A systems identification approach using Bayes factors to deconstruct the brain bases of emotion regulation

Cognitive reappraisal is fundamental to cognitive therapies and everyday emotion regulation. Analyses using Bayes factors and an axiomatic systems identification approach identified four reappraisal-related components encompassing distributed neural activity patterns across two independent functional magnetic resonance imaging (fMRI) studies (n = 182 and n = 176): (1) an anterior prefrontal system selectively involved in cognitive reappraisal; (2) a fronto-parietal-insular system engaged by both reappraisal and emotion generation, demonstrating a general role in appraisal; (3) a largely subcortical system activated during negative emotion generation but unaffected by reappraisal, including amygdala, hypothalamus and periaqueductal gray; and (4) a posterior cortical system of negative emotion-related regions downregulated by reappraisal. These systems covaried with individual differences in reappraisal success and were differentially related to neurotransmitter binding maps, implicating cannabinoid and serotonin systems in reappraisal. These findings challenge 'limbic'-centric models of reappraisal and provide new systems-level targets for assessing and enhancing emotion regulation.

Economic impact of managing invasive mold disease with isavuconazole compared with liposomal amphotericin B followed by posaconazole in Spain

BACKGROUND

Invasive fungal infections (IFI) are associated with significant morbidity and mortality. The objective of this work was to compare the costs per adult patient, associated with intravenous isavuconazole (ISAV) followed by oral ISAV versus the regimen of liposomal amphotericin B followed by posaconazole (L-AMB→POSA) in the treatment of IFI. The comparison was conducted from the perspective of the Spanish National Health System (SNS).

METHODS

As indirect comparisons have demonstrated similar efficacy between the comparators, a cost-minimization approach was taken. Drug acquisition, administration, hospitalization, laboratory tests and adverse events costs were evaluated from SNS perspective. Deterministic and probabilistic sensitivity analyzes were performed.

RESULTS

Total costs per-patient were €24,715.54 with ISAV versus €29,753.53 with L-AMB→POSA, resulting in cost-savings per patient treated with ISAV of €5,037.99 (-16.9%). Treatment costs of IFI remained lower for ISAV than for L-AMB→POSA across all sensitivity analyses (-7,968.89€ to -326.59€), being treatment duration the most influential parameter.

CONCLUSION

According to the present model, the treatment of IFIs with ISAV would generate savings for the SNS compared to L-AMB→POSA. These savings are attributed to the shorter duration of IV treatment, reduced use of healthcare resources and lower costs associated with managing adverse effects when ISAV was employed.

Detection of novel drug-adverse drug reaction signals in rheumatoid arthritis and ankylosing spondylitis: analysis of Korean real-world biologics registry data

This study aimed to detect signals of adverse drug reactions (ADRs) associated with biological disease-modifying antirheumatic drugs (DMARDs) and targeted therapies in rheumatoid arthritis (RA) and ankylosing spondylitis (AS) patients. Utilizing the KOrean College of Rheumatology BIOlogics & Targeted Therapy Registry (KOBIO) data, we calculated relative risks, excluded previously reported drug-ADR pairs, and externally validated remaining pairs using US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) and single centre's electronic health records (EHR) data. Analyzing data from 2279 RA and 1940 AS patients, we identified 35 significant drug-ADR pairs in RA and 26 in AS, previously unreported in drug labels. Among the novel drug-ADR pairs from KOBIO, 15 were also significant in the FAERS data. Additionally, 2 significant drug-laboratory abnormality pairs were found in RA using CDM MetaLAB analysis. Our findings contribute to the identification of 14 novel drug-ADR signals, expanding our understanding of potential adverse effects related to biological DMARDs and targeted therapies in RA and AS. These results emphasize the importance of ongoing pharmacovigilance for patient safety and optimal therapeutic interventions.

Multilayer Coating with Red Ginseng Dietary Fiber Improves Intestinal Adhesion and Proliferation of Probiotics in Human Intestinal Epithelial Models

To exert their beneficial effects, it is essential for the commensal bacteria of probiotic supplements to be sufficiently protected as they pass through the low pH environment of the stomach, and effectively colonize the intestinal epithelium downstream. Here, we investigated the effect of a multilayer coating containing red ginseng dietary fiber, on the acid tolerance, and the adhesion and proliferation capacities of three Lactobacillus strains (Limosilactobacillus reuteri KGC1901, Lacticaseibacillus casei KGC1201, Limosilactobacillus fermentum KGC1601) isolated from Panax ginseng, using HT-29 cells, mucin-coated plates, and human pluripotent stem cell-derived intestinal epithelial cells as in vitro models of human gut physiology. We observed that the multilayer-coated strains displayed improved survival rates after passage through gastric juice, as well as high adhesion and proliferation capacities within the various gut epithelial systems tested, compared to their uncoated counterparts. Our findings demonstrated that the multilayer coat effectively protected commensal microbiota and led to improved adhesion and colonization of intestinal epithelial cells, and consequently to higher probiotic efficacy.

Recommendations on the use of azole antifungals in hematology-oncology patients

The administration of antifungals for therapeutic and, especially, prophylactic purposes is virtually a constant in patients requiring hematology-oncology treatment. Any attempt to prevent or treat Aspergillus or Mucor infections requires the administration of some drugs in the azole group, which include voriconazole, posaconazole and isavuconazole, noted for their activity against these pathogens. One very relevant aspect is the potential risk of interaction when associated with one of the antineoplastic drugs used to treat hematologic tumors, with serious complications. In this regard, acalabrutinib, bortezomib, bosutinib, carfilzomib, cyclophosphamide, cyclosporine A, dasatinib, duvelisib, gilteritinib, glasdegib, ibrutinib, imatinib, nilotinib, ponatinib, prednisone, ruxolitinib, tacrolimus, all-transretinoic acid, arsenic trioxide, venetoclax, or any of the vinca alkaloids, are very clear examples of risk, in some cases because their clearance is reduced and in others because of increased risk of QTc prolongation, which is particularly evident when the drug of choice is voriconazole or posaconazole.

Probiotic Characteristics and Safety Assessment of Lacticaseibacillus casei KGC1201 Isolated from Panax ginseng

Panax ginseng is one of the most important herbal medicinal plants consumed as health functional food and can be fermented to achieve better efficacy. Lacticaseibacillus, one of the representative genera among lactic acid bacteria (LAB), has also been used as a probiotic material for health functional foods due to its beneficial effects on the human body. To achieve a synergistic effect by using these excellent dietary supplement ingredients together, a novel LAB strain was isolated from the root of 6-year-old ginseng. Through similarity analysis of 16S rRNAs and whole-genome sequences, the strain was confirmed as belonging to the genus Lacticaseibacillus and was named L. casei KGC1201. KGC1201 not only met all safety standards as food, but also showed excellent probiotic properties such as acid resistance, bile salt resistance, and intestinal adhesion. In particular, KGC1201 exhibited superior acid resistance through morphological observation identifying that the cell surface damage of KGC1201 was less than that of the L. casei type strain KCTC3109. Gene expression studies were conducted to elucidate the molecular mechanisms of KGC1201's acid resistance, and the expression of the glycosyltransferase gene was found to be significantly elevated under acidic conditions. Exopolysaccharides (EPSs) biosynthesized by glycosyltransferase were also increased in KGC1201 compared to KCTC3109, which may contribute to better protection of KGC1201 cells from strong acidity. Therefore, KGC1201, with its increased acid resistance through molecular mechanisms and excellent probiotic properties, can be used in health functional foods to provide greater benefit to overall human health and well-being.

EZH2 mutations at diagnosis in follicular lymphoma: a promising biomarker to guide frontline treatment

EZH2 is mutated in nearly 25% of follicular lymphoma (FL) cases. Little is known about how EZH2 affects patients’ response to therapy. In this context, the aim of this study was to retrospectively analyze the frequency of mutations in EZH2 at diagnosis in tissue and ctDNA in patients with FL and to assess the patients’ outcomes after receiving immunochemotherapy, depending on the EZH2 mutation status. Among the 154 patients included in the study, 27% had mutated EZH2 (46% with high-grade and 26% with low-grade FL). Of the mutated tissue samples, the mutation in ctDNA was identified in 44% of cases. EZH2 mutation in ctDNA was not identified in any patient unmutated in the tissue.

Unmutated patients who received R-CHOP had significantly more relapses than patients who received R-Bendamustine (16/49 vs. 2/23, p = 0.040). Furthermore, our results show that patients with mutated EZH2 treated with R-CHOP vs. those treated with R-Bendamustine present a lower incidence of relapse (10% vs. 42% p = 0.09 at 4 years), a higher PFS (92% vs. 40% p = 0.039 at 4 years), and higher OS (100% vs. 78% p = 0.039 at 4 years). Based on these data, RCHOP could be a more suitable regimen for mutated patients, and R-bendamustine for unmutated patients. These findings could mean the first-time identification of a useful biomarker to guide upfront therapy in FL.

Exopolysaccharide of Enterococcus faecium L15 promotes the osteogenic differentiation of human dental pulp stem cells via p38 MAPK pathway

Background

Bone has important functions in the body. Several researchers have reported that the polysaccharides and lipopolysaccharide derived from microbes can promote osteogenic differentiation of stem cells. Enterococcus faecium, a lactic acid bacterium (LAB), produces several bioactive metabolites and has been widely applied in the food and nutraceutical industries. The exopolysaccharide (EPS) from LAB has also been extensively examined for its postbiotic effects and for its in vivo and in vitro functionalities. However, studies on promoting bone differentiation using polysaccharides from LAB are lacking. Therefore, the purpose of this study was to investigate the effect of E. faecium L15 extract and EPS on osteogenic differentiation of human dental pulp stem cells (hDPSCs) and to identify the underlying mechanisms.

Methods

hDPSCs were obtained from dental pulp tissue, and L15 extract and EPS were isolated from L15. Gene and protein expression of the osteogenic differentiation markers were analyzed with qPCR and western blotting and the possible signaling pathways were also investigated using western blotting. Osteogenic differentiation potential was examined by alkaline phosphatase (ALP) staining and alizarin red s (ARS) staining. In addition, osteogenic differentiation potential of L15 EPS was explored in ex vivo culture of neonate murine calvaria.

Results

The calcium deposition and ALP activity were enhanced by addition of L15 extract or EPS. The expression levels of RUNX2, ALP, and COL1A1 mRNA and the protein expression levels of RUNX2, ALP, and BMP4 were increased in hDPSCs treated with the L15 extract or EPS. The L15 EPS treatment enhanced phosphorylation of the p38 mitogen-activated protein kinase (MAPK). The L15 EPS-induced increases in RUNX2, ALP, and BMP4 expression were suppressed by the p38 MAPK inhibitor SB203580. The promoting effect of L15 EPS on osteogenic differentiation was not only seen in hDPSCs, but also in osteoblast precursors. ALP activity and the expression of RUNX2, ALP, and COL1A1 increased in the L15 EPS-treated osteoblast precursors. In addition, L15 EPS increased bone thickness of neonate murine calvaria in ex vivo culture.

Conclusions

The stimulatory effect of L15 extract and EPS on osteogenic differentiation occurred through the p38 MAPK pathway, and L15 EPS enhanced new bone formation in neonate murine calvaria. These data suggest that L15 EPS has therapeutic potential applicable to bone regeneration.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13287-022-03151-0.

Phase II study of ceralasertib (AZD6738) in combination with durvalumab in patients with advanced/metastatic melanoma who have failed prior anti-PD-1 therapy

BACKGROUND

Modulating the DNA damage response and repair (DDR) pathways is a promising strategy for boosting cancer immunotherapy. Ceralasertib (AZD6738) is an oral inhibitor of the serine/threonine protein kinase ataxia telangiectasia and Rad3-related protein, which is crucial for DDR.

PATIENTS AND METHODS

This phase II trial evaluated ceralasertib plus durvalumab for the treatment of patients with metastatic melanoma who had failed anti-programmed cell death protein 1 therapy.

RESULTS

Among the 30 patients, we observed an overall response rate of 31.0% and a disease control rate of 63.3%. Responses were evident across patients with acral, mucosal, and cutaneous melanoma. The median duration of response was 8.8 months (range, 3.8-11.7 months). The median progression-free survival was 7.1 months (95% confidence interval, 3.6-10.6 months), and the median overall survival was 14.2 months (95% confidence interval, 9.3-19.1 months). Common adverse events were largely hematologic and manageable with dose interruptions and reductions. Exploratory biomarker analysis suggested that tumors with an immune-enriched microenvironment or alterations in the DDR pathway were more likely to respond to the study treatment.

CONCLUSION

We conclude that ceralasertib in combination with durvalumab has promising antitumor activity among patients with metastatic melanoma who have failed anti-programmed cell death protein 1 therapy, and constitute a population with unmet needs.

Oral intake of Lactobacillus plantarum L-14 extract alleviates TLR2- and AMPK-mediated obesity-associated disorders in high-fat-diet-induced obese C57BL/6J mice

OBJECTIVES

Whether periodic oral intake of postbiotics positively affects weight regulation and prevents obesity-associated diseases in vivo is unclear. This study evaluated the action mechanism of Lactobacillus plantarum L-14 (KTCT13497BP) extract and the effects of its periodic oral intake in a high-fat-diet (HFD) mouse model.

MATERIALS AND METHODS

Mouse pre-adipocyte 3T3-L1 cells and human bone marrow mesenchymal stem cells (hBM-MSC) were treated with L-14 extract every 2 days during adipogenic differentiation, and the mechanism underlying anti-adipogenic effects was analysed at cellular and molecular levels. L-14 extract was orally administrated to HFD-feeding C57BL/6J mice every 2 days for 7 weeks. White adipose tissue was collected and weighed, and liver and blood serum were analysed. The anti-adipogenic mechanism of exopolysaccharide (EPS) isolated from L-14 extract was also analysed using Toll-like receptor 2 (TLR2) inhibitor C29.

RESULTS

L-14 extract inhibited 3T3-L1 and hBM-MSC differentiation into mature adipocytes by upregulating AMPK signalling pathway in the early stage of adipogenic differentiation. The weight of the HFD + L-14 group (31.51 ± 1.96 g) was significantly different from that of the HFD group (35.14 ± 3.18 g). L-14 extract also significantly decreased the serum triacylglycerol/high-density lipoprotein cholesterol ratio (an insulin resistance marker) and steatohepatitis. In addition, EPS activated the AMPK signalling pathway by interacting with TLR2, consequently inhibiting adipogenesis.

CONCLUSIONS

EPS from L-14 extract inhibits adipogenesis via TLR2 and AMPK signalling pathways, and oral intake of L-14 extract improves obesity and obesity-associated diseases in vivo. Therefore, EPS can be used to prevent and treat obesity and metabolic disorders.

Molecular profiling of Asian patients with advanced melanoma receiving check-point inhibitor treatment

Objective

Melanoma is major medical challenge and being able to monitor treatment response is critical. This study aimed to use molecular profiling of Asian patients with advanced melanoma who were receiving treatment with check-point inhibitors (CPIs) to identify novel biomarkers of tumor response.

Methods

Next-generation sequencing (NGS) was performed using tumor specimens collected from 178 Asian patients with metastatic melanoma receiving CPIs. The NGS data and clinical-pathological factors were analyzed for potential genetic biomarkers of tumor response to CPI treatment.

Results

The most common melanoma subtype was acral melanoma (40%), followed by cutaneous melanoma (32%), mucosal melanoma (26%), and others (2%). For calculation of treatment efficacy, 164 of the patients could be evaluated. The overall response rate was 45.7%, of which 41 cases exhibited complete responses (25.0%) and 34 showed partial responses (20.7%). There were no significant differences in tumor responses based on melanoma subtype (P = 0.295). Genetically, NRAS mutations, TP53 mutations, and NF2 deletions were significantly associated with resistance to CPIs (P < 0.05). In contrast, MYC and RPS6KB1 amplifications were associated with responsiveness to CPIs (P < 0.05). Median progression-free survival (PFS) for patients treated with CPIs was 5.9 months (95% CI, 3.8-8.05 months). Univariate analysis identified TP53 and BRAF mutations, NF2 deletions, and BIRC2 amplifications as poor prognostic factors for PFS (P < 0.05).

Conclusions

This study determined the integrated genomic profiles of Asian patients with metastatic melanoma receiving CPIs and identified candidate biomarkers that reflected treatment outcomes.

•

The molecular characterization of Asian melanoma patients receiving check-point inhibitors (CPIs) using NGS has not been reported.

•

NRAS and TP53 mutations and NF2 deletions were significantly associated with resistance to CPIs.

•

MYC and RPS6KB1 amplifications were associated with responsiveness to CPIs.

•

TP53 and BRAF mutations, NF2 deletions, and BIRC2 amplifications were poor prognostic factors for progression-free survival.

•

This is the largest integrated genomic study to date that identifying novel biomarkers of CPIs in Asian melanoma patients.

The Multiple Ingredients Effect: The More Diverse (Un)Healthy Ingredients, the More (Un)Healthy the Food

Background

Although previous research has demonstrated that ingredient information plays a significant role in consumers’ healthier food choices, none of the research has investigated how the number of ingredients (ie, single vs multiple) influences consumer perceptions of food healthiness. However, this research argues that consumers have lay belief that the greater the number of (un)healthy ingredients in food, the more (un)healthy the food is perceived and they rely on the lay belief when judging food healthiness. Thus, this paper proposes and examines the multiple ingredients effect that people make inferences about food (un)healthiness based on the diversity of (un)healthy ingredients.

Methods and Results

Four studies test our hypotheses using ANOVAs and regression analyses. Study 1 examines that people indicate a higher perception of food unhealthiness when the number of unhealthy ingredients is presented as multiple rather than single. Study 2 replicates the multiple ingredients effect in the healthy food domain and eliminates an alternative explanation based on the subadditivity effect. Study 3 also finds that the difference in food healthiness perception between people who have high and low health consciousness is driven by the salience of each ingredient. Finally, Study 4 identifies the evaluability of the nutritional value as a boundary condition for our effect in an AI-based self-service context.

Conclusion

The current research demonstrates the multiple ingredients effect that people perceive higher food (un)healthiness when the number of (un)healthy ingredients is greater although nutritional information is identically presented. Moreover, this effect is moderated by the extent to which people are conscious of health-related issues. This finding is because ingredient information is highly accessible and salient for health-conscious people .

Exopolysaccharide Isolated from Lactobacillus plantarum L-14 Has Anti-Inflammatory Effects via the Toll-Like Receptor 4 Pathway in LPS-Induced RAW 264.7 Cells

Inflammation is a biological response of the immune system to defend the body from negative stimulation. However, the excessive inflammatory response can damage host tissues and pose serious threats. Exopolysaccharide (EPS), one of the postbiotics, is secreted from lactic acid bacteria. Although many studies have described the beneficial effects of EPS, such as its anti-inflammatory and anti-oxidant effects, its underlying mechanisms have remained to be poorly understood. Thus, we identified that EPS obtained from Lactobacillus plantarum L-14 was a homogeneous polysaccharide primarily comprised of glucose. To examine these anti-inflammatory effects, an inflammatory response was induced by lipopolysaccharide (LPS) administration to mouse macrophage RAW 264.7 cells that were pretreated with EPS. The anti-inflammatory effects of EPS were identified by analyzing the changes within inflammatory markers at the molecular level. We demonstrate here that EPS suppressed proinflammatory mediators, such as cyclooxygenase-2, interleukin-6, tumor necrosis factor-α, and interleukin-1β, and downregulated the expression of an inducible nitric oxide synthase known to lead to oxidative stress. It was also confirmed that EPS had anti-inflammatory effects by blocking the interaction of LPS with Toll-like receptor 4 (TLR4), as demonstrated by using the known TLR4 inhibitor TAK-242. In addition, we found that EPS itself could suppress the expression of TLR4. Consequently, our data suggest that EPS can be a potential target for the development of natural product-derived medicine for treating inflammatory diseases related to TLR4.

0268 Development of an Integrated Model of Sleep Deprivation in Adolescence

Introduction

Sleep deprivation is a consistently and widely concerning problem among adolescents. Although a few models have been proposed to explain the relationships and pathways through which factors influence sleep in adolescents, there are lack of theoretical models that apply both biological and behavioral factors that contribute to sleep deprivation across the trajectory of adolescent development. The current study proposes an integrated model that draws upon constructs from several influential theories with an aim to re-conceptualize factors associated with sleep deprivation as a chronic and cyclic problem that emerges from biological and behavioral changes in youth.

Methods

The Two Process Model of Sleep Regulation, Spielman’s 3p model, the theory of planned behavior, dual systems model, and sleep health framework are used to develop an integrated model of factors that lead to sleep deprivation in adolescents.

Results

The resulting integrated model highlights the importance of adolescent’s inherent nature of delayed sleep phase at pubertal onset (two process model); increased reward-seeking that precedes the structural maturation of their cognitive control and emotions (dual systems model); and their attitudes/perceptions towards sleep (theory of planned behavior), which is often geared toward not prioritizing sleep. Sleep health framework adequately frames the pattern of sleep-wakefulness in adolescents using a multidimensional approach of sleep. Moreover, the new model presents contextual factors (Spielman’s 3p model) and the way that these constructs interact in order to maintain a vicious cycle of insufficient sleep which leads to chronic sleep deprivation.

Conclusion

The current model portrays a wide-ranging view of mechanisms underlying sleep deprivation among adolescence by integrating both biological and behavioral aspects. The model is proposed to encourage researchers to explore these conceptual elements of biological and neurobiological changes, and behavioral problems in order to operationalize relevant measures to relate the concepts to sleep deprivation and subsequent health outcomes in adolescents.

Support

None

1051 Level Of Agreement Between Objective And Subjective Sleep Measures In Lung Cancer Survivors With Insomnia

Introduction

Lung cancer survivors (LCS) have the second-highest incidence of impaired sleep among cancer population. Clinical studies use self-reported and objective measures to assess insomnia in LCS. However, negative beliefs of sleep patterns may impair sleep perception, impact psychological state, and influence insomnia treatment and survivorship outcomes. This study aims to assess the level of agreement between subjective and objective sleep measures in LCS.

Methods

Forty-four non-small cell lung cancer survivors, stage I-III, at least 6 weeks after treatment completion, with Insomnia Severity Index &gt;7, were recruited from two sites from 2014-2016. Individuals with sleep apnea, menopause, rotating shift work, uncontrolled substance abuse, or unstable medical/psychiatric illnesses were excluded from the study. Agreement between total sleep time (TST), sleep latency (SL) and sleep efficiency (SE) from Sleep Diary and wrist-actigraphy (i.e. CamNtech) were assessed with Intraclass Correlation (ICC) and Bland-Altman plots. Analysis of ICC, mean difference, standard deviation (SD) and 95% confidence interval (CI) were conducted using SPSS 24.

Results

LCS were male (63.6%), 60-69 years old (52.3%), married or living with a partner (50%). Self-reported measurements underestimated TST (-68.2 minutes, ICC 0.45, CI 95%, SD 108.1) and SL (-25.9 minutes, ICC 95%, ICC -0.54, DS 17.5). Objective and self-reported measurements largely overlapped for SE, with a small actigraphy-based overestimation (9.2, ICC 0.2, CI95%, SD 7.3). Bland-Altman plots revealed that the agreement increased with lower SE values.

Conclusion

LCS tended to underestimate TST and SL. An apparent agreement between objective and self-reported measures for SE may indicate sleep state misperception. Differences in various sleep parameters and potential covariates should be investigated for contribution to the unexplained considerable individual variability in behavioral treatment response among cancer survivors in larger sample sizes.

Support

1R01NR018215-01 (GED); T32GM099607(CW).

Rydberg-Mediated Entanglement in a Two-Dimensional Neutral Atom Qubit Array

We demonstrate high fidelity two-qubit Rydberg blockade and entanglement on a pair of sites in a large two-dimensional qubit array. The qubit array is defined by a grid of blue detuned lines of light with 121 sites for trapping atomic qubits. Improved experimental methods have increased the observed Bell state fidelity to F_{Bell}=0.86(2). Accounting for errors in state preparation and measurement we infer a fidelity of F_{Bell}^{-SPAM}=0.88. Accounting for errors in single qubit operations we infer that a Bell state created with the Rydberg mediated C_{Z} gate has a fidelity of F_{Bell}^{C_{Z}}=0.89. Comparison with a detailed error model based on quantum process matrices indicates that finite atom temperature and laser noise are the dominant error sources contributing to the observed gate infidelity.

Diagnostic Accuracy and Scope of Intraoperative Transoral Ultrasound and Transoral Ultrasound-Guided Fine-Needle Aspiration of Retropharyngeal Masses

The use of transoral sonography-guided fine-needle aspiration for intraoperative localization of retropharyngeal masses has been described by Fornage et al. The purpose of this study was to assess the accuracy of this technique. We reviewed the images and medical records of 26 patients with a retropharyngeal lesion suspicious for a metastatic lymph node of Rouviere identified on CT and/or PET/CT. There were 14 patients with a history of thyroid cancer, 7 with mucosal squamous cell carcinoma, 1 with renal cell carcinoma, 1 with parotid acinic cell cancer, 1 with metastatic colon adenocarcinoma, and 2 with no history of cancer. Intraoperative transoral sonography was performed using a commercially available endovaginal transducer. A transoral sonography-guided fine-needle aspiration was performed with a 25-cm-long 20-ga Chiba needle through a needle guide attached to the transducer shaft. Cytopathologic results were categorized as malignant, benign, or nondiagnostic. Transoral sonography and transoral sonography-guided fine-needle aspiration were performed in all patients. A diagnostic specimen was obtained in 25 of 26 (96%) patients with a 100% overall accuracy. Twelve patients underwent subsequent transoral resection of the retropharyngeal mass. In each patient, surgical pathology confirmed the fine-needle aspiration biopsy result. In 4 patients, transoral sonography-guided injection of methylene blue was used to facilitate intraoperative localization of the metastatic retropharyngeal mass. Transoral sonography and transoral sonography-guided fine-needle aspiration of suspicious masses in the retropharyngeal space are highly accurate procedures for identification and cytologic evaluation of benign and metastatic lymph nodes of Rouviere and for presurgical localization.

CODA-ML: context-specific biological knowledge representation for systemic physiology analysis

Background

Computational analysis of complex diseases involving multiple organs requires the integration of multiple different models into a unified model. Different models are often constructed in heterogeneous formats. Thus, the integration of the models requires a standard language format that can effectively represent essential biological information. However, the previously introduced formats have limitations that prevent from adequately representing essential biological information, particularly specifications of bio-molecules and biological contexts.

Results

We defined an XML-based markup language called context-oriented directed association markup language (CODA-ML), which better represents essential biological information. The CODA-ML has two major strengths in designating molecular specifications and biological contexts. It can cover heterogeneous entity types involved in biological events (e.g. gene/protein, compound, cellular function, disease). Molecular types of entities can have molecular specifications which include detailed information of a molecule from isoforms to modifications, enabling high-resolution representation of molecules. In addition, it can distinguish biological events that vary depending on different biological contexts such as cell types or disease conditions. Especially representation of inter-cellular events as well as intra-cellular events is available. These two major strengths can resolve contradictory associations when different models are integrated into one unified model, which improves the accuracy of the model.

Conclusions

With the CODA-ML, diverse models such as signaling pathways, metabolic pathways, and gene regulatory pathways can be represented in a unified language format. Heterogeneous entity types can be covered by the CODA-ML, thus it enables detailed description for the mechanisms of diseases or drugs from multiple perspectives (e.g., molecule, function or disease). The CODA-ML is expected to help integrate different models into one systemic model in an efficient and effective. The unified model can be used to perform computational analysis not only for cancer but also for other complex diseases involving multiple organs beyond a single cell.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2812-7) contains supplementary material, which is available to authorized users.

Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy

Background

Muscle atrophy, an involuntary loss of muscle mass, is involved in various diseases and sometimes leads to mortality. However, therapeutics for muscle atrophy thus far have had limited effects. Here, we present a new approach for therapeutic target prediction using Petri net simulation of the status of phosphorylation, with a reasonable assumption that the recovery of abnormally phosphorylated proteins can be a treatment for muscle atrophy.

Results

The Petri net model was employed to simulate phosphorylation status in three states, i.e. reference, atrophic and each gene-inhibited state based on the myocyte-specific phosphorylation network. Here, we newly devised a phosphorylation specific Petri net that involves two types of transitions (phosphorylation or de-phosphorylation) and two types of places (activation with or without phosphorylation). Before predicting therapeutic targets, the simulation results in reference and atrophic states were validated by Western blotting experiments detecting five marker proteins, i.e. RELA, SMAD2, SMAD3, FOXO1 and FOXO3. Finally, we determined 37 potential therapeutic targets whose inhibition recovers the phosphorylation status from an atrophic state as indicated by the five validated marker proteins. In the evaluation, we confirmed that the 37 potential targets were enriched for muscle atrophy-related terms such as actin and muscle contraction processes, and they were also significantly overlapping with the genes associated with muscle atrophy reported in the Comparative Toxicogenomics Database (p-value < 0.05). Furthermore, we noticed that they included several proteins that could not be characterized by the shortest path analysis. The three potential targets, i.e. BMPR1B, ROCK, and LEPR, were manually validated with the literature.

Conclusions

In this study, we suggest a new approach to predict potential therapeutic targets of muscle atrophy with an analysis of phosphorylation status simulated by Petri net. We generated a list of the potential therapeutic targets whose inhibition recovers abnormally phosphorylated proteins in an atrophic state. They were evaluated by various approaches, such as Western blotting, GO terms, literature, known muscle atrophy-related genes and shortest path analysis. We expect the new proposed strategy to provide an understanding of phosphorylation status in muscle atrophy and to provide assistance towards identifying new therapies.

Electronic supplementary material

The online version of this article (10.1186/s12918-018-0555-0) contains supplementary material, which is available to authorized users.

HIDEEP: a systems approach to predict hormone impacts on drug efficacy based on effect paths

Experimental evidence has shown that some of the human endogenous hormones significantly affect drug efficacy. Since hormone status varies with individual physiological states, it is essential to understand the interplay of hormones and drugs for precision medicine. Here, we developed an in silico method to predict interactions between 283 human endogenous hormones and 590 drugs for 20 diseases including cancers and non-cancer diseases. We extracted hormone effect paths and drug effect paths from a large-scale molecular network that contains protein interactions, transcriptional regulations, and signaling interactions. If two kinds of effect paths for a hormone-drug pair intersect closely, we expect that the influence of the hormone on the drug efficacy is significant. It has been shown that the proposed method correctly distinguishes hormone-drug pairs with known interactions from random pairs in blind experiments. In addition, the method can suggest underlying interaction mechanisms at the molecular level so that it helps us to better understand the interplay of hormones and drugs.

CODA: Integrating multi-level context-oriented directed associations for analysis of drug effects

In silico network-based methods have shown promising results in the field of drug development. Yet, most of networks used in the previous research have not included context information even though biological associations actually do appear in the specific contexts. Here, we reconstruct an anatomical context-specific network by assigning contexts to biological associations using protein expression data and scientific literature. Furthermore, we employ the context-specific network for the analysis of drug effects with a proximity measure between drug targets and diseases. Distinct from previous context-specific networks, intercellular associations and phenomic level entities such as biological processes are included in our network to represent the human body. It is observed that performances in inferring drug-disease associations are increased by adding context information and phenomic level entities. In particular, hypertension, a disease related to multiple organs and associated with several phenomic level entities, is analyzed in detail to investigate how our network facilitates the inference of drug-disease associations. Our results indicate that the inclusion of context information, intercellular associations, and phenomic level entities can contribute towards a better prediction of drug-disease associations and provide detailed insight into understanding of how drugs affect diseases in the human body.