bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Writing of Daily Life
Authors: Werlin Julianne 
Published: August 2021

Abstract
This chapter argues that the growing importance of financial documentation in early modernity shaped the form and content of vernacular writing. Focusing on the diary, it traces links between journals and accounts from early Renaissance Florence through seventeenth-century England, showing how notebook culture spread in response to financial pressures. Ultimately, the extension of monetary relations in early capitalist England gave men and women new reasons to record apparently trivial details of their daily lives, which now appeared in lists of expenses, debts, and accounts. The chapter thus contributes to debates about English economic individualism and the origins of realist prose; in addition, it shows how practical documents served as a vector for transmitting financial imperatives to literary history.
Exploratory Data Analysis and Data Summarization
Authors: Touchon Justin C. 
Published: August 2021

Abstract
The third chapter introduces the dataset that readers will work with for the remainder of the book: the RxP data. Students are taught how to import the data and how to use indexing and packages like dplyr to navigate this large, real, and somewhat messy set of ecological data. Basic plotting is introduced as a tool for exploratory data analysis. Lastly, students are taught how to summarize a dataset quickly and efficiently.
Introduction to Plotting
Authors: Touchon Justin C. 
Published: August 2021

Abstract
R is one of the most powerful programs available for graphically representing your data, and chapter 4 begins the important process of teaching how this is done. Base graphics are introduced but the main focus is on teaching the package ggplot2, which has become the principal method of making figures in R. Various types of graphics are taught, including box-and-whisker plots, scatterplots, histograms, and density plots. In addition, the ways to customize these figures with colors, shapes, and faceting are also covered. The chapter ends by walking readers step-by-step through the process of creating a professional looking bar graph in both base graphics and ggplot2
Advanced Data Wrangling and Plotting
Authors: Touchon Justin C. 
Published: August 2021

Abstract
The advent of the packages in the tidyverse such as dplyr, tidyr, and ggplot2, has made the process of navigating, summarizing, transforming and plotting data increasing easy. Chapter 9 teaches readers the most important basics of data wrangling, such as how to summarize, spread, and gather your data, and how to use to the do() function to automate running functions. A detailed run through of plotting with ggplot2 is also undertaken, as is the connectivity of data wrangling and plotting.
‘Wang’s Paradox’
Authors: Wright Crispin 
Published: August 2021

Abstract
This chapter, specially written for the 2007 Schilp volume in his honour, revisits Sir Michael Dummett’s seminal contribution to the debates about vagueness in his ipsonymous 1975 paper. The chapter again rejects both the conception of vagueness as any kind of semantic incompleteness and Epistemicism, and critiques Dummett’s own suggestion of Incoherentism, returning again to the governing view and the question of the sense, if any, in which vague expressions should be thought of as governed by semantic rules. The Sorites for phenomenal predicates, ‘looks red’ and its ilk, receives special focus. It is argued that the correct response is that the competent use of these and other vague expressions is, in a certain sense, unprincipled: their vagueness is a phenomenon of reactive judgement unsupported by reasons. This conception enforces Agnosticism about Bivalence and a consequent repudiation of the validity of double negation elimination.
Fermionic topological phases and bosonization in higher dimensions
Authors: Kobayashi Ryohei 
Published: August 2021

Abstract
We review a recipe to produce a lattice construction of fermionic phases of matter in the presence of time reversal symmetry by extending the fermionization and bosonization known in (1+1) dimensions to various setups including higher spacetime dimensions in the presence of global symmetries. As an application, we provide a state sum lattice path integral for a (1+1)-dimensional topological superconductor with time reversal symmetry generating the $\mathbb{Z}_8$ classification of the symmetry-protected topological phase. We also illustrate a state sum path integral for a (3+1)-dimensional topological superconductor with time reversal symmetry that generates the $\mathbb{Z}_{16}$ classification.
Concentrated growth factor regulates the macrophage-mediated immune response
Authors: Luo Haiyun , Liu Wenjing , Zhou Yachuan , Jiang Xiao , Liu Yeungyeung , Yang Qin , Shao Longquan 
Published: August 2021

AbstractConcentrated growth factor (CGF) is a promising regenerative material that serves as a scaffold and adjunct growth factor for tissue engineering. The host immune response, particularly macrophage activity, plays a critical role in injury repair and tissue regeneration. However, the biological effect of CGF on the immune response is not clear. To enrich the theoretical groundwork for clinical application, the present study examined the immunoregulatory role of CGF in macrophage functional activities in vitro. The CGF scaffold appeared as a dense fibrin network with multiple embedded leukocytes and platelets, and it was biocompatible with macrophages. Concentrated bioactive factors in the CGF extract enhanced THP-1 monocyte recruitment and promoted the maturation of suspended monocytes into adherent macrophages. CGF extract also promoted THP-1 macrophage polarization toward the M2 phenotype with upregulated CD163 expression, as detected by cell morphology and surface marker expression. A cytokine antibody array showed that CGF extract exerted a regulatory effect on macrophage functional activities by reducing secretion of the inflammatory factor interleukin-1β while inducing expression of the chemokine regulated on activation, normal T cell expressed and secreted. Mechanistically, the AKT signaling pathway was activated, and an AKT inhibitor partially suppressed the immunomodulatory effect of CGF. Our findings reveal that CGF induces a favorable immune response mediated by macrophages, which represents a promising strategy for functional tissue regeneration.
Complete Genome Sequence of the Plant-Pathogenic Fungus Colletotrichum lupini
Authors: Baroncelli Riccardo , Pensec Flora , Da Lio Daniele , Boufleur Thais , Vicente Isabel , Sarrocco Sabrina , Picot Adeline , Baraldi Elena , Sukno Serenella , Thon Michael , Le Floch Gaetan 
Published: August 2021

Colletotrichum is a fungal genus (Ascomycota, Sordariomycetes, Glomerellaceae) that includes many economically important plant pathogens that cause devastating diseases of a wide range of plants. In this work, using a combination of long- and short-read sequencing technologies, we sequenced the genome of Colletotrichum lupini RB221, isolated from white lupin (Lupinus albus) in France during a survey in 2014. The genome was assembled into 11 nuclear chromosomes and a mitochondrial genome with a total assembly size of 63.41 Mb and 36.55 kb, respectively. In total, 18,324 protein-encoding genes have been predicted, of which only 39 are specific to C. lupini. This resource will provide insight into pathogenicity factors and will help provide a better understanding of the evolution and genome structure of this important plant pathogen. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Koumiss promotes Mycobacterium bovis infection by disturbing intestinal flora and inhibiting endoplasmic reticulum stress
Authors: Wang Haoran , Hussain Tariq , Yao Jiao , Li Jing , Sabir Naveed , Liao Yi , Liang Zhengmin , Wang Yuanzhi , Liu Yiduo , Zhao Deming , Zhou Xiangmei 
Published: August 2021

AbstractMycobacterium bovis is the causative agent of bovine tuberculosis and also responsible for serious threat to public health. Koumiss is a fermented mare's milk product, used as traditional drink. Here, we explored the effect of koumiss on gut microbiota and the host immune response against M bovis infection. Therefore, mice were treated with koumiss and fresh mare milk for 14 days before M bovis infection and continue for 5 weeks after infection. The results showed a clear change in the intestinal flora of mice treated with koumiss, and the lungs of mice treated with koumiss showed severe edema, inflammatory infiltration, and pulmonary nodules in M bovis‐infected mice. Notably, we found that the content of short‐chain fatty acids was significantly lower in the koumiss‐treated group compared with the control group. However, the expression of endoplasmic reticulum stress and apoptosis‐related proteins in the lungs of koumiss‐treated mice were significantly decreased. Collectively, these findings suggest that koumiss treatment disturb the intestinal flora of, which is associated with disease severity and the possible mechanism that induces lungs pathology. Our current findings can be exploited further to establish the “gut‐lung” axis which might be a novel strategy for the control of tuberculosis.
New mechanism-based approaches to treating and evaluating the vasculopathy of scleroderma
Authors: Flavahan Nicholas A. 
Published: August 2021

Purpose of review
Utilizing recent insight into the vasculopathy of scleroderma (SSc), the review will highlight new opportunities for evaluating and treating the disease by promoting stabilization and protection of the microvasculature.

Recent findings
Endothelial junctional signaling initiated by vascular endothelial-cadherin (VE-cadherin) and Tie2 receptors, which are fundamental to promoting vascular health and stability, are disrupted in SSc. This would be expected to not only diminish their protective activity, but also increase pathological processes that are normally restrained by these signaling mediators, resulting in pathological changes in vascular function and structure. Indeed, key features of SSc vasculopathy, from the earliest signs of edema and puffy fingers to pathological disruption of hemodynamics, nutritional blood flow, capillary structure and angiogenesis are all consistent with this altered endothelial signaling. It also likely contributes to further progression of the disease including tissue fibrosis, and organ and tissue injury.

Summary
Restoring protective endothelial junctional signaling should combat the vasculopathy of SSc and prevent further deterioration in vascular and organ function. Indeed, this type of targeted approach has achieved remarkable results in preclinical models for other diseases. Furthermore, tracking this endothelial junctional signaling, for example by assessing vascular permeability, should facilitate insight into disease progression and its response to therapy.
Lymphocyte immunophenotyping in inflammatory myositis: a review
Authors: Franco Chiara , Gatto Mariele , Iaccarino Luca , Ghirardello Anna , Doria Andrea 
Published: August 2021

Purpose of review
This is a comprehensive review of the current knowledge on predominant immune cell phenotypes involved in idiopathic inflammatory myopathies (IIM).

Recent findings
Major circulating immune cell subpopulations described in IIM encompass the lymphocyte compartment. An unbalance in T cell subsets seems to consistently affect the peripheral and muscle compartment, with a predominance of CD4+ T and B cells in dermatomyositis, CD8+ T cells in polymyositis/inclusion body myositis (IBM) and novel findings highlighting novel proinflammatory T subsets, that is, CD8+Tbet+ and CD28− T cells across different IIM subsets. On the other hand, an impairment in Treg cells number and function has been described especially across polymyositis/dermatomyositis and IBM. Total T follicular helper (Tfh) cells, increased in immune-mediated necrotizing myopathy, skewed toward Tfh2 and Tfh17 in dermatomyositis, polymyositis, and juvenile dermatomyositis. B cell compartment is more rarely described in IIM, yet an unbalance in this pool is as well likely. Evidence of plasma cells increased in polymyositis, dermatomyositis, IBM, and Bregs decreased in dermatomyositis have been reported. Perturbations in the memory and naïve subsets are common in dermatomyositis/polymyositis and antisynthetase syndrome.

Summary
Protean immune cell abnormalities characterize different IIM subsets, reflecting the complexity of these autoimmune conditions. A deeper understanding of B-cell and T-cell immunophenotyping may promote early diagnosis and identification of new potential therapeutic targets.
Preexisting opioid use disorder is associated with poor outcomes in hospitalized acute pancreatitis patients
Authors: Shaikh Abdullah S. , Al Mouslmani Mhd Yassin , Raza Shah Aun , Hassan Khan Zarak , Tausif Siddiqui Mohamed , Saraireh Hamzeh , Chandan Saurabh , Umar Shifa , Arora Sumant , Desai Madhav , Guturu Praveen , Bilal Mohammad 
Published: August 2021

Introduction
Although opioids are widely used for pain management in acute pancreatitis, the impact of opioid use disorder (OUD) on outcomes in patients with acute pancreatitis remains unknown. In the current study, we aimed to evaluate the impact of the OUD on outcomes in patients hospitalized with acute pancreatitis and delineate the trends associated with OUD and acute pancreatitis using a nationally representative sample.

Methods
This is a retrospective cohort study of patients with acute pancreatitis using the combined releases of the year 2005–2014 of the National (Nationwide) Inpatient Sample (NIS) database. Patients over the age of 18 years with a principal diagnosis of acute pancreatitis were divided into cohorts of patients with opioid use disorders and those without. The primary measured outcome was in-hospital mortality and secondary outcomes were healthcare utilization measures, including length of stay (LOS) and hospitalization costs.

Results
A total of 2 593 831 hospitalizations of acute pancreatitis were included; of which, 37 849 (1.46%) had a secondary diagnosis of OUD. Total acute pancreatitis-related hospitalizations increased from 237 882 in 2005 to 274 006 in 2014. At the same time prevalence of OUD in acute pancreatitis patients also increased from 1 to 2.1%. Patients with OUD had significantly increased mortality as compared to patients without OUD (aOR: 1.4; P < 0.001). At the same time, acute pancreatitis patients with OUD were associated with 1.3 days longer LOS as compared to other acute pancreatitis patients (P < 0.001]. The mean adjusted difference in total hospitalization costs was $2353 (P < 0.001).

Conclusion
OUD is associated with a significant increase in LOS, healthcare utilization cost and in-hospital mortality in patients admitted for acute pancreatitis. Therefore, clinicians should exercise caution in prescribing opioid medications to this high-risk patient population and other modalities such as nonopioid pain medications should be tried as alternatives to opioid analgesics.
Pediatric Endoscopy Quality Improvement Network Quality Standards and Indicators for Pediatric Endoscopists and Endoscopists in Training
Authors: Walsh Catharine M. , Lightdale Jenifer R. , Leibowitz Ian H. , Lerner Diana G. , Liu Quin Y. , Mack David R. , Mamula Petar , Narula Priya , Oliva Salvatore , Riley Matthew R. , Rosh Joel R. , Tavares Marta , Utterson Elizabeth C. , Amil‐Dias Jorge , Bontems Patrick , Brill Herbert , Croft Nicholas M. , Fishman Douglas S. , Furlano Raoul I. , Gillett Peter M. , Hojsak Iva , Homan Matjaž , Huynh Hien Q. , Jacobson Kevan , Ambartsumyan Lusine , Otley Anthony R. , Kramer Robert E. , McCreath Graham A. , Connan Veronik , Thomson Mike A. ,   PEnQuIN Working Group
Published: August 2021

ABSTRACTIntroduction:High‐quality pediatric endoscopy requires reliable performance of procedures by competent individual providers who consistently uphold all standards determined to assure optimal patient outcomes. Establishing consensus expectations for ongoing monitoring and assessment of individual pediatric endoscopists is a method for confirming the highest possible quality of care for such procedures worldwide. We aim to provide guidance to define and measure quality of endoscopic care for children.Methods:With support from the North American and European Societies of Pediatric Gastroenterology Hepatology and Nutrition (NASPGHAN and ESPGHAN), an international working group of the Pediatric Endoscopy Quality Improvement Network (PEnQuIN) used the methodological strategy of the Appraisal of Guidelines for REsearch and Evaluation (AGREE) II instrument to develop standards and indicators relevant for assessing the quality of endoscopists. Consensus was sought via an iterative online Delphi process and finalized at an in‐person conference. The quality of evidence and strength of recommendations were rated according to the GRADE (Grading of Recommendation Assessment, Development, and Evaluation) approach.Results:The PEnQuIN working group achieved consensus on 6 standards that all providers who perform pediatric endoscopy should uphold and 2 standards for pediatric endoscopists in training, with 7 corresponding indicators that can be used to identify high‐quality endoscopists. Additionally, these can inform continuous quality improvement at the provider level. Minimum targets for defining high‐quality pediatric ileocolonoscopy were set for 2 key indicators: cecal intubation rate (≥90%) and terminal ileal intubation rate (≥85%).Discussion:It is recommended that all individual providers performing or training to perform pediatric endoscopy initiate and engage with these international endoscopist‐related standards and indicators developed by PEnQuIN.
Analysis of key genes and pathways associated with the pathogenesis of Type 2 diabetes mellitus
Authors: Alur Varun , Raju Varshita , Vastrad Basavaraj , Vastrad Chanabasayya , Kotturshetti Shivakumar 
Published: August 2021

AbstractType 2 diabetes mellitus (T2DM) is the most common endocrine disorder which poses a serious threat to human health. This investigation aimed to screen the candidate genes differentially expressed in T2DM by bioinformatics analysis. The expression profiling by high throughput sequencing of GSE81608 dataset was retrieved from the gene expression omnibus (GEO) database and analyzed to identify the differentially expressed genes (DEGs) between T2DM and normal controls. Then, Gene Ontology (GO) and pathway enrichment analysis, protein-protein interaction (PPI) network, modules, miRNA-hub gene regulatory network construction and TF-hub gene regulatory network construction, and topological analysis were performed. Receiver operating characteristic curve (ROC) analysis was also performed to verify the diagnostics value and expression of identified hub genes. A total of 927 DEGs (461 were up regulated and 466 down regulated genes) were identified in T2DM. GO and REACTOME results showed that DEGs mainly enriched in protein metabolic process, establishment of localization, metabolism of proteins and metabolism. The top centrality hub genes APP, MYH9, TCTN2, USP7, SYNPO, GRB2, HSP90AB1, UBC, HSPA5 and SQSTM1 were screened out as the critical genes among the DEGs from the PPI network, modules, miRNA-hub gene regulatory network construction and TF-hub gene regulatory network. ROC analysis provide diagnostics value of hub genes. This study identified key genes, signal pathways and therapeutic agents, which might help us, improve our understanding of the mechanisms of HGPS and identify some new therapeutic agents for T2DM.
Proteogenomic Discovery of Neoantigens Facilitates Personalized Multi-antigen Targeted T cell Immunotherapy for Brain Tumors
Authors: Rivero-Hinojosa Samuel , Grant Melanie , Panigrahi Aswini , Zhang Huizhen , Caisova Veronika , Bollard Catherine M. , Rood Brian R. 
Published: August 2021

ABSTRACTNeoantigen discovery in pediatric brain tumors is hampered by their low mutational burden and scant tissue availability. We developed a low-input proteogenomic approach combining tumor DNA/RNA sequencing and mass spectrometry proteomics to identify tumor-restricted (neoantigen) peptides arising from multiple genomic aberrations to generate a highly target-specific, autologous, personalized T cell immunotherapy. Our data indicate that novel splice junctions are the primary source of neoantigens in medulloblastoma, a common pediatric brain tumor. Proteogenomically identified tumor-specific peptides are immunogenic and generate MHC II-based T cell responses. Moreover, polyclonal and polyfunctional T cells specific for tumor-specific peptides effectively eliminated tumor cells in vitro. Targeting novel tumor-specific antigens obviates the issue of central immune tolerance while potentially providing a safety margin favoring combination with other immune-activating therapies. These findings demonstrate the proteogenomic discovery of immunogenic tumor-specific peptides and lay the groundwork for personalized targeted T cell therapies for children with brain tumors.
In silico Analysis of Transcriptomic Profiling and Affected Biological pathways in Multiple Sclerosis
Authors: Vaja Rutvi , Kaur Harpreet , Mazumder Mohit , Brodsky Elia 
Published: August 2021

AbstractMultiple sclerosis (MS) is a chronic autoimmune, inflammatory neurological disease that is widely associated with Grey and white matter degradation due to the demyelination of axons. Thus exposing the underlying causes of this condition can lead to a novel treatment approach for Multiple Sclerosis. The total RNA microarray processed data from GEO for Multiple sclerotic patients was comprehensively analyzed to find out underlying differences between Grey Matter lesions (GML), Normal appearing Grey Matter (NAGM), and Control Grey matter at the transcriptomics level. Thus, in the current study, we performed various bioinformatics analyses on transcriptional profiles of 184 samples including 105 NAGM, 37 GML, and 42 Controls obtained from the NCBI-Bio project (PRJNA543111). First, exploratory data analysis based on gene expression data using principal component analysis (PCA) depicted distinct patterns between GML and CG samples. Subsequently, the Welch’s T-test differential gene expression analysis identified 15,525 significantly differentially expressed genes (p.adj value <0.05, Fold change(>=+/-1.5) between these conditions. This study reveals the genes like CREB3L2, KIF5B, WIPI1, EP300, NDUFA1, ATG101, AND TAF4 as the key features that may substantially contribute to loss of cognitive functions in Multiple sclerosis and several other neurodegenerative disorders. Further, this study also proposes genes associated with Huntington’s disease in Multiple sclerotic patients. Eventually, the results presented here reveal new insights into MS and how it affects the development of male primary sexual characteristics.