综合性期刊最新文献

{"title":"Chromosome-scale genome assembly and gene annotation of the Alligator Gar (Atractosteus spatula).","authors":"Qing Wang, Qianqian Yu, Xiangqian Dong, Hengjin Chen, Xue Tian, Peng Qi, Haitao Wu, Yuxiang Yuan","doi":"10.1038/s41597-024-04256-2","DOIUrl":"https://doi.org/10.1038/s41597-024-04256-2","url":null,"abstract":"<p><p>Given the aggressive nature and robust survival capabilities of the alligator gar (Atractosteus spatula), if it was to exist in a new environment as an invasive species, it could cause significant disruption to the invaded ecosystem. Building on the continuity and completeness of the existing draft genome were not optimal, this study has updated a high-quality genome of the alligator gar at the chromosome level, which was assembled using Oxford Nanopore Technology and chromatin interaction mapping (Hi-C) sequencing techniques. In summary, the alligator gar genome in this study was 1.05 Gb in size with a contig N50 of 15.7 Mb and scaffold N50 of 56.8 Mb. We captured 98.26% of assembled bases in 28 pseudochromosomes. The completeness of the final chromosome-level genome reached 96.7%. Meanwhile, a total of 19,103 protein-coding genes were predicted, of which 99.83% could be predicted with functions. Taken together, the present high-quality alligator gar chromosome-level genome provides a valuable resource for exploring the underlying genomic basis to comprehend the functional genomics, chromosome evolution, and population management of this species.</p>","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"11 1","pages":"1337"},"PeriodicalIF":5.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthetic dataset of ID and Travel Documents.","authors":"Carlos Boned, Maxime Talarmain, Nabil Ghanmi, Guillaume Chiron, Sanket Biswas, Ahmad Montaser Awal, Oriol Ramos Terrades","doi":"10.1038/s41597-024-04160-9","DOIUrl":"https://doi.org/10.1038/s41597-024-04160-9","url":null,"abstract":"<p><p>This paper presents a new synthetic dataset of ID and travel documents, called SIDTD. The SIDTD dataset is created to help training and evaluating forged ID documents detection systems. Such a dataset has become a necessity as ID documents contain personal information and a public dataset of real documents can not be released. Moreover, forged documents are scarce, compared to legit ones, and the way they are generated varies from one fraudster to another resulting in a class of high intra-variability. In this paper we introduce a dataset, synthetically generated, that simulates the most common, and easiest, forgeries to be made by common users of ID documents and travel documents. The creation of this dataset will help to document image analysis community to progress in the task of automatic ID document verification in online onboarding systems.</p>","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"11 1","pages":"1356"},"PeriodicalIF":5.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasma metabolomics profiling of EGFR-mutant NSCLC patients treated with third-generation EGFR-TKI.","authors":"Ning Lou, Ruyun Gao, Yuankai Shi, Xiaohong Han","doi":"10.1038/s41597-024-04169-0","DOIUrl":"https://doi.org/10.1038/s41597-024-04169-0","url":null,"abstract":"<p><p>Third-generation epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) are the latest and a vital treatment option for non-small cell lung cancer (NSCLC) patients. Although EGFR-sensitive mutations are an indication for third-generation EGFR-TKI therapy, 30% of NSCLC patients lack response and all patients inevitably progress. There is a lack of biomarkers to predict the efficacy of EGFR-TKI therapy. In this report, we performed comprehensive plasma metabolomic profiling on 186 baseline and 20 post-treatment samples, analyzing 1,019 metabolites using four ultrahigh performance liquid chromatography-tandem mass spectroscopy (UPLC-MS/MS) methods. The dataset contains detailed clinical and metabolic information for 186 patients. Rigorous quality control measures were implemented. No significant differences in body mass index and biochemical metabolic parameters were observed between responders and non-responders. The datasets were utilized to characterize the responsive metabolic traits of third-generation EGFR-TKI therapy. All datasets are available for download on the OMIX website. We anticipate that these datasets will serve as valuable resources for future studies investigating NSCLC metabolism and for the development of personalized therapeutic strategies.</p>","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"11 1","pages":"1369"},"PeriodicalIF":5.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Primate Phenotypes: A Multi-Institution Collection of 3D Morphological Data Housed in MorphoSource.","authors":"Sergio Almécija, Kelsey D Pugh, Alisha Anaya, Christopher M Smith, Nancy B Simmons, Robert S Voss, Neil Duncan, Darrin P Lunde, Megan K Viera, Teresa Hsu, Emmanuel Gilissen, Stephanie A Maiolino, Julie M Winchester, Biren A Patel, Caley M Orr, Matthew W Tocheri, Eric Delson, Ashley S Hammond, Doug M Boyer, Santiago A Catalano","doi":"10.1038/s41597-024-04261-5","DOIUrl":"https://doi.org/10.1038/s41597-024-04261-5","url":null,"abstract":"<p><p>The field of phenomics is experiencing unprecedented advances thanks to the rapid growth of morphological quantification based on three-dimensional (3D) imaging, online data repositories, team-oriented collaborations, and open data-sharing policies. In line with these progressions, we present an extensive primate phenotypic dataset comprising >6,000 3D scans (media) representing skeletal morphologies of 386 individual specimens covering all hominoid genera (except humans) and other selected primates. The digitized specimens are housed in physical collections at the American Museum of Natural History, the National Museum of Natural History, the Royal Museum for Central Africa (Belgium), the Cleveland Museum of Natural History, and Stony Brook University. Our technical validation indicates that despite the diverse digitizing devices used to produce the scans, the final 3D models (meshes) can be safely combined to collect comparable morphometric data. The entire dataset (and detailed associated metadata) is freely available through MorphoSource. Hence, these data contribute to empowering the future of primate phenomics and providing a roadmap for future digitization and archiving of digital data from other collections.</p>","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"11 1","pages":"1391"},"PeriodicalIF":5.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"QM40, Realistic Quantum Mechanical Dataset for Machine Learning in Molecular Science.","authors":"Ayesh Madushanka, Renaldo T Moura, Elfi Kraka","doi":"10.1038/s41597-024-04206-y","DOIUrl":"https://doi.org/10.1038/s41597-024-04206-y","url":null,"abstract":"<p><p>The growing popularity of machine learning (ML) and deep learning (DL) in scientific fields is hindered by the scarcity of high-quality datasets. While quantum mechanical (QM) predictions using DL techniques such as graph neural networks (GNNs) and generative models are gaining traction, insufficient training data remains a bottleneck. The QM40 dataset addresses this challenge by representing 88% of the FDA-approved drug chemical space. It includes molecules containing 10 to 40 atoms and composed of elements commonly found in drug molecular structures (C, O, N, S, F, Cl). QM40 offers valuable resources for researchers which include the core QM40 main dataset, containing 16 key quantum mechanical parameters for 162,954 molecules calculated using the B3LYP/6-31G(2df,p) level of theory in Gaussian16, ensuring consistency with established datasets like QM9 and Alchemy. This compatibility allows for future concatenation of QM40 with these datasets. In addition to other valuable information, the QM40 dataset offers the initial and optimized Cartesian coordinates, Mulliken charges, and detailed bond information, including local vibrational mode force constants, which serve as indicators of bond strength. QM40 can be used to benchmark both existing and new methods for predicting QM calculations using ML and DL techniques.</p>","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"11 1","pages":"1376"},"PeriodicalIF":5.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The FLAIR-GG federated network of FAIR germplasm data resources.","authors":"Alberto Cámara Ballesteros, Elena Aguayo Jara, Evrykleia Sofia Verykaki, Germán Pastor Del Olmo, Santiago Moreno Vázquez, Elena Torres, Mark D Wilkinson","doi":"10.1038/s41597-024-04243-7","DOIUrl":"https://doi.org/10.1038/s41597-024-04243-7","url":null,"abstract":"","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"11 1","pages":"1386"},"PeriodicalIF":5.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crosstalk between mitochondrial homeostasis and AMPK pathway mediate the receptor-mediated cardioprotective effects of estradiol in ovariectomized female rats.","authors":"Mennatallah A Gowayed, Zainab Zaki Zakaraya, Nehal Abu-Samra, Reem H Elhamammy, Lobna M Abdel Moneim, Hala A Hafez, Ihab A Moneam, Ghaleb A Oriquat, Maher A Kamel","doi":"10.1371/journal.pone.0312397","DOIUrl":"https://doi.org/10.1371/journal.pone.0312397","url":null,"abstract":"<p><p>Estrogen (E2) deficiency is a risk factor for cardiovascular disease (CVD), however, the exact mechanism for the E2 protective effect on CVD remains unclear. This study aimed to investigate the estrogen receptor (ER) and non-receptor mediated effects of E2 treatment on the cardiac expression of adenosine monophosphate-dependent protein kinase (AMPK), autophagic, mitophagy and mitochondrial homeostasis-regulating genes in ovariectomized (OVX) rats. Female rats were divided into two main groups; sham and bilaterally OVX rats, then each group was subdivided into four subgroups according to treatment; untreated, subcutaneously treated with E2 (30 μg/kg), or Fulvestrant (F) (5 mg/Kg), or a combination of both drugs for 28 days. The OVX rats or F-treated sham rats showed dyslipidemia, and marked disturbances in parameters of AMPK signaling, autophagy, mitophagy, mitochondrial fission, fusion and biogenesis. E2 administration to OVX or F-treated sham rats has corrected the disturbed lipid and cardiac profiles, increased AMPK, and restored the balance of cardiac autophagy, mitophagy, and mitochondrial dynamics and homeostasis. Most of these effects in OVX rats were blocked by the ER antagonist (F). Estrogen treatment has cardioprotective effects in OVX females through modulating cardiac mitochondrial homeostasis, mitophagy and autophagy and restoring the AMPK signaling pathway. As witnessed by Fulvestrant, these effects suggest the main role of ER-mediated signaling in regulating mitophagy and plasma and cardiac lipids along with the existence of a post-translational control mechanism or the involvement of estrogenic non-receptor pathway controlling the postmenopausal cardiac mitochondrial energy production machinery that needs further investigation.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"19 12","pages":"e0312397"},"PeriodicalIF":2.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decay experiments and microbial community analysis of water lily leaf biofilms: Sediment effects on leaf preservation potential.","authors":"Brianne Palmer, Sabina Karačić, Shook Ling Low, Kathrin Janssen, Harald Färber, Moritz Liesegang, Gabriele Bierbaum, Carole T Gee","doi":"10.1371/journal.pone.0315656","DOIUrl":"https://doi.org/10.1371/journal.pone.0315656","url":null,"abstract":"<p><p>Understanding the intricate dynamics of sediment-mediated microbial interactions and their impact on plant tissue preservation is crucial for unraveling the complexities of leaf decay and preservation processes. To elucidate the earliest stages of leaf preservation, a series of decay experiments was carried out for three months on Nymphaea water lily leaves in aquariums with pond water and one of three distinctly different, sterilized, fine-grained substrates-commercially purchased kaolinite clay or fine sand, or natural pond mud. One aquarium contained only pond water as a control. We use 16S and ITS rRNA gene amplicon sequencing to identify and characterize the complex composition of the bacterial and fungal communities on leaves. Our results reveal that the pond mud substrate produces a unique community composition in the biofilms compared to other substrates. The mud substrate significantly influences microbial communities, as shown by the correlation between high concentrations of minerals in the water and bacterial abundance. Furthermore, more biofilm formers are observed on the leaves exposed to mud after two months, contrasting with declines on other substrates. The mud substrate also enhanced leaf tissue preservation compared to the other sediment types, providing insight into the role of sediment and biofilms in fossilization processes. Notably, leaves on kaolinite clay have the fewest biofilm formers by the end of the experiment. We also identify key biofilm-forming microbes associated with each substrate. The organic-rich mud substrate emerges as a hotspot for biofilm formers, showing that it promotes biofilm formation on leaves and may increase the preservation potential of leaves better than other substrates. The mud's chemical composition, rich in minerals such as silica, iron, aluminum, and phosphate, may slow or suspend decay and facilitate biomineralization, thus paving the way toward leaf preservation. Our study bridges the information gap between biofilms observed on modern leaves and the mineral encrustation on fossil leaves by analyzing the microbial response in biofilms to substrate types in which fossil leaves are commonly found.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"19 12","pages":"e0315656"},"PeriodicalIF":2.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Defining harmful news reporting on community firearm violence: A modified Delphi consensus study.","authors":"Jessica H Beard, Evan L Eschliman, Anita Wamakima, Christopher N Morrison, Jim MacMillan, Jennifer Midberry","doi":"10.1371/journal.pone.0316026","DOIUrl":"https://doi.org/10.1371/journal.pone.0316026","url":null,"abstract":"<p><p>Community firearm violence (CFV), including fatal and non-fatal shootings that result from interpersonal violence, disproportionately harms people from marginalized racial groups. News reporting on CFV can further exacerbate these harms. However, examining the effects of harmful news reporting on CFV on individuals, communities, and society is hindered by the lack of a consensus definition of harmful reporting on CFV. In this study, we aimed to define harmful reporting on CFV. We used a modified, three-round Delphi process to achieve consensus among diverse stakeholders. Round 1 sought to assess consensus on 12 potentially harmful news content elements for three levels of harm (individual, community, and society). Round 2 invited panelists to rate the severity of each news content element at each level of harm. Round 3 asked panelists to agree or disagree with the panel's median severity rating of each element at each level of harm. Twenty-one panelists were recruited from three expertise groups (lived experience of CFV, journalism practice, scholarship) and all panelists completed all three rounds. In Round 1, no negative consensus was achieved for any of the proposed news content elements. In Round 2, panelists assigned moderate to severe harm ratings for all but two news content elements, and median harm ratings for each element varied across the different levels of harm. In Round 3, panelists reported high levels of agreement for each harm rating at each level. This modified Delphi process yielded a definition of the 12 elements that comprise harmful news reporting on CFV and severity ratings of harm caused by each element at each level according to expert consensus. Future work will use these results to evaluate and intervene on harmful reporting on CFV. Reducing harm from reporting on CFV can help address this health disparity and support evidence-based approaches to this urgent public health issue.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"19 12","pages":"e0316026"},"PeriodicalIF":2.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Road side unit deployment optimization for the reliability of internet of vehicles based on information transmission model.","authors":"Jun Zhang, Guangtong Hu","doi":"10.1371/journal.pone.0315716","DOIUrl":"https://doi.org/10.1371/journal.pone.0315716","url":null,"abstract":"<p><p>The Internet of Vehicles (IoV) makes it possible to transmit information in real time between vehicles, providing a modern approach for autonomous driving, traffic safety, and other applications. Roadside units (RSUs) contribute to the enhancement of IoV's reliability and transmission efficiency, while mitigating the impact of low IoV penetration. The objective of RSU deployment optimization is to minimize the total cost with the premise of ensuring IoV reliability. We construct a distance-based reliability measure for IoV, which is expressed as the proportion of information transmitted in online mode to the total transmission distance. The distance distribution of the online and offline transmissions is computed using the information transmission model. A bi-objective optimization model is established with the objectives of minimizing the cost of RSU and maximizing the reliability of IoV. Meanwhile, based on variable probabilities of crossover and mutation, a nondomination level-based NSGA-II (NNSGA-II) is designed to improve the solving efficiency. Numerical results show the advantage of the proposed model over the models evaluated with the objective of reducing transmission time can be up to 18% in different traffic scenarios, and NNSGA-II is significantly more computationally efficient.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"19 12","pages":"e0315716"},"PeriodicalIF":2.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}