bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ownership and First-Person Authority from a Normative Pragmatist Perspective
Authors: Presti Patrizio Lo 
Published: December 2020

Abstract
Mental episodes are typically associated with subjective ownership and first-person authority. My belief that an apple is red is had by me; it is mine and I’m in a privileged position to know it. Your experience of red is had by you; it is yours and you are in a privileged position to know it. The two assumptions are that mental events are had by individuals to whom they occur, and that owners are in a privileged epistemic position to fallibly report their own. This paper asks how to understand ownership and first-person authority (section 1). It argues that the two assumptions should not be accepted by default (section 2). A normative pragmatism is specified, on which mental episodes are not owned, but owed to practices of reason articulation (section 3). Finally, a positive account of ownership and first-person authority is considered (section 4).
The Metaphysical Grounding of Logical Operations: John Dewey’s Theory of Qualitative Continuity
Authors: Cherlin Paul Benjamin 
Published: December 2020

Abstract
In John Dewey’s logical theory, qualities or qualitative relations account for the capacity to distinguish and associate the objects of reflective thought; they are antecedent to reflective analysis and necessary for coherent processes of inquiry. In Dewey’s writings that are specifically “metaphysical” in orientation, he is much more vague about the function of qualities, but does call them “generic traits of existence.” As such, they appear to be central to his mature ontological theory. In order to more fully understand the metaphysical import of qualitative relations, I first examine the details of Dewey’s logical theory, and then generalize those details in accordance with Dewey’s larger theory of nature. The end result is a novel interpretation of Dewey’s metaphysics.
The Future of Europe: The Beginning of a New Era in EU Governance?
Authors: Józon Mónika 
Published: December 2020

Abstract
The paper offers insight into the current practice of the passerelle(s), the enhanced cooperation and the flexibility clause, which may serve in the future the implementation of the Commission’s White Paper on the Future of Europe (2017) without Treaty revision, in light of recent developments in the policy of the new Commission, Council and European Parliament on the future of EU integration. The ex-ante and ex-post control mechanisms available at Member State level concerning the freedom of their governments to support such European initiatives, are also discussed from a comparative perspective. The paper concludes by presenting the risks associated with the activation of these mechanism of integration.
Autistic Communication and Imagination Sub-Traits Are Related to Audiovisual Temporal Integration in the Stream–Bounce Illusion
Authors: Yaguchi Ayako , Hidaka Souta 
Published: December 2020

Abstract
Autism spectrum disorder (ASD) is characterized by atypical social communication and restricted and repetitive behaviors; such traits are continuously distributed across nonclinical and clinical populations. Recently, relationships between ASD traits and low-level multisensory processing have been investigated, because atypical sensory reactivity has been regarded as a diagnostic criterion of ASD. Studies regarding an audiovisual illusion (the double-flash illusion) reported that social communication difficulties are related to temporal aspects of audiovisual integration. This study investigated whether similar relationships exist in another audiovisual illusion (the stream–bounce effect). In this illusion, two visual objects move toward each other, coincide, and pass each other, and the presentation of a transient sound at their coincidence induces a dominant perception that they bounce away from each other. Typically developing adults were recruited to perform experimental trials involving the stream–bounce effect. We measured their ASD traits using the Autism-Spectrum Quotient. The total quotient score was not related to any behavioral measurements of the effect. In contrast, for participants with higher difficulty in communication, the greatest magnitude of the stream–bounce effect occurred when the presentation timing of the sound tended to follow the visual coincidence. Participants with higher difficulty in imagination also showed the greatest magnitude of the effect when the presentation timing of the sound preceded that of the visual coincidence. Our findings regarding the stream–bounce effect, along with previous findings regarding the double-flash illusion, suggest that atypical temporal audiovisual integration is uniquely related to ASD sub-traits, especially in social communication.
Integrating the Thought of Mencius and Xunzi and the Problem of Modernizing Chinese Society
Authors: Huang Yushun 
Published: December 2020

Abstract
How should people today deal with the teachings of Mencius 孟子 and Xunzi 荀子? This is a question of utmost importance in reviving Confucianism. The thought of Mencius and Xunzi has many inherent complexities and contradictions. After all, they have been revised, reconstituted, and reused alongside shifts in lifestyles and social structures; their respective influence also waxed and waned accordingly. Xunzi’s teachings flourished during China’s transition from monarchical feudalism to imperial autocracy, an indication that Xunzi’s thinking has Legalist elements. The rulers in the imperial period adopted “sole veneration of Confucian learning” [du zun rushu 獨尊儒術], so the suspiciously Legalist teachings of Xunzi went into decline while the orthodox Confucian teachings of Mencius were on the rise. At the same time, Xunzi’s thought continued to play an important, perhaps even fundamental, role in hidden ways. This is the political path of being “openly Confucian, covertly Legalist” [yang ru yin fa 陽儒陰法] practiced under autocratic authority. As Chinese society began to modernize, Xunzi’s teachings enjoyed a revival, revealing that some of its strains were compatible with modern Enlightenment ideas. Further, this modern revival of Xunzi occurred on the heels of a Confucian revival. The fact that the two then more or less continued to coexist indicates the need to rethink the two schools of thought in an integrated way. To do this, I take a page from modern value systems and consider the existing distinctions between Mencius’s and Xunzi’s thinking via a “profit and loss analysis.”
First brachytherapy treatment of prostate cancer in Nigeria using low dose rate radioactive iodine 125
Authors: Adeyemi Oludare Folajimi , Mghari Rachid 
Published: December 2020

Abstract
Background
We report the first prostate brachytherapy in Nigeria, using low dose radioactive iodine 125 (I-125) permanent seeds implant.

Case Presentation
The low dose rate brachytherapy using I-125 implants was performed in a private clinic in the city of Benin, Edo state of Nigeria. This pilot study reports the case of the first two patients with prostate cancer. The patients were treated under spinal anesthesia using 2 ml of heavy bupibacaine which is equivalent to 10 mg of bupibacaine. Biopsy, total blood count, electrolytes, urea, creatinine, urinalysis, electrocardiogram, chest X-ray, prostate-specific antigen and bone scan were checked prior to the procedure. The first two prostate cancer patients who were in low risk category successfully received the treatment in the first day of the clinic’s operations. This paper describes the settings in which these clinical operations occurred, detailing the type of technology used, the clinical procedure and the obtained dose distribution.

Conclusions
The paper ends with discussing the overall cost of the investment and the challenges encountered as well as the perspectives of extending the brachytherapy practice to treat other cancer diseases, such as breast and genealogical cancers.
gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data
Authors: Ciccolella Simone , Soto Gomez Mauricio , Patterson Murray D. , Della Vedova Gianluca , Hajirasouliha Iman , Bonizzoni Paola 
Published: December 2020

AbstractBackgroundCancer progression reconstruction is an important development stemming from the phylogenetics field. In this context, the reconstruction of the phylogeny representing the evolutionary history presents some peculiar aspects that depend on the technology used to obtain the data to analyze: Single Cell DNA Sequencing data have great specificity, but are affected by moderate false negative and missing value rates. Moreover, there has been some recent evidence of back mutations in cancer: this phenomenon is currently widely ignored.ResultsWe present a new tool, , that reconstructs a tumor phylogeny from Single Cell Sequencing data, allowing each mutation to be lost at most a fixed number of times. The General Parsimony Phylogeny from Single cell () tool is open source and available athttps://github.com/AlgoLab/gpps.Conclusionsprovides new insights to the analysis of intra-tumor heterogeneity by proposing a new progression model to the field of cancer phylogeny reconstruction on Single Cell data.
iDPGK: characterization and identification of lysine phosphoglycerylation sites based on sequence-based features
Authors: Huang Kai-Yao , Hung Fang-Yu , Kao Hui-Ju , Lau Hui-Hsuan , Weng Shun-Long 
Published: December 2020

AbstractBackgroundProtein phosphoglycerylation, the addition of a 1,3-bisphosphoglyceric acid (1,3-BPG) to a lysine residue of a protein and thus to form a 3-phosphoglyceryl-lysine, is a reversible and non-enzymatic post-translational modification (PTM) and plays a regulatory role in glucose metabolism and glycolytic process. As the number of experimentally verified phosphoglycerylated sites has increased significantly, statistical or machine learning methods are imperative for investigating the characteristics of phosphoglycerylation sites. Currently, research into phosphoglycerylation is very limited, and only a few resources are available for the computational identification of phosphoglycerylation sites.ResultWe present a bioinformatics investigation of phosphoglycerylation sites based on sequence-based features. The TwoSampleLogo analysis reveals that the regions surrounding the phosphoglycerylation sites contain a high relatively of positively charged amino acids, especially in the upstream flanking region. Additionally, the non-polar and aliphatic amino acids are more abundant surrounding phosphoglycerylated lysine following the results of PTM-Logo, which may play a functional role in discriminating between phosphoglycerylation and non-phosphoglycerylation sites. Many types of features were adopted to build the prediction model on the training dataset, including amino acid composition, amino acid pair composition, positional weighted matrix and position-specific scoring matrix. Further, to improve the predictive power, numerous top features ranked by F-score were considered as the final combination for classification, and thus the predictive models were trained using DT, RF and SVM classifiers. Evaluation by five-fold cross-validation showed that the selected features was most effective in discriminating between phosphoglycerylated and non-phosphoglycerylated sites.ConclusionThe SVM model trained with the selected sequence-based features performed well, with a sensitivity of 77.5%, a specificity of 73.6%, an accuracy of 74.9%, and a Matthews Correlation Coefficient value of 0.49. Furthermore, the model also consistently provides the effective performance in independent testing set, yielding sensitivity of 75.7% and specificity of 64.9%. Finally, the model has been implemented as a web-based system, namely iDPGK, which is now freely available athttp://mer.hc.mmh.org.tw/iDPGK/.
Convolutional neural network for automated mass segmentation in mammography
Authors: Abdelhafiz Dina , Bi Jinbo , Ammar Reda , Yang Clifford , Nabavi Sheida 
Published: December 2020

Abstract
Background
Automatic segmentation and localization of lesions in mammogram (MG) images are challenging even with employing advanced methods such as deep learning (DL) methods. We developed a new model based on the architecture of the semantic segmentation U-Net model to precisely segment mass lesions in MG images. The proposed end-to-end convolutional neural network (CNN) based model extracts contextual information by combining low-level and high-level features. We trained the proposed model using huge publicly available databases, (CBIS-DDSM, BCDR-01, and INbreast), and a private database from the University of Connecticut Health Center (UCHC).

Results
We compared the performance of the proposed model with those of the state-of-the-art DL models including the fully convolutional network (FCN), SegNet, Dilated-Net, original U-Net, and Faster R-CNN models and the conventional region growing (RG) method. The proposed Vanilla U-Net model outperforms the Faster R-CNN model significantly in terms of the runtime and the Intersection over Union metric (IOU). Training with digitized film-based and fully digitized MG images, the proposed Vanilla U-Net model achieves a mean test accuracy of 92.6%. The proposed model achieves a mean Dice coefficient index (DI) of 0.951 and a mean IOU of 0.909 that show how close the output segments are to the corresponding lesions in the ground truth maps. Data augmentation has been very effective in our experiments resulting in an increase in the mean DI and the mean IOU from 0.922 to 0.951 and 0.856 to 0.909, respectively.

Conclusions
The proposed Vanilla U-Net based model can be used for precise segmentation of masses in MG images. This is because the segmentation process incorporates more multi-scale spatial context, and captures more local and global context to predict a precise pixel-wise segmentation map of an input full MG image. These detected maps can help radiologists in differentiating benign and malignant lesions depend on the lesion shapes. We show that using transfer learning, introducing augmentation, and modifying the architecture of the original model results in better performance in terms of the mean accuracy, the mean DI, and the mean IOU in detecting mass lesion compared to the other DL and the conventional models.
Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution
Authors: Kay C. , Williams T. A. , Gibson W. 
Published: December 2020

AbstractBackgroundTrypanosomes are single-celled eukaryotic parasites characterised by the unique biology of their mitochondrial DNA. African livestock trypanosomes impose a major burden on agriculture across sub-Saharan Africa, but are poorly understood compared to those that cause sleeping sickness and Chagas disease in humans. Here we explore the potential of the maxicircle, a component of trypanosome mitochondrial DNA to study the evolutionary history of trypanosomes.ResultsWe used long-read sequencing to completely assemble maxicircle mitochondrial DNA from four previously uncharacterized African trypanosomes, and leveraged these assemblies to scaffold and assemble a further 103 trypanosome maxicircle gene coding regions from published short-read data. While synteny was largely conserved, there were repeated, independent losses of Complex I genes. Comparison of pre-edited and non-edited genes revealed the impact of RNA editing on nucleotide composition, with non-edited genes approaching the limits of GC loss. African tsetse-transmitted trypanosomes showed high levels of RNA editing compared to other trypanosomes. The gene coding regions of maxicircle mitochondrial DNAs were used to construct time-resolved phylogenetic trees, revealing deep divergence events among isolates of the pathogensTrypanosoma bruceiandT. congolense.ConclusionsOur data represents a new resource for experimental and evolutionary analyses of trypanosome phylogeny, molecular evolution and function. Molecular clock analyses yielded a timescale for trypanosome evolution congruent with major biogeographical events in Africa and revealed the recent emergence ofTrypanosoma brucei gambienseandT. equiperdum, major human and animal pathogens.
Hepatic transcriptome and DNA methylation patterns following perinatal and chronic BPS exposure in male mice
Authors: Brulport Axelle , Vaiman Daniel , Bou-Maroun Elias , Chagnon Marie-Christine , Corre Ludovic Le 
Published: December 2020

Abstract
Background
Bisphenol S (BPS) is a common bisphenol A (BPA) substitute, since BPA is virtually banned worldwide. However, BPS and BPA have both endocrine disrupting properties. Their effects appear mostly in adulthood following perinatal exposures. The objective of the present study was to investigate the impact of perinatal and chronic exposure to BPS at the low dose of 1.5 μg/kg body weight/day on the transcriptome and methylome of the liver in 23 weeks-old C57BL6/J male mice.

Results
This multi-omic study highlights a major impact of BPS on gene expression (374 significant deregulated genes) and Gene Set Enrichment Analysis show an enrichment focused on several biological pathways related to metabolic liver regulation. BPS exposure also induces a hypomethylation in 58.5% of the differentially methylated regions (DMR). Systematic connections were not found between gene expression and methylation profile excepted for 18 genes, including 4 genes involved in lipid metabolism pathways (Fasn, Hmgcr, Elovl6, Lpin1), which were downregulated and featured differentially methylated CpGs in their exons or introns.

Conclusions
This descriptive study shows an impact of BPS on biological pathways mainly related to an integrative disruption of metabolism (energy metabolism, detoxification, protein and steroid metabolism) and, like most high-throughput studies, contributes to the identification of potential exposure biomarkers.

Graphical abstract
Non-O blood group is associated with lower risk of in-hospital mortality in non-surgically managed patients with type A aortic dissection
Authors: Huang Song , Chen Yequn , Huang Zhaotao , Wu Shiwan , Xiong Nianling , Huang Xiru , Wang Xin , Chen Chang , Wang Bin , Li Weiping , Hong Liangli , Ye Shu , Tan Xuerui 
Published: December 2020

AbstractBackgroundThe association between different ABO blood groups and mortality of aortic dissection (AD) remains controversial. This study aimed to examine whether different ABO blood groups affect the prognosis of AD.MethodsDemographic and clinical data were collected from 877 patients diagnosed with AD from 2015 to 2019 in the First Affiliated Hospital of Shantou University Medical College. The association between in-hospital mortality of AD patients and ABO blood group was analyzed using Cox proportional hazards regression models.ResultsThis retrograde cohort study demonstrated that for 877 patients, male gender, non-O blood group, Stanford type B AD (TBAD), higher presenting systolic and diastolic blood pressure, and being a recipient of aortic arch replacement surgery (surgery) or endovascular stent-graft implantation (stent-graft) were associated with decreased in-hospital mortality of AD. In Cox proportional hazards models, non-O blood group was associated with lower risk of early mortality regardless of adjustment (HR = 0.668, 95% confidence interval [CI] 0.473–0.944 before adjustment, HR = 0.662, 95% CI 0.468–0.935 after adjustment for age and sex, and HR = 0.641, 95% CI 0.453–0.906 after adjustment for AD types, SBP and surgery). Further analyses revealed that for patients diagnosed with type A AD (TAAD), non-O blood group renders a significant 34.3% decrease in the risk of in-hospital mortality compared with blood group O. Specifically, this difference in mortality risk was found among TAAD patients who did not undergo surgery (HR = 0.579, 95% CI 0.377–0.889), rather than those who did. There was no significant difference in early mortality for patients with TBAD, whether or not stent-grafts were implanted.ConclusionsNon-O blood type decreases the risk of in-hospital mortality, especially for TAAD, in AD patients without surgical intervention. More attention must be paid to blood type O TAAD patients without surgical interventions, and early surgical intervention may be an effective means to decrease in-hospital mortality of TAAD.
Genetic determinants of clinical phenotype in hypertrophic cardiomyopathy
Authors: Velicki Lazar , Jakovljevic Djordje G. , Preveden Andrej , Golubovic Miodrag , Bjelobrk Marija , Ilic Aleksandra , Stojsic Snezana , Barlocco Fausto , Tafelmeier Maria , Okwose Nduka , Tesic Milorad , Brennan Paul , Popovic Dejana , Ristic Arsen , MacGowan Guy A. , Filipovic Nenad , Maier Lars S. , Olivotto Iacopo 
Published: December 2020

AbstractBackgroundHypertrophic cardiomyopathy (HCM) is the most common inherited cardiovascular disease that affects approximately one in 500 people. HCM is a recognized genetic disorder most often caused by mutations involving myosin-binding protein C (MYBPC3) and β-myosin heavy chain (MYH7) which are responsible for approximately three-quarters of the identified mutations.MethodsAs a part of the international multidisciplinary SILICOFCM project (www.silicofcm.eu) the present study evaluated the association between underlying genetic mutations and clinical phenotype in patients with HCM. Only patients with confirmed single pathogenic mutations in either MYBPC3 or MYH7 genes were included in the study and divided into two groups accordingly. The MYBPC3 group was comprised of 48 patients (76%), while the MYH7 group included 15 patients (24%). Each patient underwent clinical examination and echocardiography.ResultsThe most prevalent symptom in patients with MYBPC3 was dyspnea (44%), whereas in patients with MYH7 it was palpitations (33%). The MYBPC3 group had a significantly higher number of patients with a positive family history of HCM (46% vs. 7%;p = 0.014). There was a numerically higher prevalence of atrial fibrillation in the MYH7 group (60% vs. 35%,p = 0.085). Laboratory analyses revealed normal levels of creatinine (85.5 ± 18.3 vs. 81.3 ± 16.4 µmol/l;p = 0.487) and blood urea nitrogen (10.2 ± 15.6 vs. 6.9 ± 3.9 mmol/l;p = 0.472) which were similar in both groups. The systolic anterior motion presence was significantly more frequent in patients carrying MYH7 mutation (33% vs. 10%;p = 0.025), as well as mitral leaflet abnormalities (40% vs. 19%;p = 0.039). Calcifications of mitral annulus were registered only in MYH7 patients (20% vs. 0%;p = 0.001). The difference in diastolic function, i.e. E/e′ ratio between the two groups was also noted (MYBPC3 8.8 ± 3.3, MYH7 13.9 ± 6.9,p = 0.079).ConclusionsMajor findings of the present study corroborate the notion that MYH7 gene mutation patients are presented with more pronounced disease severity than those with MYBPC3.