Kenta , Okamoto Shuichiro , Igarashi Mika , Sato Yukino , Okamoto Hikaru , Kamezaki Ayasa , Itadani Masumi , Kuribayashi Futoshi , Yamauchi Akira 
Published: May 2024

AbstractAvoiding fatigue is a long-standing challenge in both healthy and diseased individuals. Establishing objective standard markers of fatigue is essential to evaluate conditions in spatiotemporally different locations and individuals and identify agents to fight against fatigue. Herein, we introduced a novel method for evaluating fatigue using nervous system markers (including dopamine, adrenaline, and noradrenaline), various cytokine levels (such as interleukin [IL]-1β, tumor necrosis factor [TNF]-α, IL-10, IL-2, IL-5 and IL-17A), and oxidative stress markers (such as diacron-reactive oxygen metabolites [d-ROMs] and biological antioxidant potential [BAP]) in a rat fatigue model. Using this method, the anti-fatigue effects of methyl dihydrojasmonate (MDJ) and linalool, the fragrance/flavor compounds used in various products, were assessed. Our method evaluated the anti-fatigue effects of the aforementioned compounds based on the changes in levels of the nerves system markers, cytokines, and oxidative stress markers. MDJ exerted more potent anti-fatigue effects than linalool. In conclusion, the reported method could serve as a useful tool for fatigue studies and these compounds may act as effective therapeutic agents for abrogating fatigue symptoms.
Preparation of orodispersible tablets of bosentan using xylitol and menthol as dissolution enhancers
Authors: Sakr Rania Mohamed , Abdelaziz Abdelaziz El Sayed , Mazyed Eman Ahmed , El Maghraby Gamal Mohamed 
Published: May 2024

AbstractBosentan is a drug used to treat pulmonary hypertension via dual endothelial receptor antagonism. Bosentan has a restricted oral bioavailability, a problem that's mostly due to poor solubility and hepatic metabolism. It is extensively used for the elderly and children who require a friendly dosage form like orodispersible tablets. So, the goal of this research work was to hasten the dissolution rate of bosentan to produce an orodispersible tablet with immediate drug release. Bosentan was exposed to ethanol-assisted kneading with a rise of xylitol or menthol concentrations (1:1 and 1:2 molar ratio of bosentan with excipient). In addition to observing the dissolution behavior, the resulting dry products were investigated using Fourier transform infrared spectroscopy (FTIR), differential thermal analysis (DTA), and X-ray diffraction (XRD). The FTIR reflected possible hydrogen bonding with xylitol and menthol. DSC studies reflected a reduction in the enthalpy and Tm. These results with XRD data reflected partial co-amorphization in the case of xylitol and eutaxia in the case of menthol. These modifications were related to an accelerated dissolving rate. The developed systems were fabricated as orodispersible tablets which exhibited immediate release of bosentan. Thus, the current study offered simple co-processing for the preparation of orodispersible bosentan tablets.
Assessment of modified chitosan composite in acidic reservoirs through pilot and field-scale simulation studies
Authors: Khattab Hamid , Gawish Ahmed A. , Gomaa Sayed , Hamdy Abdelnaser , El-hoshoudy A. N. 
Published: May 2024

AbstractChemical flooding through biopolymers acquires higher attention, especially in acidic reservoirs. This research focuses on the application of biopolymers in chemical flooding for enhanced oil recovery in acidic reservoirs, with a particular emphasis on modified chitosan. The modification process involved combining chitosan with vinyl/silane monomers via emulsion polymerization, followed by an assessment of its rheological behavior under simulated reservoir conditions, including salinity, temperature, pressure, and medium pH. Laboratory-scale flooding experiments were carried out using both the original and modified chitosan at conditions of 2200 psi, 135,000 ppm salinity, and 196° temperature. The study evaluated the impact of pressure on the rheological properties of both chitosan forms, finding that the modified composite was better suited to acidic environments, showing enhanced resistance to pressure effects with a significant increase in viscosity and an 11% improvement in oil recovery over the 5% achieved with the unmodified chitosan. Advanced modeling and simulation techniques, particularly using the tNavigator Simulator on the Bahariya formations in the Western Desert, were employed to further understand the polymer solution dynamics in reservoir contexts and to predict key petroleum engineering metrics. The simulation results underscored the effectiveness of the chitosan composite in increasing oil recovery rates, with the composite outperforming both its native counterpart and traditional water flooding, achieving a recovery factor of 48%, compared to 39% and 37% for native chitosan and water flooding, thereby demonstrating the potential benefits of chitosan composites in enhancing oil recovery operations.
Silver and gold nanoparticles as a novel approach to fight Sarcoptic mange in rabbits
Authors: Hassanen Eman I. , Morsy Eman A. , Abuowarda Mai , Ibrahim Marwa A. , Shaalan Mohamed 
Published: May 2024

AbstractVarious kinds of pets have been known to contract the ectoparasite Sarcoptes scabiei. Current acaricides are becoming less effective because of the resistance developed by the mite besides their adverse effects on the general activity and reproductive performance of domestic pets. For this reason, the present study aims to discover a novel and safe approach using silver and gold nanoparticles to fight Sarcoptic mange in rabbits as well as to explain their mechanism of action. 15 pet rabbits with clinical signs of Sarcoptic mange that were confirmed by the microscopic examination were used in our study. All rabbits used in this study were assessed positive for the presence of different developing stages of S. scabiei. Three groups of rabbits (n = 5) were used as follows: group (1) didn’t receive any treatment, and group (2 and 3) was treated with either AgNPs or GNPs, respectively. Both nanoparticles were applied daily on the affected skin areas via a dressing and injected subcutaneously once a week for 2 weeks at a dose of 0.5 mg/kg bwt. Our results revealed that all rabbits were severely infested and took a mean score = 3. The skin lesions in rabbits that didn’t receive any treatments progressed extensively and took a mean score = of 4. On the other hand, all nanoparticle-treated groups displayed marked improvement in the skin lesion and took an average score of 0–1. All NPs treated groups showed remarkable improvement in the microscopic pictures along with mild iNOS, TNF-α, and Cox-2 expression. Both nanoparticles could downregulate the m-RNA levels of IL-6 and IFγ and upregulate IL-10 and TGF-1β genes to promote skin healing. Dressing rabbits with both NPs didn’t affect either liver and kidney biomarkers or serum Ig levels indicating their safety. Our residual analysis detected AgNPs in the liver of rabbits but did not detect any residues of GNPs in such organs. We recommend using GNPs as an alternative acaricide to fight rabbit mange.
Generating an organ-deficient animal model using a multi-targeted CRISPR-Cas9 system
Authors: Lim Jonathan Jun-Yong , Murata Yamato , Yuri Shunsuke , Kitamuro Kohei , Kawai Taro , Isotani Ayako 
Published: May 2024

AbstractGene-knockout animal models with organ-deficient phenotypes used for blastocyst complementation are generally not viable. Animals need to be maintained as heterozygous mutants, and homozygous mutant embryos yield only one-fourth of all embryos. In this study, we generated organ-deficient embryos using the CRISPR-Cas9-sgRNAms system that induces cell death with a single-guide RNA (sgRNAms) targeting multiple sites in the genome. The Cas9-sgRNAms system interrupted cell proliferation and induced cell ablation in vitro. The mouse model had Cas9 driven by the Foxn1 promoter with a ubiquitous expression cassette of sgRNAms at the Rosa26 locus (Foxn1Cas9; Rosa26_ms). It showed an athymic phenotype similar to that of nude mice but was not hairless. Eventually, a rat cell-derived thymus in an interspecies chimera was generated by blastocyst complementation of Foxn1Cas9; Rosa26_ms mouse embryos with rat embryonic stem cells. Theoretically, a half of the total embryos has the Cas9-sgRNAms system because Rosa26_ms could be maintained as homozygous.
Reducing childhood mortality extends mothers’ lives
Authors: Zipple Matthew N. 
Published: May 2024

AbstractDuring the twentieth century, childhood mortality was dramatically reduced globally, falling by more than 90% in the United States and much of Europe. Total fertility also fell, with the combined result that many parents who otherwise would have experienced the loss of a child were spared the trauma and negative health consequences that accompany such a loss. Here I use mathematical modeling to argue that the reduction in the frequency of child death that occurred in the twentieth century indirectly led to a substantial reduction in female mortality, resulting in an extension of female lifespan. I estimate that the reduction in maternal bereavement in the US during the twentieth century indirectly increased mean female lifespan after age 15 by approximately 1 year. I discuss implications for our understanding of the persistence of the sex gap in longevity and approaches to improving maternal health outcomes in countries that still face high levels of childhood mortality.
Association of fat-to-muscle mass ratio with physical activity and dietary protein, carbohydrate, sodium, and fiber intake in a cross-sectional study
Authors: Nishikori Shu , Fujita Satoshi 
Published: May 2024

AbstractHigher fat-to-muscle mass ratio (FMR) is reported to be a risk factor for various diseases, including type 2 diabetes and cardiovascular diseases, and mortality. Although this association suggests that reducing FMR may help to prevent certain diseases and mortality, the relationship between FMR and lifestyle factors is unclear. Therefore, we performed a cross-sectional study with the aim to elucidate this relationship. This cross-sectional study included 1518 healthy Japanese adults aged 30 to 64 years. We measured FMR in the whole body, arms, legs, and trunk and assessed various lifestyle factors. Then, we performed forced entry multiple regression analyses for FMR with the following variables: sex, age, physical activity, dietary intake, sleep quality, cigarette smoking, stress levels, and body mass index. As a result, whole-body and regional FMRs were correlated with female sex (β = 0.71); age (β = 0.06); physical activity (β = − 0.07); dietary intake of protein (β = − 0.12), carbohydrate (β = 0.04), sodium (β = 0.13), and fiber (β = − 0.16); and body mass index (β = 0.70). The results suggest that in the Japanese middle-aged population, low FMR is associated with certain lifestyle factors, i.e. higher physical activity and a diet with higher protein and fiber and lower carbohydrate and sodium, independent of age, sex, and body mass index.
A dual-branch selective attention capsule network for classifying kiwifruit soft rot with hyperspectral images
Authors: Guo Zhiqiang , Ni Yingfang , Gao Hongsheng , Ding Gang , Zeng Yunliu 
Published: May 2024

AbstractKiwifruit soft rot is highly contagious and causes serious economic loss. Therefore, early detection and elimination of soft rot are important for postharvest treatment and storage of kiwifruit. This study aims to accurately detect kiwifruit soft rot based on hyperspectral images by using a deep learning approach for image classification. A dual-branch selective attention capsule network (DBSACaps) was proposed to improve the classification accuracy. The network uses two branches to separately extract the spectral and spatial features so as to reduce their mutual interference, followed by fusion of the two features through the attention mechanism. Capsule network was used instead of convolutional neural networks to extract the features and complete the classification. Compared with existing methods, the proposed method exhibited the best classification performance on the kiwifruit soft rot dataset, with an overall accuracy of 97.08% and a 97.83% accuracy for soft rot. Our results confirm that potential soft rot of kiwifruit can be detected using hyperspectral images, which may contribute to the construction of smart agriculture.
A combined observational and Mendelian randomization investigation reveals NMR-measured analytes to be risk factors of major cardiovascular diseases
Authors: Zheng Rui , Lind Lars 
Published: May 2024

AbstractDyslipidaemias is the leading risk factor of several major cardiovascular diseases (CVDs), but there is still a lack of sufficient evidence supporting a causal role of lipoprotein subspecies in CVDs. In this study, we comprehensively investigated several lipoproteins and their subspecies, as well as other metabolites, in relation to coronary heart disease (CHD), heart failure (HF) and ischemic stroke (IS) longitudinally and by Mendelian randomization (MR) leveraging NMR-measured metabolomic data from 118,012 UK Biobank participants. We found that 123, 110 and 36 analytes were longitudinally associated with myocardial infarction, HF and IS (FDR < 0.05), respectively, and 25 of those were associated with all three outcomes. MR analysis suggested that genetically predicted levels of 70, 58 and 7 analytes were associated with CHD, HF and IS (FDR < 0.05), respectively. Two analytes, ApoB/ApoA1 and M-HDL-C were associated with all three CVD outcomes in the MR analyses, and the results for M-HDL-C were concordant in both observational and MR analyses. Our results implied that the apoB/apoA1 ratio and cholesterol in medium size HDL were particularly of importance to understand the shared pathophysiology of CHD, HF and IS and thus should be further investigated for the prevention of all three CVDs.