bluuebunny/crossref_metadata_2025_split huggingface dataset:
S9.6-based hybrid capture immunoassay for pathogen detection
Authors: Bothra Ankur , Perry Megan L. , Wei Elena , Moayeri Mahtab , Ma Qian , Biamonte Marco A. , Siirin Marina , Leppla Stephen H. 
Published: December 2023

AbstractThe detection of pathogens is critical for clinical diagnosis and public health surveillance. Detection is usually done with nucleic acid-based tests (NATs) and rapid antigen tests (e.g., lateral flow assays [LFAs]). Although NATs are more sensitive and specific, their use is often limited in resource-poor settings due to specialized requirements. To address this limitation, we developed a rapid DNA-RNA Hybrid Capture immunoassay (HC) that specifically detects RNA from pathogens. This assay utilizes a unique monoclonal antibody, S9.6, which binds DNA-RNA hybrids. Biotinylated single-stranded DNA probes are hybridized to target RNAs, followed by hybrid capture on streptavidin and detection with S9.6. The HC-ELISA assay can detect as few as 104 RNA molecules that are 2.2 kb in length. We also adapted this assay into a LFA format, where captured Bacillus anthracis rpoB RNA of 3.5 kb length was detectable from a bacterial load equivalent to 107 CFU per 100 mg of mouse tissue using either HC-ELISA or HC-LFA. Importantly, we also demonstrated the versatility of HC by detecting other pathogens, including SARS-CoV-2 and Toxoplasma gondii, showing its potential for broad pathogen detection. Notably, HC does not require amplification of the target nucleic acid and utilizes economical formats like ELISA and LFA, making it suitable for use in sentinel labs for pathogen detection or as a molecular tool in basic research laboratories. Our study highlights the potential of HC as a sensitive and versatile method for RNA-based pathogen detection.
Analyzing the impact of feature selection methods on machine learning algorithms for heart disease prediction
Authors: Noroozi Zeinab , Orooji Azam , Erfannia Leila 
Published: December 2023

AbstractThe present study examines the role of feature selection methods in optimizing machine learning algorithms for predicting heart disease. The Cleveland Heart disease dataset with sixteen feature selection techniques in three categories of filter, wrapper, and evolutionary were used. Then seven algorithms Bayes net, Naïve Bayes (BN), multivariate linear model (MLM), Support Vector Machine (SVM), logit boost, j48, and Random Forest were applied to identify the best models for heart disease prediction. Precision, F-measure, Specificity, Accuracy, Sensitivity, ROC area, and PRC were measured to compare feature selection methods' effect on prediction algorithms. The results demonstrate that feature selection resulted in significant improvements in model performance in some methods (e.g., j48), whereas it led to a decrease in model performance in other models (e.g. MLP, RF). SVM-based filtering methods have a best-fit accuracy of 85.5. In fact, in a best-case scenario, filtering methods result in + 2.3 model accuracy. SVM-CFS/information gain/Symmetrical uncertainty methods have the highest improvement in this index. The filter feature selection methods with the highest number of features selected outperformed other methods in terms of models' ACC, Precision, and F-measures. However, wrapper-based and evolutionary algorithms improved models' performance from sensitivity and specificity points of view.
Early childhood SARS experience leads to long-lasting impacts on adulthood mental health in China
Authors: Yuan Ye , Chen Litian , Yang Chao , Xie Tingting 
Published: December 2023

AbstractThe association between pandemic experience and immediate mental health risks, such as depression, is well-documented, yet the long-term effects remain unclear. This study examines the impact of early childhood exposure to the 2003 SARS pandemic on adulthood mental health after 17 years in China, using data from the 2020 China Family Panel Studies (CFPS). The analysis included 6289 participants, aged 3 to 30 years during the SARS outbreak, with an average age of 35.3 years at the time of survey. Adulthood mental health was assessed using Center for Epidemiologic Studies Depression Scale (CESD) and an indicator of clinical depression. The severity of local SARS outbreaks was assessed by cumulative cases per 10,000 population. Results show that each additional case per 10,000 population was linked to a 1.617-fold (95% confidence interval (CI): 1.425–1.836) increase in odds of depression after 17 years for younger children (aged 3–12 years in 2003) relative to older cohorts (aged 13-30). This risk was higher in children from rural areas (adjusted odds ratio (aOR) 3.64; 95% CI 2.92–4.55), with poor physical health (1.98; 1.59–2.48), and from low-income families (2.87; 2.03–4.05). The childhood pandemic experience elevated the probability of developing depression-prone personality traits, which contributes to the enduring impact of childhood pandemic experiences on adulthood mental health. These findings highlight the long-lasting psychological impact of early-childhood pandemic exposure, underscoring the need for targeted interventions to mitigate its effects on the younger generation and emphasizing the importance of monitoring long-term mental health and personality development in children post-pandemics, particularly in light of COVID-19.
Discovery of novel neutral glycosphingolipids in cereal crops: rapid profiling using reversed-phased HPLC–ESI–QqTOF with parallel reaction monitoring
Authors: Yu Dingyi , Boughton Berin A. , Rupasinghe Thusitha W. T. , Hill Camilla B. , Herrfurth Cornelia , Scholz Patricia , Feussner Ivo , Roessner Ute 
Published: December 2023

AbstractThis study explores the sphingolipid class of oligohexosylceramides (OHCs), a rarely studied group, in barley (Hordeum vulgare L.) through a new lipidomics approach. Profiling identified 45 OHCs in barley (Hordeum vulgare L.), elucidating their fatty acid (FA), long-chain base (LCB) and sugar residue compositions; and was accomplished by monophasic extraction followed by reverse-phased high performance liquid chromatography electrospray ionisation quadrupole-time-of-flight tandem mass spectrometry (HPLC–ESI–QqTOF–MS/MS) employing parallel reaction monitoring (PRM). Results revealed unknown ceramide species and highlighted distinctive FA and LCB compositions when compared to other sphingolipid classes. Structurally, the OHCs featured predominantly trihydroxy LCBs associated with hydroxylated FAs and oligohexosyl residues consisting of two–five glucose units in a linear 1 → 4 linkage. A survey found OHCs in tissues of major cereal crops while noting their absence in conventional dicot model plants. This study found salinity stress had only minor effects on the OHC profile in barley roots, leaving questions about their precise functions in plant biology unanswered.
Impact of climatic oscillations on marlin catch rates of Taiwanese long-line vessels in the Indian Ocean
Authors: Mondal Sandipan , Ray Aratrika , Osuka Kennedy Edeye , Sihombing Riah Irawati , Lee Ming-An , Chen Yu‑Kai 
Published: December 2023

AbstractThis study explored the influence of climatic oscillations on the striped, blue, and silver marlin catch rates in the Indian Ocean by using logbook data from Taiwanese large-scale fishing vessels and climate records from 1994 to 2016. Only the Madden–Julian oscillation (MJO) and the subtropical Indian Ocean dipole (SIOD) had immediate effects on the striped and silver marlin catch rates. The positive and negative phases of the IOD at the lags of 7 and 3 years corresponded to increased and decreased catch rates, respectively, for both the striped and blue marlin, contrasting to the reverse pattern for the silver marlin. Similarly, all three marlin species experienced decreased and increased catch rates respectively during the positive and negative phases of the Pacific decadal oscillation. The striped and blue marlin catch rates decreased and increased during the positive and negative phases, respectively, of the SIOD and MJO with various lags. Our results suggest that the impacts of climatic oscillations on fish species are crucial for policymakers and coastal communities for managing marine resources, forecasting changes in marine ecosystems, and developing strategies to adapt to and mitigate the effects of climate variability.
Circulating ESR1, long non-coding RNA HOTAIR and microRNA-130a gene expression as biomarkers for breast cancer stage and metastasis
Authors: Abdel-hamid Noura R. , Mohammed Eman A. , Toraih Eman A. , Kamel Mahmoud M. , Abdelhafiz Ahmed Samir , Badr Fouad M. 
Published: December 2023

AbstractBreast cancer, the most prevalent cancer among women, has posed a significant challenge in identifying biomarkers for early diagnosis and prognosis. This study aimed to elucidate the gene expression profile of Estrogen Receptor-1 (ESR-1), long non-coding RNA HOTAIR, and microRNA-130a in the serum of Egyptian breast cancer patients, evaluating the potential of HOTAIR and miR-130a as biomarkers for predicting pathological parameters in BC. The study involved 45 patients with primary BC, with serum samples collected preoperatively and postoperatively twice. The expression levels of ESR-1, HOTAIR, and miR-130a were quantified using real-time PCR and analyzed for correlations with each other and with the clinical and pathological parameters of the patients. Serum HOTAIR levels exhibited a strong positive association with metastasis and demonstrated a significant increase after 6 months in all patients with locally advanced and stage IV BC. Conversely, tumors with advanced stages and metastatic lesions showed significantly lower expression levels of miR-130a. Notably, a significant positive correlation was observed between preoperative ESR-1 expression and both HOTAIR and miR-130a levels. Serum HOTAIR and miR-130a levels have emerged as promising non-invasive biomarkers with the potential to predict the pathological features of BC patients. HOTAIR, an oncogenic long non-coding RNA (lncRNA), and miR-130a, a tumor suppressor miRNA, play crucial roles in tumor progression. Further investigations are warranted to elucidate the intricate interplay between HOTAIR and miR-130a and to fully comprehend the contribution of HOTAIR to BC recurrence and its potential utility in early relapse prediction.
Depletion of muscularis macrophages ameliorates inflammation-driven dysmotility in murine colitis model
Authors: Ferenczi Szilamér , Mogor Fruzsina , Takacs Peter , Kovacs Tamas , Toth Viktoria E. , Varga Zoltán V. , Kovács Krisztina , Lohinai Zoltan , Vass Koppány Csaba , Nagy Nandor , Dora David 
Published: December 2023

AbstractPreviously, the presence of a blood-myenteric plexus barrier and its disruption was reported in experimentally induced colitis via a macrophage-dependent process. The aim of this study is to reveal how myenteric barrier disruption and subsequent neuronal injury affects gut motility in vivo in a murine colitis model. We induced colitis with dextran sulfate sodium (DSS), with the co-administration of liposome-encapsulated clodronate (l-clodronate) to simultaneously deplete blood monocytes contributing to macrophage infiltration in the inflamed muscularis of experimental mice. DSS-treated animals receiving concurrent l-clodronate injection showed significantly decreased blood monocyte numbers and colon muscularis macrophage (MM) density compared to DSS-treated control (DSS-vehicle). DSS-clodronate-treated mice exhibited significantly slower whole gut transit time than DSS-vehicle-treated animals and comparable to that of controls. Experiments with oral gavage-fed Evans-blue dye showed similar whole gut transit times in DSS-clodronate-treated mice as in control animals. Furthermore, qPCR-analysis and immunofluorescence on colon muscularis samples revealed that factors associated with neuroinflammation and neurodegeneration, including Bax1, Hdac4, IL-18, Casp8 and Hif1a are overexpressed after DSS-treatment, but not in the case of concurrent l-clodronate administration. Our findings highlight that MM-infiltration in the muscularis layer is responsible for colitis-associated dysmotility and enteric neuronal dysfunction along with the release of mediators associated with neurodegeneration in a murine experimental model.
CRISPR/Cas9-mediated nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo
Authors: Hofeichner Janessa , Gahr Bernd Martin , Huber Magdalena , Boos Alena , Rottbauer Wolfgang , Just Steffen 
Published: December 2023

AbstractNexilin (NEXN) plays a crucial role in stabilizing the sarcomeric Z-disk of striated muscle fibers and, when mutated, leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice, the detailed impact of the constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated. Here, we characterized a constitutive homozygous CRISPR/Cas9-mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably, in contrast to nexn morphants, CRISPR/Cas9 nexn−/− knockout embryos showed a milder phenotype without the development of a pronounced pericardial edema or blood congestion. nexn-specific expression analysis as well as whole transcriptome profiling suggest some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced and may mediate a sarcomere stabilizing function in nexn−/− knockout embryos. Our findings demonstrate the successful generation and characterization of a constitutive homozygous nexn knockout line enabling the detailed investigation of the role of nexn on heart and skeletal muscle development and function as well as to assess putative compensatory mechanisms induced by the loss of Nexn.
Effects of plant-based proteins and handling stress on intestinal mucus microbiota in rainbow trout
Authors: Suhr Marvin , Fichtner-Grabowski Finn-Thorbjörn , Seibel Henrike , Bang Corinna , Franke Andre , Schulz Carsten , Hornburg Stéphanie C. 
Published: December 2023

AbstractVia 16S rRNA gene amplicon sequencing, this study explores whether the gut mucus microbiota of rainbow trout is affected by the interaction of a plant-protein-based diet and a daily handling stressor (chasing with a fishing net) across two genetic lines (A, B). Initial body weights of fish from lines A and B were 124.7 g and 147.2 g, respectively. Fish were fed 1.5% of body weight per day for 59 days either of two experimental diets, differing in their fish meal [fishmeal-based diet (F): 35%, plant-based diet (V): 7%] and plant-based protein content (diet F: 47%, diet V: 73%). No diet- or stress-related effect on fish performance was observed at the end of the trial. However, we found significantly increased observed ASVs in the intestinal mucus of fish fed diet F compared to diet V. No significant differences in Shannon diversity could be observed between treatments. The autochthonous microbiota in fish fed with diet V was dominated by representatives of the genera Mycoplasma, Cetobacterium, and Ruminococcaceae, whereas Enterobacteriaceae and Photobacterium were significantly associated with diet F. The mucus bacteria in both genetic lines were significantly separated by diet, but neither by stress nor an interaction, as obtained via PERMANOVA. However, pairwise comparisons revealed that the diet effect was only significant in stressed fish. Therefore, our findings indicate that the mucus-associated microbiota is primarily modulated by the protein source, but this modulation is mediated by the stress status of the fish.
Fracture identification and characteristics of carbonate underground gas storage: an example from the eastern area of Sulige gas field, ordos Basin, China
Authors: Xie Jun , Hao Xiaofan , Zhang Yuanpei , Zhang Jianguo , Xia Yong , He Yilin 
Published: December 2023

AbstractThe carbonate rock formations have obvious dual media characteristics, fracture development and good physical conditions, which are the main seepage channels and storage spaces for gas after the reconstruction of underground gas storage. The carbonate strata of the Ordovician system are important natural gas reservoirs in the eastern area of Sulige Gas Field in the Ordos Basin, and the identification and characterization of their fractures are of great significance for the modeling of fractures in the later stage and the improvement of the operation scheme of the gas storage. At present, there is little research on fractures, which restricts exploration and development. Therefore, taking the 39–61 gas storage reservoir in the eastern area of Sulige Gas Field in the Ordos Basin as the research object, this paper identifies and studies the characteristics of the fractures by core, microscopic, conventional logging curves, and imaging logging identification. The results show that the fracture length ranges from 5 to 15 cm and the width ranges from 0.1 to 3 mm. The fracture angles are mostly between 75° and 90° and the main direction is NW–SE. In conventional logging curves, porosity logging has a good response to fractures, while resistivity logging has a general response to fractures; In layers with more developed fractures, natural gamma values are mostly higher than 40API, rock volume density is less than 2.8 g/cm3, neutron porosity is greater than 12.5%, and acoustic time difference is greater than 160 μ s/m. This study is of great significance for improving the identification of carbonate fractures, enriching the relevant theories, and providing guidance for the construction of carbonate gas storage.
Dynamic response of axle box bearing for high-speed train considering wheelset flexibility and polygonal wear
Authors: Guan Tiantian , Deng Xiaoyu , Wang Jiangwen 
Published: December 2023

AbstractIn this study, a flexible wheelset was added to a rigid-flexible coupled vehicle dynamics model, in which the axle box bearings are accurately modeled. The measured wheel’s polygon wear profile and Wuhan-Guangzhou track spectrum are used in the model to define the wheel tread and track irregularity, respectively. We conducted a field test on the Wuhan-Guangzhou railway line to validate the model. Then, we investigate how the dynamic properties of the axle box bearing are impacted by the wheelset flexibility and polygonal wear of wheel. We found that the polygonal wheel with a rigid wheelset causes high-frequency vibration in wheelset and axle box, and increases the axle box bearing’s internal contact force. Additionally, the flexible wheelset with a normal wheel tread can alleviate the wheel/rail impact and reduce the axle box’s vertical vibration as well as the axle box bearing’s internal contact force. When the vehicle is running at v = 300 km/h, the excitation frequency caused by the wheel's 20th-order polygon is 576.5 Hz, and the flexible wheelset's 20th-order modal frequency is 577 Hz. The two frequencies are similar, when considering the polygonal wheel and flexible wheelset simultaneously, the wheelset will resonate. And the resonate of wheelset will increase the local deformation of the axle end and deteriorate the bearing operating environment, causing a significant increase in the bearing contact force. Finally, the axle box bearing’s dynamic characteristics are summarized when vehicle velocity varies from 50 to 350 km/h and wheel polygon wear amplitude ranges from 0.01 to 0.05 mm.
YTHDC1 delays cellular senescence and pulmonary fibrosis by activating ATR in an m6A-independent manner
Authors: Zhang Canfeng , Chen Liping , Xie Chen , Wang Fengwei , Wang Juan , Zhou Haoxian , Liu Qianyi , Zeng Zhuo , Li Na , Huang Junjiu , Zhao Yong , Liu Haiying 
Published: December 2023

AbstractAccumulation of DNA damage in the lung induces cellular senescence and promotes age-related diseases such as idiopathic pulmonary fibrosis (IPF). Hence, understanding the mechanistic regulation of DNA damage repair is important for anti-aging therapies and disease control. Here, we identified an m6A-independent role of the RNA-binding protein YTHDC1 in counteracting stress-induced pulmonary senescence and fibrosis. YTHDC1 is primarily expressed in pulmonary alveolar epithelial type 2 (AECII) cells and its AECII expression is significantly decreased in AECIIs during fibrosis. Exogenous overexpression of YTHDC1 alleviates pulmonary senescence and fibrosis independent of its m6A-binding ability, while YTHDC1 deletion enhances disease progression in mice. Mechanistically, YTHDC1 promotes the interaction between TopBP1 and MRE11, thereby activating ATR and facilitating DNA damage repair. These findings reveal a noncanonical function of YTHDC1 in delaying cellular senescence, and suggest that enhancing YTHDC1 expression in the lung could be an effective treatment strategy for pulmonary fibrosis.
eIF4E1b is a non-canonical eIF4E protecting maternal dormant mRNAs
Authors: Lorenzo-Orts Laura , Strobl Marcus , Steinmetz Benjamin , Leesch Friederike , Pribitzer Carina , Roehsner Josef , Schutzbier Michael , Dürnberger Gerhard , Pauli Andrea 
Published: December 2023

AbstractMaternal mRNAs are essential for protein synthesis during oogenesis and early embryogenesis. To adapt translation to specific needs during development, maternal mRNAs are translationally repressed by shortening the polyA tails. While mRNA deadenylation is associated with decapping and degradation in somatic cells, maternal mRNAs with short polyA tails are stable. Here we report that the germline-specific eIF4E paralog, eIF4E1b, is essential for zebrafish oogenesis. eIF4E1b localizes to P-bodies in zebrafish embryos and binds to mRNAs with reported short or no polyA tails, including histone mRNAs. Loss of eIF4E1b results in reduced histone mRNA levels in early gonads, consistent with a role in mRNA storage. Using mouse and human eIF4E1Bs (in vitro) and zebrafish eIF4E1b (in vivo), we show that unlike canonical eIF4Es, eIF4E1b does not interact with eIF4G to initiate translation. Instead, eIF4E1b interacts with the translational repressor eIF4ENIF1, which is required for eIF4E1b localization to P-bodies. Our study is consistent with an important role of eIF4E1b in regulating mRNA dormancy and provides new insights into fundamental post-transcriptional regulatory principles governing early vertebrate development.
Extended-Synaptotagmin-1 and -2 control T cell signaling and function
Authors: Benavides Nathalia , Giraudo Claudio G 
Published: December 2023

AbstractUpon T-cell activation, the levels of the secondary messenger diacylglycerol (DAG) at the plasma membrane need to be controlled to ensure appropriate T-cell receptor signaling and T-cell functions. Extended-Synaptotagmins (E-Syts) are a family of inter-organelle lipid transport proteins that bridge the endoplasmic reticulum and the plasma membrane. In this study, we identify a novel regulatory mechanism of DAG-mediated signaling for T-cell effector functions based on E-Syt proteins. We demonstrate that E-Syts downmodulate T-cell receptor signaling, T-cell-mediated cytotoxicity, degranulation, and cytokine production by reducing plasma membrane levels of DAG. Mechanistically, E-Syt2 predominantly modulates DAG levels at the plasma membrane in resting-state T cells, while E-Syt1 and E-Syt2 negatively control T-cell receptor signaling upon stimulation. These results reveal a previously underappreciated role of E-Syts in regulating DAG dynamics in T-cell signaling.