bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atlas of eccDNA in Mus musculus reveals intron and isoform gene-density dependent protection of transcription-induced eccDNA formation
Authors: Regenberg Birgitte , Tané Gerard , Liang Xue , Qin Yating , González Lucía , Tümmler Maria , Ma Jie , Holt Sylvester , Han Peng , Luo Yonglun , Ruiz-Herrera Aurora , Pilegaard Henriette 
Published: February 2024

Abstract

EccDNA is a driver of many cancers and a potential intermediate in other age-related disorders. However, little is known about the mechanisms underlying eccDNA formation in healthy tissue and how age affects these processes. We generated an Atlas of eccDNA across seven tissues of mice spanning four ages. EccDNA was overrepresented from open chromatin characterized by signatures of H3K27ac and H3K4me1 in 3 and 12-month-old mice but not in 22-month-old mice. The mutational load of eccDNA on genes increased logarithmically as a function of transcription and this phenomenon was enhanced as mitotically active tissue aged. Still, a population of intron-dense genes with many splice forms was sheltered from eccDNA formation. We also found that the number of eccDNA did not increase as mice aged, unlike other types of mutations. Our data reveal a link between eccDNA formation, transcript level and aging that might have driven gene architecture in mammals.
Physicochemical, Micronutrient and Fatty Acid Compositions of Some Selected Mayonnaise Samples in Nsukka, Nigeria
Authors: Chinenye Chinelo Nkwocha , Felix Joshua Ogah , Ekeanyanwu Raphael 
Published: February 2024

Abstract
Introduction: The chemical makeup of mayonnaise, a distinctive type of spread and food dressing formed with an oil-in-water emulsion, was examined.
Methods: For this investigation, a total of six distinct mayonnaise samples were used. Standard techniques and GCMS were used to examine the physicochemical, fatty acid, and micronutrient contents of the mayonnaise samples.
Results: The findings indicated that the mayonnaise samples contained the following range of physicochemical characteristics: iodine value (33.1098 ± 0.473 to 35.1022 ± 0.620 g I2/100g), acid value (27.7824 ± 0.5774 to 29.1121 ± 0.588 mgKOH/g), peroxide value (14.6000 ± 0.5774 to 16.4000 ± 0.5774 meqO2/kg), saponification value (190.9843 ± 0.5774 to 225.1288 ± 3.0550 mgKOH/g), melting point (8.0000 ± 0.5774 to 10.2214 ± 0.5774 ᵒC). According to the fatty acid profile, the different mayonnaise samples differ in their proportions of linolenic acid, lauric acid, tetracosapentanoic acid, docosahexaenoic acid, myristic acid, eicosadecanoic acid, oleic acid, and docosapentanoic acid. The mayonnaise samples contained various levels of vitamins A, C, D, E, and K as well as minerals like copper, iron, zinc, and manganese. Conclusion: The results of the nutritional features of the various mayonnaise samples, showed that it contained various essential nutrients useful in developing healthy – oriented diets and improve food quality.
Machine learning-based exploration of enzyme-substrate networks: SET8-mediated methyllysine and its changing impact within cancer proteomes
Authors: Biggar Kyle , Ridgeway Nashira , Chopra Anand , Lukinovic Valentina , Feldman Michal , Charih Francois , Levy Dan , Green James 
Published: February 2024

Abstract
The exploration of post-translational modifications (PTMs) within the proteome is pivotal for advancing disease and cancer therapeutics. However, identifying genuine PTM sites amid numerous candidates is challenging. Integrating machine learning (ML) models with high-throughput in vitro peptide synthesis has introduced an ML-hybrid search methodology, enhancing enzyme-substrate selection prediction. In this study we have developed a ML-hybrid search methodology to better predict enzyme-substrate selection. This model achieved a 37.4% experimentally validated precision, unveiling 885 SET8 candidate methylation sites in the human proteome—marking a 19-fold accuracy increase over traditional in vitro methods. Mass spectrometry analysis confirmed the methylation status of several sites, responding positively to SET8 overexpression in mammalian cells. This approach to substrate discovery has also shed light on the changing SET8-regulated substrate network in breast cancer, revealing a predicted gain (376) and loss (62) of substrates due to missense mutations. By unraveling enzyme selection features, this approach offers transformative potential, revolutionizing enzyme-substrate discovery across diverse PTMs while capturing crucial biochemical substrate properties.
Carbon-Free Fuels Can Increase Aviation-Induced Cloudiness
Authors: Vasel-Be-Hagh Ahmad , Cannon Trevor , Hagan Ty , Kramer Trevor , Schafer David , Meeks Spencer , Medlin Ryan , Roland Devin , Roberts Rory 
Published: February 2024

Abstract

This study evaluates the potential of a newly introduced carbon-free, ammonia-powered propulsion system in contrast to conventional propulsions powered by jet fuel in forming condensation trails (contrails). Contrail formation in an airplane's wake relies on two main prerequisites. Firstly, the system's thermodynamics must lead to supersaturation. Secondly, aerosol particles must be present to provide surfaces for solidification, enabling the formation of visible ice crystals. While this study primarily analyzes the first requirement, it leverages the insights gained to comment on the second prerequisite, arguing that although ammonia does not generate soot particles, it dramatically warms the critical temperature required for supersaturation. Therefore, given that aerosol particles are consistently generated or released into the atmosphere through natural and human-made processes, which is why natural clouds can form anyway, increased critical temperatures caused by ammonia result in contrails that would not occur if jet fuel were employed. Hence, while ammonia's contrail might not be as dense as jet fuel's as it lacks soot particles in the exhaust gas, it can form at lower altitudes where the air is warmer. Moreover, it can endure longer due to the increased water content, which preserves supersaturation for longer as fresh air dilutes the contrail.
Engineering TadA ortholog-derived cytosine base editor without motif preference and adenosine activity limitation
Authors: Zhou Yingsi , Li Guoling , Dong Xue , Luo Jiamin , Li Tong , Zhao Guoli , Zhang Hainan , Zhou Jingxing , Cui Shuna , Zeng Zhenhai , Wang Haoqiang , Wang Yin , Yu Yuyang , Yuan Yuan , Xu Chunlong , Huang Jinhai 
Published: February 2024

Abstract

The engineered TadA variants used in cytosine base editors (CBEs) present unique advantages, including a smaller size and fewer off-target effects compared to cytosine base editors that rely on natural deaminases. However, the current TadA variants demonstrate a preference for base editing in DNA with specific motif sequences and possess dual deaminase activity, acting on both cytosine and adenosine in adjacent positions, limiting their application scope. To address these issues, we employed TadA orthologs screening and multi sequence alignment (MSA)-guided protein engineering techniques to create a highly effective cytosine base editor (aTdCBE) without motif and adenosine deaminase activity limitations. Notably, the delivery of aTdCBE to a humanized mouse model of Duchenne muscular dystrophy (DMD) mice achieved robust exon 55 skipping and restoration of dystrophin expression. Our advancement in engineering TadA ortholog for cytosine editing enrich the base editing toolkits for gene-editing therapy and other potential applications.
Combining clinically common drugs with hindlimb stretching in spinal cord injured rodents
Authors: Magnuson David , Forston Morgan , Jordan Savannah , Cesarz Greta , Burke Darlene , Shum-Siu Alice , Petruska Jeffrey C. 
Published: February 2024

Abstract

Study Design: Preclinical pilot study.
Objectives: To explore peripheral and central nociceptive mechanisms that contribute to muscle stretch-induced locomotor deficits following spinal cord injury.
Setting: Kentucky Spinal Cord Injury Research Center, Louisville, KY, USA
Methods: Ten female Sprague-Dawley rats received moderate, 25 g/cm T10 contusion injuries and recovered for 4 weeks. Rats were divided into three groups: Morphine/Ibuprofen-treated, Acetaminophen/Baclofen-treated, and saline control. Each group received daily hindlimb muscle stretching during weeks 4, 5, 9, and 10 post-injury and drugs were administered with stretching during weeks 4 and 9 only. Locomotor function was assessed throughout the experiment using the BBB Open Field Locomotor Scale. Hindlimb responses including spasticity, writhing, and clonic-like vibrations during muscle stretching were classified and scored.
Results: Consistent with our previous studies, hindlimb muscle stretching caused significant deficits in locomotor recovery following spinal cord injury. Baclofen and Ibuprofen partially mitigated the stretching effect, but none of the drugs significantly prevented the drop in locomotor function during stretching. Interestingly, treatment with Baclofen or Ibuprofen significantly reduced hindlimb responses such as spasticity and writhing during stretching, while Morphine exacerbated clonic-like vibrations in response to stretching maneuvers.
Conclusions: These findings suggest that stretching may inhibit locomotor recovery through combined mechanisms of peripheral inflammation and sensitization of nociceptive afferents. When combined with central sprouting and loss of descending controls after SCI, this results in exaggerated nociceptive input during stretching. The inability of the applied clinical drugs to mitigate the detrimental effects of stretching highlights the complexity of the stretching phenomenon and emphasizes the need for further investigation.
Transradial access for hepatic artery infusion chemotherapy: a single center retrospective study
Authors: Huang Jian , Zeng Genghua , Wei Huijun , Xu Zhangqi , Zhong Guihong , Pan Weihua , Jian Yizeng 
Published: February 2024

Abstract

Background
The purpose of this study was to investigate the safety, efficacy and feasibility of transradial approach (TRA) for hepatic arterial infusion chemotherapy in patients with unresectable hepatocellular carcinoma.
Methods
A total of 100 patients with unresectable hepatocellular carcinoma who received hepatic artery infusion chemotherapy in the department of hepatobiliary surgery, Longyan Second Hospital from January 2018 to June 2023 were retrospectively collected. The patients were divided into two groups according to the arterial puncture approach: TRA group (n = 35) and transfemoral approach group (TFA) (n = 65). The operation time, radiation dose, success rate of puncture and operation, intraoperative and postoperative complications of the two groups were observed and recorded.
Results
All patients received hepatic arterial infusion chemotherapy. The success rate of TFA group was higher than that of TRA group (100% vs 85.7%, P = 0.002). In terms of operation time and radiation dose to patients, the TRA group was higher than the TFA group (P < 0.001). In terms of postoperative complications, there was no significant difference between the two groups. The comfort and satisfaction of the TRA group were significantly higher than those of the TFA group (P < 0.05).
Conclusion
Transradial approach is safe, effective and feasible for hepatic artery infusion chemotherapy in patients with unresectable hepatocellular carcinoma. The comfort and satisfaction of patients are significantly improved, but the technique is difficult.
Efficient estimating and clustering Lithium-ion batteries with a deep-learning approach
Authors: He Xin , Sun Zhongxian , He Weilin , Li Dingquan , Geng Xin , Yang Dongchen , Wang Hailong , Hu Linyu , Tu Haiyan 
Published: February 2024

Abstract

Identifying the state of health (SOH) of batteries is critical for estimating batteries from unknown states or grouping retired batteries for secondary utilization to promote recycling sustainability. However, batteries perform distinct capacity fading behaviours in real scenarios and service activities. The energy conversion process is reflected by electrical signals, but proceeds via electrochemical reactions associated with temperature and strain variation. Herein, we develop a deep-learning framework for rapid, accurate, and transferable estimation of battery SOH. This framework incorporates deep neural networks with interconnected electrochemical, mechanical and thermal features as expanded segments. Our model delivers optimal accuracy with mean absolute error (MAE) of 0.519% and root mean square error (RMSE) of 0.795% based on combined features. The model is valid in various conditions and is capable of realizing rapid and accurate prediction merely with one previous cycle. More importantly, the well-trained material domain could be transferred to other electrode systems with few samples. Our work highlights the value of relevant features on battery SOH estimation, and provides guidance on efficient and reliable classification of batteries in the sustainable cycle.
Comprehensive Nontargeted Analysis of Fluorosurfactant Byproducts and Reaction Products in Wastewater from Semiconductor Manufacturing
Authors: Chen YiJu , Yang Jheng-Sian , Lin Angela Yu-Chen 
Published: February 2024

Abstract

Semiconductor manufacturing employs per- and polyfluoroalkyl substances (PFAS) as fluoroasurfactants to enhance the quality of photolithography lines. Our research, employing a fragment-based approach to investigate nontarget PFAS, overcomes conventional homologous series limitations. We identified 80 PFAS in wastewater and effluent samples from semiconductor industry, including 29 newly discovered compounds, categorized into three groups. First, primary PFAS formulations, such as perfluorobutane sulfonamide and perfluorobutane sulfonamido (di)ethanols, are accompanied by byproducts comprising approximately 0.1% of the total height compared to the main components. These byproducts, which exhibit variations in fluoroalkyl chains such as hydro-substituted, unsaturated, or ether structures, were reported for the first time to exist in commercially authentic standards, indicating their possible origin as byproducts of chemical manufacturing process. Second, transformation products from perfluorobutane sulfonamido ethanol during oxidation, including the first identified intermediate transformation compounds, perfluorobutane sulfonamido acetaldehyde and its hydrate, were obtained. Third, diverse reaction products are generated from the intricate processes of semiconductor manufacturing, which utilize strong acids, bases, and solvents under UV light or heated conditions. These processes include the formation of PFAS-related compounds through hydration, sulfonation, oxidation, and nitrification. This study revealed 22 isomeric PFAS, encompassing headgroup isomers and functional tail group isomers. These findings underscore the importance of comprehending diverse reactions and the overall emission compositions of PFAS in semiconductor wastewater, highlighting its complexity and presenting challenges for subsequent wastewater treatment.
Epigenetic age acceleration is associated with blood lipid levels in a multi-ancestry sample of older U.S. adults
Authors: Lin Lisha , Kiryakos Jenna , Ammous Farah , Ratliff Scott M. , Ware Erin B. , Faul Jessica D. , Kardia Sharon L.R. , Zhao Wei , Birditt Kira S. , Smith Jennifer A. 
Published: February 2024

Abstract
Background
Dyslipidemia, which is characterized by an unfavorable lipid profile, is a key risk factor for cardiovascular disease (CVD). Understanding the relationships between epigenetic aging and lipid levels may help guide early prevention and treatment efforts for dyslipidemia.
Methods
We used weighted linear regression to cross-sectionally investigate the associations between five measures of epigenetic age acceleration estimated from whole blood DNA methylation (HorvathAge Acceleration, HannumAge Acceleration, PhenoAge Acceleration, GrimAge Acceleration, and DunedinPACE) and four blood lipid measures (total cholesterol (TC), LDL-C, HDL-C, and triglycerides (TG)) in 3,813 participants (mean age = 70 years) from the Health and Retirement Study (HRS). As a sensitivity analysis, we examined the same associations in participants who fasted prior to the blood draw (n = 2,531) and in participants who did not take lipid-lowering medication (n = 1,869). Using interaction models, we also examined whether the relationships between epigenetic age acceleration and blood lipids differ by demographic factors including age, sex, and educational attainment.
Results
After adjusting for age, race/ethnicity, sex, fasting status, and lipid-lowering medication use, greater epigenetic age acceleration was associated with lower TC, HDL-C, and LDL-C, and higher TG (p < 0.05). GrimAge acceleration and DunedinPACE associations with all lipids remained significant after further adjusting for body mass index, smoking status, and educational attainment. These associations were stronger in participants who fasted and who did not use lipid-lowering medication, particularly for LDL-C. We observed the largest number of interactions between DunedinPACE and demographic factors, where the associations with lipids were stronger in younger participants, females, and those with higher educational attainment.
Conclusion
Epigenetic age acceleration, a powerful biomarker of cellular aging, is highly associated with blood lipid levels in older adults. A greater understanding of how these associations differ across demographic groups can help shed light on the relationships between aging and downstream cardiovascular diseases. The inverse associations between epigenetic age and TC and LDL-C could be due to sample limitations or the non-linear relationship between age and these lipids, as both TC and LDL-C decrease faster at older ages. More studies are needed to further understand the temporal relationships between epigenetic age acceleration on blood lipids and other health outcomes.
Impact of COVID-19 Pandemic on Bone and Soft Tissue Sarcoma Patients’ Consultation and Diagnosis
Authors: Oyama Ryunosuke , Endo Makoto , Shimada Eijiro , Kanahori Masaya , Matsunobu Tomoya , Kawaguchi Kengo , Setsu Nokitaka , Hirose Takeshi , Maekawa Akira , Nabeshima Akira , Fujiwara Toshifumi , Yoshimoto Masato , Ishihara Shin , Hanada Masuo , Yokoyama Nobuhiko , Matsumoto Yoshihiro , Oda Yoshinao , Nakashima Yasuharu 
Published: February 2024

Abstract

The coronavirus disease (COVID-19) pandemic negatively affected the diagnosis and treatment of several cancer types. However, the exact impact and extent of this pandemic on bone and soft tissue sarcomas have not been clarified. We aimed to investigate the impact of the COVID-19 pandemic on consultation behavior and clinical stage at diagnosis of bone and soft tissue sarcoma. A total of 403 patients diagnosed with bone and soft tissue sarcoma who initially visited three sarcoma treatment hospitals between January 2018 and December 2021 were included. The monthly number of newly diagnosed primary bone and soft tissue sarcoma cases was significantly decreased by 43% during the state of emergency declaration (6.9 vs. 3.9; p<0.001). Furthermore, the monthly number of new primary soft tissue sarcoma cases was reduced by 25% during the COVID-19 pandemic compared to before the COVID-19 pandemic (6.0 vs. 4.5; p=0.020), especially for painless soft tissue sarcoma cases (4.5 vs. 3.1; p=0.014). The proportion of patients with stage IV disease at diagnosis significantly was increased by 9% during the COVID-19 pandemic (10 vs. 19%. p=0.032). The COVID-19 pandemic had a negative impact on bone and soft tissue sarcoma patients’ consultation behavior, especially for those with painless soft tissue sarcoma.
Analysis of coinfections in patients with hematologic malignancies and COVID-19 by next-generation sequencing of bronchoalveolar lavage fluid
Authors: Shu Wenxiu , Yang Qianqian , Le Jing , Cai Qianqian , Dai Hui , Luo Liufei , Tong Jiaqi , Song Yanping , Chen Bingrong , Tang Yaodong , Jin Dian 
Published: February 2024

Abstract

Background
Coinfections in patients with coronavirus disease 2019 (COVID-19) affect patient prognosis. Patients with hematologic malignancies (HMs) are usually immunosuppressed and may be at high risk of coinfection, but few related data have been reported. Here, we conducted a retrospective study to explore coinfections in patients with HMs and COVID-19 by next-generation sequencing (NGS) of bronchoalveolar lavage fluid (BALF).
Methods
The data of hospitalized patients with pneumonia who underwent NGS analysis of BALF were reviewed. COVID-19 patients with HMs were enrolled in the HM group, and those without HMs were enrolled in the non-HM group. The coinfections of the two groups identified by NGS were analyzed.
Results
Fifteen patients were enrolled in the HM group, and 14 patients were enrolled in the non-HM group. The coinfection rates in the HM group and non-HM group were 80.0% and 85.7%, respectively. The percentage of coinfected bacteria in the HM group was significantly lower than that in the non-HM group (20.0% vs 71.4%, p = 0.005). The coinfection rates of fungi and viruses were 60.0% and 35.7%, respectively, in the HM group and 35.7% and 78.6%, respectively, in the non-HM group, with no significant differences. The most common coexisting pathogen in patients with HMs was Pneumocystis jirovecii (33.3%), and the most common coexisting pathogen in patients without HMs was human gammaherpesvirus 4 (50%). Coinfection with herpesviruses occurred frequently in both groups.
Conclusions
Our study showed that hospitalized patients with COVID-19 had a high incidence of coinfection. Pneumocystis jiroveci and herpesvirus are commonly coinfected pathogens in patients with HMs. Bacterial coinfection is rare in patients with HMs but is more common in patients without HMs.
Navigating Soundscapes: Attractant effect of reef sound on oyster settlement may be attenuated by vessel noise
Authors: Schmidlin Sarah , Parcerisas Clea , Hubert Jeroen , Watson Maryann S. , Mees Jan , Botteldooren Dick , Devos Paul , Debusschere Elisabeth , Hablützel Pascal I. 
Published: February 2024

Abstract
Settlement is a critical period in the life cycle of benthic species with planktonic larval stages and for reef building invertebrates such as oysters and corals; settlement rates are predictive for reef restoration and long-term survival. Increasing evidence suggests that marine invertebrates use information from ocean soundscapes to inform settlement decisions. Sessile marine invertebrates with a settlement stage are particularly reliant on environmental cues to direct them to ideal habitats as settlement location is permanent. As gregarious settlers, oysters prefer to settle amongst members of the same species. It has been hypothesized that planktonic larvae use distinct oyster reef sounds to navigate to ideal habitats. In controlled laboratory experiments, we show that sounds recorded at conspecific reefs induce higher percentages of settlement in larvae of the Pacific Oyster Magallana gigas. Additionally, we exposed larvae to anthropogenic sounds from several different vessels, combined reef-vessel sounds as well as off-reef and no sound controls. Our results suggest that attractive reef noises may be masked by vessel sounds, however, this observation is substantiated by a nonsignificant trend. Examining the acoustic characteristics of the preferred reef sounds, we hypothesize that spectro-temporal patterns are the driving attractive quality in reef sounds for this species.