Yao, Lixia

Abstract Background: It is estimated that 10-25% of patients with hypothyroidism use desiccated thyroid extract (DTE) as their primary thyroid hormone replacement medication, despite concerns about the risk of thyrotoxicosis associated with DTE use. It is unclear why many patients prefer the use of DTE as a thyroid hormone replacement formulation over guideline-concordant therapies such as levothyroxine (LT4). Methods: We conducted a mixed-methods study by analyzing patient-reported information from patient online forums to better understand patient preferences for and attitudes toward the use of DTE to treat hypothyroidism. We searched the 10 most popular patient forums based on number of users (WebMD, Topix, Health questions, Patients like me, Drugs.com, Endocrine Web, Everyday Health, Talk Health Partnership, Spark People and Patients.info) using the key terms: desiccated thyroid extract, desiccated thyroid treatment, thyroid USP, commercial names of DTE (Armour Thyroid® or Natural Thyroid®), thyroid extract, AND hypothyroidism. Unique posts were retrieved from those websites between each forum’s inception to March 2018. From these posts, we extracted descriptive information on patient demographics and clinical characteristics and qualitatively analyzed posts’ content to further explore patient perceptions on DTE and other thyroid hormone replacement therapies. Results: Unique 1,235 posts were initially retrieved from the included patient forums. After the initial screening, we selected data from three of these forums (WebMD, Patients Like Me, and Drugs.com) based on the completeness of the available information (673 posts). Nearly half (45%) of patients reported that a clinician initially drove their interest in trying DTE. Patients described many reasons for switching from a previous therapeutic approach to DTE, including lack of improvement in symptoms (58%) and the development of side effects (22%). Among a majority of patients, DTE was described as moderately-to-majorly effective overall (81%) and more effective than the previous therapy (77%). The most frequently described benefits associated with DTE use were an improvement in clinical symptoms (56%) as well as a change in overall well-being (34%). One-fifth of patients described side effects related to the use of DTE. Qualitative analysis of posts’ content supported these findings and raised additional issues around the need for individualizing therapy approaches for hypothyroidism as well as difficulties obtaining DTE. Conclusions: Among patients with hypothyroidism, a subset may prefer DTE over guideline-concordant therapies for many reasons, including perceived effectiveness, despite the risks associated with DTE. Future work should incorporate patient-reported outcomes to better elucidate the mechanisms responsible for therapy preferences in this subset of patients.

Background and objectives: It is unclear why many patients with hypothyroidism prefer the use of desiccated thyroid extract (DTE) as a thyroid hormone replacement formulation over levothyroxine (LT4) treatment, as recommended by clinical practice guidelines. We analyzed patient-reported information from patient online forums to better understand patient preferences for and attitudes toward the use of DTE to treat hypothyroidism. Materials and Methods: We conducted a mixed-methods study by evaluating the content of online posts from three popular hypothyroidism forums from patients currently taking DTE (n = 673). From these posts, we extracted descriptive information on patient demographics and clinical characteristics and qualitatively analyzed posts’ content to explore patient perceptions on DTE and other therapies further. Results: Nearly half (46%) of the patients reported that a clinician initially drove their interest in trying DTE. Patients described many reasons for switching from a previous therapeutic approach to DTE, including lack of improvement in hypothyroidism-related symptoms (58%) and the development of side effects (22%). The majority of patients described DTE as moderately to majorly effective overall (81%) and more effective than the previous therapy (77%). The most frequently described benefits associated with DTE use were an improvement in symptoms (56%) and a change in overall well-being (34%). One-fifth of patients described side effects related to the use of DTE. Qualitative analysis of posts’ content supported these findings and raised additional issues around the need for individualizing therapy approaches for hypothyroidism (e.g., a sense of each patient has different needs), as well as difficulties obtaining DTE (e.g., issues with pharmacy availability). Conclusions: Lack of individualized treatment and a feeling of not been listened to were recurrent themes among DTE users. A subset of patients may prefer DTE to LT4 for many reasons, including perceived better effectiveness and improved overall well-being, despite the risks associated with DTE.

Drug safety is a severe clinical pharmacology and toxicology problem that has caused immense medical and social burdens every year. Regretfully, a reproducible method to assess drug safety systematically and quantitatively is still missing. In this study, we developed an advanced machine learning model for de novo drug safety assessment by solving the multilayer drug‐gene‐adverse drug reaction (ADR) interaction network. For the first time, the drug safety was assessed in a broad landscape of 1,156 distinct ADRs. We also designed a parameter ToxicityScore to quantify the overall drug safety. Moreover, we determined association strength for every 3,807,631 gene‐ADR interactions, which clues mechanistic exploration of ADRs. For convenience, we deployed the model as a web service ADRAlert‐gene at http://www.bio-add.org/ADRAlert/. In summary, this study offers insights into prioritizing safe drug therapy. It helps reduce the attrition rate of new drug discovery by providing a reliable ADR profile in the early preclinical stage.

Rationale: GWAS (Genome-Wide Association Studies) have identified hundreds of genetic loci associated with atrial fibrillation (AF). However, these loci explain only a small proportion of AF heritability. Objective: To develop an approach to identify additional AF-related genes by integrating multiple omics data. Methods and Results: Three types of omics data were integrated: (1) summary statistics from the AFGen 2017 GWAS; (2) a whole blood EWAS (Epigenome-Wide Association Study) of AF; and (3) a whole blood TWAS (Transcriptome-Wide Association Study) of AF. The variant-level GWAS results were collapsed into gene-level associations using fast set-based association analysis. The CpG-level EWAS results were also collapsed into gene-level associations by an adapted SNP-set Kernel Association Test approach. Both GWAS and EWAS gene-based associations were then meta-analyzed with TWAS using a fixed-effects model weighted by the sample size of each data set. A tissue-specific network was subsequently constructed using the NetWAS (Network-Wide Association Study). The identified genes were then compared with the AFGen 2018 GWAS that contained more than triple the number of AF cases compared with AFGen 2017 GWAS. We observed that the multiomics approach identified many more relevant AF-related genes than using AFGen 2018 GWAS alone (1931 versus 206 genes). Many of these genes are involved in the development and regulation of heart- and muscle-related biological processes. Moreover, the gene set identified by multiomics approach explained much more AF variance than those identified by GWAS alone (10.4% versus 3.5%). Conclusions: We developed a strategy to integrate multiple omics data to identify AF-related genes. Our integrative approach may be useful to improve the power of traditional GWAS, which might be particularly useful for rare traits and diseases with limited sample size.

Data on disease burden are often used for assessing population health, evaluating the effectiveness of interventions, formulating health policies, and planning future resource allocation. We investigated whether Internet usage and social media data, specifically the search volume on Google, page view count on Wikipedia, and disease mentioning frequency on Twitter, correlated with the disease burden, measured by prevalence and treatment cost, for 1633 diseases over an 11-year period. We also applied least absolute shrinkage and selection operator to predict the burden of diseases. We found that Google search volume is relatively strongly correlated with the burdens for 39 of 1633 diseases, including viral hepatitis, diabetes mellitus, multiple sclerosis, and hemorrhoids. Wikipedia and Twitter data strongly correlated with the burdens of 15 and 7 diseases, respectively. However, an accurate analysis must consider each condition’s characteristics, including acute/chronic nature, severity, familiarity to the public, and the presence of stigma.

The interaction of death-associated protein kinase 1 (DAPK1) with the 2B subunit (GluN2B) C-terminus of N-methyl-D-aspartate receptor (NMDAR) plays a critical role in the pathophysiology of depression and is considered a potential target for the structure-based discovery of new antidepressants. However, the 3D structures of C-terminus residues 1290–1310 of GluN2B (GluN2B-CT1290-1310) remain elusive and the interaction between GluN2B-CT1290-1310 and DAPK1 is unknown. In this study, the mechanism of interaction between DAPK1 and GluN2B-CT1290-1310 was predicted by computational simulation methods including protein–peptide docking and molecular dynamics (MD) simulation. Based on the equilibrated MD trajectory, the total binding free energy between GluN2B-CT1290-1310 and DAPK1 was computed by the mechanics generalized born surface area (MM/GBSA) approach. The simulation results showed that hydrophobic, van der Waals, and electrostatic interactions are responsible for the binding of GluN2B-CT1290–1310/DAPK1. Moreover, through per-residue free energy decomposition and in silico alanine scanning analysis, hotspot residues between GluN2B-CT1290-1310 and DAPK1 interface were identified. In conclusion, this work predicted the binding mode and quantitatively characterized the protein–peptide interface, which will aid in the discovery of novel drugs targeting the GluN2B-CT1290-1310 and DAPK1 interface.

Background: Due to its ability to provide quantitative and dynamic information on tumor genesis and development by directly profiling protein expression, the proteomics has become intensely popular for characterizing the functional proteins driving the transformation of malignancy, tracing the large-scale protein alterations induced by anticancer drug, and discovering the innovative targets and first-in-class drugs for oncologic disorders. Objective: To quantify cancer proteomics data, the label-free quantification (LFQ) is frequently employed. However, low precision, poor reproducibility and inaccuracy of the LFQ of proteomics data have been recognized as the key “technical challenge” in the discovery of anticancer targets and drugs. In this paper, the recent advances and development in the computational perspective of LFQ in cancer proteomics were therefore systematically reviewed and analyzed. Methods: PubMed and Web of Science database were searched for label-free quantification approaches, cancer proteomics and computational advances. Results: First, a variety of popular acquisition techniques and state-of-the-art quantification tools are systematically discussed and critically assessed. Then, many processing approaches including transformation, normalization, filtering and imputation are subsequently discussed, and their impacts on improving LFQ performance of cancer proteomics are evaluated. Finally, the future direction for enhancing the computation-based quantification technique for cancer proteomics are also proposed. Conclusion: There is a dramatic increase in LFQ approaches in recent year, which significantly enhance the diversity of the possible quantification strategies for studying cancer proteomics.

Background: The human Monoamine Transporters (hMATs), primarily including hSERT, hNET and hDAT, are important targets for the treatment of depression and other behavioral disorders with more than the availability of 30 approved drugs. Objective: This paper is to review the recent progress in the binding mode and inhibitory mechanism of hMATs inhibitors with the central or allosteric binding sites, for the benefit of future hMATs inhibitor design and discovery. The Structure-Activity Relationship (SAR) and the selectivity for hit/lead compounds to hMATs that are evaluated by in vitro and in vivo experiments will be highlighted. Methods: PubMed and Web of Science databases were searched for protein-ligand interaction, novel inhibitors design and synthesis studies related to hMATs. Results: Literature data indicate that since the first crystal structure determinations of the homologous bacterial Leucine Transporter (LeuT) complexed with clomipramine, a sizable database of over 100 experimental structures or computational models has been accumulated that now defines a substantial degree of structural variability hMATs-ligands recognition. In the meanwhile, a number of novel hMATs inhibitors have been discovered by medicinal chemistry with significant help from computational models. Conclusion: The reported new compounds act on hMATs as well as the structures of the transporters complexed with diverse ligands by either experiment or computational modeling have shed light on the poly-pharmacology, multimodal and allosteric regulation of the drugs to transporters. All of the studies will greatly promote the Structure-Based Drug Design (SBDD) of structurally novel scaffolds with high activity and selectivity for hMATs.

Binge drinking is a severe health problem faced by many US colleges and universities. College students often post drinking-related text and images on social media, portraying their alcohol use as socially desirable. In this project, we investigated the feasibility of mining the heterogeneous data (e.g. text, images, and videos) on Facebook to identify drinking-related contents. We manually annotated 4266 posts during 21 October 2011 and 3 November 2014 from “I’m Shmacked” group on Facebook, where 511 posts were drinking-related. Our machine learning models show that by combining heterogeneous data types, we were able to identify drinking-related posts with an F1-score of 0.81. Prediction models built on text data were more reliable compared to those built on image and video data for predicting drinking-related contents. As the first step of our efforts in this direction, this feasibility study showed promise toward unleashing the potential of mining social media to identify students who binge drink.