Additional file 1: of Constructing tissue-specific transcriptional regulatory networks via a Markov random field

Figure S1. The directed acyclic subgraph of the human cell hierarchical taxonomy graph. Figure S2 The similarity of Th2 cell and Crohn’s disease. Figure S3 The enrichment degree for target set of NFKB1 in 110 cell lines. Table S1 TFs and corresponding GO terms that alter between normal and cancer cell lines. TableS2 Top ranked TFs based on their differential regulating edges. (DOC 501 kb

Table_1_Emerging trends and hot spots in subacute thyroiditis research from 2001 to 2022: A bibliometric analysis.docx

BackgroundSubacute thyroiditis (SAT) is the most prevalent self-limiting thyroid disease that causes pain, accounting for about 5% of all clinical thyroid disorders. Numerous clinically noteworthy results have been published in this area over the last 20 years. However, no article has comprehensively assessed the relevant literature yet. We conducted a bibliometric analysis of SAT to provide light on the dynamic nature of scientific advancement and aid researchers in gaining a global perspective while examining research core themes and hotspots.MethodsSAT-related articles and reviews from 2001 to 2022 were retrieved from the Science Citation Index-Expanded of Web of Science Core Collection (WoSCC). We analyzed current research trends and hotspots in this area using CiteSpace and Vosviewer.ResultsA total of 568 studies associated with SAT research were published in 282 academic journals by 2,473 authors in 900 institutions from 61 countries/regions. The United States was a crucial link in inter-country/region collaboration and was the most frequently involved country in international cooperation. The University of Missouri System was the top organization, and Braley-Mullen H. was the most productive researcher. Thyroid published the most papers, with 36 publications. The most co-cited article was “Clinical features and outcome of subacute thyroiditis in an incidence cohort: Olmsted County, Minnesota, study” (by Fatourechi V., 2003). The clustered network and timeline view of keywords showed that the prevalence, diagnosis, and treatment of SAT were the research core themes during the past 20 years. Analysis of keyword bursts indicated that the clinical characteristic and the influence of COVID-19 on SAT appeared to be the current research hotspots.ConclusionThis bibliometric analysis conducted a thorough review of the SAT research. The clinical characteristics and the genetic background of SAT under the influence of COVID-19 are current research hotspots. However, there is still a need for further study and global collaboration. Our findings can aid researchers in understanding the current status of SAT research and immediately pinpoint new directions for further investigation.</p

Estimated false positive rates under different <i>q</i>-value cut-offs when using neutral SNVs in the Swiss-Prot database and exomes of the eight HapMap individuals as negative control sets.

<p>Estimated false positive rates under different <i>q</i>-value cut-offs when using neutral SNVs in the Swiss-Prot database and exomes of the eight HapMap individuals as negative control sets.</p

Presentation_1_Emerging trends and hot spots in subacute thyroiditis research from 2001 to 2022: A bibliometric analysis.zip

BackgroundSubacute thyroiditis (SAT) is the most prevalent self-limiting thyroid disease that causes pain, accounting for about 5% of all clinical thyroid disorders. Numerous clinically noteworthy results have been published in this area over the last 20 years. However, no article has comprehensively assessed the relevant literature yet. We conducted a bibliometric analysis of SAT to provide light on the dynamic nature of scientific advancement and aid researchers in gaining a global perspective while examining research core themes and hotspots.MethodsSAT-related articles and reviews from 2001 to 2022 were retrieved from the Science Citation Index-Expanded of Web of Science Core Collection (WoSCC). We analyzed current research trends and hotspots in this area using CiteSpace and Vosviewer.ResultsA total of 568 studies associated with SAT research were published in 282 academic journals by 2,473 authors in 900 institutions from 61 countries/regions. The United States was a crucial link in inter-country/region collaboration and was the most frequently involved country in international cooperation. The University of Missouri System was the top organization, and Braley-Mullen H. was the most productive researcher. Thyroid published the most papers, with 36 publications. The most co-cited article was “Clinical features and outcome of subacute thyroiditis in an incidence cohort: Olmsted County, Minnesota, study” (by Fatourechi V., 2003). The clustered network and timeline view of keywords showed that the prevalence, diagnosis, and treatment of SAT were the research core themes during the past 20 years. Analysis of keyword bursts indicated that the clinical characteristic and the influence of COVID-19 on SAT appeared to be the current research hotspots.ConclusionThis bibliometric analysis conducted a thorough review of the SAT research. The clinical characteristics and the genetic background of SAT under the influence of COVID-19 are current research hotspots. However, there is still a need for further study and global collaboration. Our findings can aid researchers in understanding the current status of SAT research and immediately pinpoint new directions for further investigation.</p

sj-docx-1-ajr-10.1177_19458924221124363 - Supplemental material for Daphnetin Mitigates Ovalbumin-Induced Allergic Rhinitis in Mice by Regulating Nrf2/HO-1 and TLR4/NF-kB Signaling

Supplemental material, sj-docx-1-ajr-10.1177_19458924221124363 for Daphnetin Mitigates Ovalbumin-Induced Allergic Rhinitis in Mice by Regulating Nrf2/HO-1 and TLR4/NF-kB Signaling by Bo Tian, Xin Ma and Rui Jiang in American Journal of Rhinology & Allergy</p

Validation results for synthesized exomes.

<p>(A) Distributions of ranks for test SNVs. (B) Boxplots of MRRs. (C) Boxplots of AUCs.</p

Integrating Multiple Genomic Data to Predict Disease-Causing Nonsynonymous Single Nucleotide Variants in Exome Sequencing Studies

<div><p>Exome sequencing has been widely used in detecting pathogenic nonsynonymous single nucleotide variants (SNVs) for human inherited diseases. However, traditional statistical genetics methods are ineffective in analyzing exome sequencing data, due to such facts as the large number of sequenced variants, the presence of non-negligible fraction of pathogenic rare variants or <i>de novo</i> mutations, and the limited size of affected and normal populations. Indeed, prevalent applications of exome sequencing have been appealing for an effective computational method for identifying causative nonsynonymous SNVs from a large number of sequenced variants. Here, we propose a bioinformatics approach called SPRING (<i>Snv PRioritization via the INtegration of Genomic data</i>) for identifying pathogenic nonsynonymous SNVs for a given query disease. Based on six functional effect scores calculated by existing methods (SIFT, PolyPhen2, LRT, MutationTaster, GERP and PhyloP) and five association scores derived from a variety of genomic data sources (gene ontology, protein-protein interactions, protein sequences, protein domain annotations and gene pathway annotations), SPRING calculates the statistical significance that an SNV is causative for a query disease and hence provides a means of prioritizing candidate SNVs. With a series of comprehensive validation experiments, we demonstrate that SPRING is valid for diseases whose genetic bases are either partly known or completely unknown and effective for diseases with a variety of inheritance styles. In applications of our method to real exome sequencing data sets, we show the capability of SPRING in detecting causative <i>de novo</i> mutations for autism, epileptic encephalopathies and intellectual disability. We further provide an online service, the standalone software and genome-wide predictions of causative SNVs for 5,080 diseases at <a href="http://bioinfo.au.tsinghua.edu.cn/spring" target="_blank">http://bioinfo.au.tsinghua.edu.cn/spring</a>.</p></div

sj-tif-2-ajr-10.1177_19458924221124363 - Supplemental material for Daphnetin Mitigates Ovalbumin-Induced Allergic Rhinitis in Mice by Regulating Nrf2/HO-1 and TLR4/NF-kB Signaling

Supplemental material, sj-tif-2-ajr-10.1177_19458924221124363 for Daphnetin Mitigates Ovalbumin-Induced Allergic Rhinitis in Mice by Regulating Nrf2/HO-1 and TLR4/NF-kB Signaling by Bo Tian, Xin Ma and Rui Jiang in American Journal of Rhinology & Allergy</p

Workflow of SPRING.

<p>Given a query disease and a set of candidate SNVs as inputs, SPRING calculates a <i>q</i>-value for each candidate and generates a ranking list of the candidates as the output. A <i>q</i>-value is calculated by using Fisher's method with dependence correction to integrate six functional effect <i>p</i>-values and five association <i>p</i>-values.</p

Rank distributions of the test SNVs.

<p>(A–C) Results for diseases with partly known genetic bases when validating against the neutral, disease, and combined control sets, respectively. (D–F) Results for diseases of unknown genetic bases when validating against the neutral, disease, and combined control sets, respectively.</p