BondGraphs.jl: composable energy-based modelling in systems biology.

SUMMARY: BondGraphs.jl is a Julia implementation of bond graphs. Bond graphs provide a modelling framework that describes energy flow through a physical system and by construction enforce thermodynamic constraints. The framework is widely used in engineering and has recently been shown to be a powerful approach for modelling biology. Models are mutable, hierarchical, multiscale, and multiphysics, and BondGraphs.jl is compatible with the Julia modelling ecosystem. AVAILABILITY AND IMPLEMENTATION: BondGraphs.jl is freely available under the MIT license. Source code and documentation can be found at https://github.com/jedforrest/BondGraphs.jl.

SuPAR, biomarkers of inflammation, and severe outcomes in patients hospitalized for COVID-19: The International Study of Inflammation in COVID-19.

Severe coronavirus disease 2019 (COVID-19) is a hyperinflammatory syndrome. The biomarkers of inflammation best suited to triage patients with COVID-19 are unknown. We conducted a prospective multicenter observational study of adult patients hospitalized specifically for COVID-19 from February 1, 2020 to October 19, 2022. Biomarkers measured included soluble urokinase plasminogen activator receptor (suPAR), C-reactive protein, interleukin-6, procalcitonin, ferritin, and D-dimer. In-hospital outcomes examined include death and the need for mechanical ventilation. Patients admitted in the United States (US, n = 1962) were used to compute area under the curves (AUCs) and identify biomarker cutoffs. The combined European cohorts (n = 1137) were used to validate the biomarker cutoffs. In the US cohort, 356 patients met the composite outcome of death (n = 197) or need for mechanical ventilation (n = 290). SuPAR was the most important predictor of the composite outcome and had the highest AUC (0.712) followed by CRP (0.642), ferritin (0.619), IL-6 (0.614), D-dimer (0.606), and lastly procalcitonin (0.596). Inclusion of other biomarkers did not improve discrimination. A suPAR cutoff of 4.0 ng/mL demonstrated a sensitivity of 95.4% (95% CI: 92.4%-98.0%) and negative predictive value (NPV) of 92.5% (95% CI: 87.5%-96.9%) for the composite outcome. Patients with suPAR < 4.0 ng/mL comprised 10.6% of the cohort and had a 0.8% probability of the composite outcome. Applying this cutoff to the validation cohort yielded a sensitivity of 93.8% (90.4%-96.7%) and NPV of 95.5% (93.1%-97.8%) for the composite outcome. Among commonly measured biomarkers, suPAR offered stronger discriminatory ability and may be useful in triaging low-risk patients with COVID-19.

Direct Thermal Growth of Gold Nanopearls on 3D Interweaved Hydrophobic Fibers as Ultrasensitive Portable SERS Substrates for Clinical Applications.

Surface-enhanced Raman spectroscopy (SERS)-based biosensors have attracted much attention for their label-free detection, ultrahigh sensitivity, and unique molecular fingerprinting. In this study, a wafer-scale, ultrasensitive, highly uniform, paper-based, portable SERS detection platform featuring abundant and dense gold nanopearls with narrow gap distances, are prepared and deposited directly onto ultralow-surface-energy fluorosilane-modified cellulose fibers through simple thermal evaporation by delicately manipulating the atom diffusion behavior. The as-designed paper-based SERS substrate exhibits an extremely high Raman enhancement factor (3.9 × 1011 ), detectability at sub-femtomolar concentrations (single-molecule level) and great signal reproductivity (relative standard deviation: 3.97%), even when operated with a portable 785-nm Raman spectrometer. This system is used for fingerprinting identification of 12 diverse analytes, including clinical medicines (cefazolin, chloramphenicol, levetiracetam, nicotine), pesticides (thiram, paraquat, carbaryl, chlorpyrifos), environmental carcinogens (benzo[a]pyrene, benzo[g,h,i]perylene), and illegal drugs (methamphetamine, mephedrone). The lowest detection concentrations reach the sub-ppb level, highlighted by a low of 16.2 ppq for nicotine. This system appears suitable for clinical applications in, for example, i) therapeutic drug monitoring for individualized medication adjustment and ii) ultra-early diagnosis for pesticide intoxication. Accordingly, such scalable, portable and ultrasensitive fibrous SERS substrates open up new opportunities for practical on-site detection in biofluid analysis, point-of-care diagnostics and precision medicine.

Modular assembly of dynamic models in systems biology.

It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces. To this end, both modelling and software frameworks are required to enable modular modelling. While there has been consistent progress in the development of software tools to enhance model reusability, there has been a relative lack of consideration for how underlying biophysical principles can be applied to this space. Bond graphs combine the aspects of both modularity and physics-based modelling. In this paper, we argue that bond graphs are compatible with recent developments in modularity and abstraction in systems biology, and are thus a desirable framework for constructing large-scale models. We use two examples to illustrate the utility of bond graphs in this context: a model of a mitogen-activated protein kinase (MAPK) cascade to illustrate the reusability of modules and a model of glycolysis to illustrate the ability to modify the model granularity.

Hierarchical semantic composition of biosimulation models using bond graphs.

Simulating complex biological and physiological systems and predicting their behaviours under different conditions remains challenging. Breaking systems into smaller and more manageable modules can address this challenge, assisting both model development and simulation. Nevertheless, existing computational models in biology and physiology are often not modular and therefore difficult to assemble into larger models. Even when this is possible, the resulting model may not be useful due to inconsistencies either with the laws of physics or the physiological behaviour of the system. Here, we propose a general methodology for composing models, combining the energy-based bond graph approach with semantics-based annotations. This approach improves model composition and ensures that a composite model is physically plausible. As an example, we demonstrate this approach to automated model composition using a model of human arterial circulation. The major benefit is that modellers can spend more time on understanding the behaviour of complex biological and physiological systems and less time wrangling with model composition.

Catheter-based therapies in acute and chronic pulmonary embolism.

PURPOSE OF REVIEW: The aim of this study is to summarize currently available catheter-based therapies in acute and chronic pulmonary embolic disease. RECENT FINDINGS: Catheter-based therapies to treat acute pulmonary embolism and its sequelae such as chronic thromboembolic pulmonary hypertension (CTEPH) are emerging as the next frontier within interventional cardiology. However, the true benefit of these catheter-based therapies in intermediate-risk and high-risk pulmonary embolism and CTEPH remains unclear. The current evidence supporting such interventions comes primarily from small single-arm studies in acute pulmonary embolism and case series in CTEPH. SUMMARY: Appropriately powered randomized controlled trials with meaningful clinical outcomes as endpoints are needed to elucidate the true benefit of catheter-based therapies in pulmonary embolism compared with other treatment modalities such as anticoagulation and systemic thrombolysis in acute pulmonary embolism and riociguat and pulmonary endarterectomy in CTEPH.

Analysing and simulating energy-based models in biology using BondGraphTools.

Like all physical systems, biological systems are constrained by the laws of physics. However, mathematical models of biochemistry frequently neglect the conservation of energy, leading to unrealistic behaviour. Energy-based models that are consistent with conservation of mass, charge and energy have the potential to aid the understanding of complex interactions between biological components, and are becoming easier to develop with recent advances in experimental measurements and databases. In this paper, we motivate the use of bond graphs (a modelling tool from engineering) for energy-based modelling and introduce, BondGraphTools, a Python library for constructing and analysing bond graph models. We use examples from biochemistry to illustrate how BondGraphTools can be used to automate model construction in systems biology while maintaining consistency with the laws of physics.

Soluble Urokinase Receptor (SuPAR) in COVID-19-Related AKI.

BACKGROUND: AKI commonly occurs in patients with coronavirus disease 2019 (COVID-19). Its pathogenesis is poorly understood. The urokinase receptor system is a key regulator of the intersection between inflammation, immunity, and coagulation, and soluble urokinase plasminogen activator receptor (suPAR) has been identified as an immunologic risk factor for AKI. Whether suPAR is associated with COVID-19-related AKI is unknown. METHODS: In a multinational observational study of adult patients hospitalized for COVID-19, we measured suPAR levels in plasma samples from 352 adult patients that had been collected within 48 hours of admission. We examined the association between suPAR levels and incident in-hospital AKI. RESULTS: Of the 352 patients (57.4% were male, 13.9% were black, and mean age was 61 years), 91 (25.9%) developed AKI during their hospitalization, of whom 25 (27.4%) required dialysis. The median suPAR level was 5.61 ng/ml. AKI incidence rose with increasing suPAR tertiles, from a 6.0% incidence in patients with suPAR <4.60 ng/ml (first tertile) to a 45.8% incidence of AKI in patients with suPAR levels >6.86 ng/ml (third tertile). None of the patients with suPAR <4.60 ng/ml required dialysis during their hospitalization. In multivariable analysis, the highest suPAR tertile was associated with a 9.15-fold increase in the odds of AKI (95% confidence interval [95% CI], 3.64 to 22.93) and a 22.86-fold increase in the odds of requiring dialysis (95% CI, 2.77 to 188.75). The association was independent of inflammatory markers and persisted across subgroups. CONCLUSIONS: Admission suPAR levels in patients hospitalized for COVID-19 are predictive of in-hospital AKI and the need for dialysis. SuPAR may be a key component of the pathophysiology of AKI in COVID-19.

Copy number variation analysis reveals variants associated with milk production traits in dairy goats.

Copy number variation (CNV) is a major type of genomic structural variation. We investigated their impacts on goat dairy traits using the CaprineSNP50 array. From 120 samples of five dairy goat breeds, we totally identified 42 CNVs ranging from 56,044 bp to 4,337,625 bp. We found significant associations between two CNVs (CNV5 and CNV25) and two milk production traits (mean of milk fat yield and mean of milk protein yield) after false discovery rate (FDR) correction (P < 0.05). CNV5 overlaps the ADAMTS20 gene, which is involved in the differentiation of mammary cell and plays a crucial role in lactogenic activity of bovine mammary epithelial cells. CNV25 overlaps with PAPPA2, which has been found to be associated with bovine reproduction and milk production traits. Our results revealed that CNVs overlapped with ADAMTS20 and PAPPA2 could be involved in goat dairy traits and function as candidate markers for further genetic selection.

Genome-wide CNV analysis revealed variants associated with growth traits in African indigenous goats.

Using the CaprineSNP50 data generated by the AGIN consortium, we detected common CNVs in 126 samples from four African indigenous goat breeds. A total of 30 CNVs ranging from 30,237 bp to 4,910,757 bp were identified. These CNVs were then associated with six growth traits by a linear regression analysis. Three significant associations were identified between two CNVs and two body traits after false discovery rate (FDR) correction (P < .05). One of them (CNV27) was significantly associated with both chest width and width of pin bones. It overlaps the SNX29 gene, the Gene Ontology (GO) annotations of which indicate CNV27 could be a potential functional candidate for meat production, health and reproduction traits. To our knowledge, this study is the first CNV-based association test of growth traits using SNP chip data in African meat goats.

Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins.

BACKGROUND: Copy number variations (CNVs) are structural variants consisting of large-scale insertions and deletions of genomic fragments. Exploring CNVs and estimating their effects on phenotypes are useful for genome selection but remain challenging in the livestock. RESULTS: We identified 1043 CNV regions (CNVRs) from array comparative genomic hybridization (CGH) data of 47 Holstein bulls. Using a probe-based CNV association approach, we detected 87 CNVRs significantly (Bonferroni-corrected P value < 0.05) associated with at least one out of 41 complex traits. Within them, 39 CNVRs were simultaneously associated with at least 2 complex traits. Notably, 24 CNVRs were markedly related to daughter pregnancy rate (DPR). For example, CNVR661 containing CYP4A11 and CNVR213 containing CTR9, respectively, were associated with DPR and other traits related to reproduction, production, and body conformation. CNVR758 was also significantly related to DPR, with a nearby gene CAPZA3, encoding one of F-actin-capping proteins which play a role in determining sperm architecture and male fertility. We corroborated these CNVRs by examining their overlapped quantitative trait loci and comparing with previously published CNV results. CONCLUSION: To our knowledge, this is one of the first genome-wide association studies based on CNVs called by array CGH in Holstein cattle. Our results contribute substantial information about the potential CNV impacts on reproduction, health, production, and body conformation traits, which lay the foundation for incorporating CNV into the future dairy cattle breeding program.

A thermodynamic framework for modelling membrane transporters.

Membrane transporters contribute to the regulation of the internal environment of cells by translocating substrates across cell membranes. Like all physical systems, the behaviour of membrane transporters is constrained by the laws of thermodynamics. However, many mathematical models of transporters, especially those incorporated into whole-cell models, are not thermodynamically consistent, leading to unrealistic behaviour. In this paper we use a physics-based modelling framework, in which the transfer of energy is explicitly accounted for, to develop thermodynamically consistent models of transporters. We then apply this methodology to model two specific transporters: the cardiac sarcoplasmic/endoplasmic Ca2+ ATPase (SERCA) and the cardiac Na+/K+ ATPase.

Performance of robotic simulated skills tasks is positively associated with clinical robotic surgical performance.

OBJECTIVE: To compare user performance of four fundamental inanimate robotic skills tasks (FIRST) as well as eight da Vinci Skills Simulator (dVSS) virtual reality tasks with intra-operative performance (concurrent validity) during robot-assisted radical prostatectomy (RARP) and to show that a positive correlation exists between simulation and intra-operative performance. MATERIALS AND METHODS: A total of 21 urological surgeons with varying robotic experience were enrolled. Demographics were captured using a standardized questionnaire. User performance was assessed concurrently in simulated (FIRST exercises and dVSS tasks) and clinical environments (endopelvic dissection during RARP). Intra-operative robotic clinical performance was scored using the previously validated six-metric Global Evaluative Assessment of Robotic Skills (GEARS) tool. The relationship between simulator and clinical performance was evaluated using Spearman's rank correlation. RESULTS: Performance was assessed in 17 trainees and four expert robotic surgeons with a median (range) number of previous robotic cases (as primary surgeon) of 0 (0-55) and 117 (58-600), respectively (P = 0.001). Collectively, the overall FIRST (ρ = 0.833, P < 0.001) and dVSS (ρ = 0.805, P < 0.001) simulation scores correlated highly with GEARS performance score. Each individual FIRST and dVSS task score also demonstrated a significant correlation with intra-operative performance, with the exception of Energy Switcher 1 exercise (P = 0.063). CONCLUSIONS: This is the first study to show a significant relationship between simulated robotic performance and robotic clinical performance. Findings support implementation of these robotic training tools in a standardized robotic training curriculum.

Multi-Institutional Validation of Fundamental Inanimate Robotic Skills Tasks.

PURPOSE: Our group has previously reported the development and validation of FIRST (Fundamental Inanimate Robotic Skills Tasks), a series of 4 inanimate robotic skills tasks. Expanding on the initial validation, we now report face, content and construct validity of FIRST in a large multi-institutional cohort of experts and trainees. MATERIALS AND METHODS: A total of 96 residents, fellows and attending surgeons completed the FIRST exercises at participating institutions. Participants were classified based on previous robotic experience and task performance was compared across groups to establish construct validity. Face and content validity was assessed from participant ratings of the tasks on a 5-point Likert scale. RESULTS: A total of 51 novice, 22 intermediate and 23 expert participants with a median previous robotic experience of 0 (range 0 to 3), 10 (range 5 to 30) and 200 cases (range 55 to 2,000), respectively (p<0.001), were assessed across all 4 inanimate robotic skills tasks. Expert and intermediate groups reliably outperformed novices (p<0.01). Experts also performed better than intermediates on all exercises (p<0.01). A survey of participants on their perceptions of the tasks yielded excellent face and content validity. CONCLUSIONS: We confirm robust face, content and construct validity of 4 inanimate robotic training tasks in a large multi-institutional cohort. FIRST tasks are reliably able to discern among expert, intermediate and novice robotic surgeons. Validation data from this large multi-institutional cohort is useful as we incorporate these tasks into a comprehensive robotic training curriculum.

External validation of Global Evaluative Assessment of Robotic Skills (GEARS).

BACKGROUND: We demonstrate the construct validity, reliability, and utility of Global Evaluative Assessment of Robotic Skills (GEARS), a clinical assessment tool designed to measure robotic technical skills, in an independent cohort using an in vivo animal training model. METHODS: Using a cross-sectional observational study design, 47 voluntary participants were categorized as experts (>30 robotic cases completed as primary surgeon) or trainees. The trainee group was further divided into intermediates (≥5 but ≤30 cases) or novices (<5 cases). All participants completed a standardized in vivo robotic task in a porcine model. Task performance was evaluated by two expert robotic surgeons and self-assessed by the participants using the GEARS assessment tool. Kruskal-Wallis test was used to compare the GEARS performance scores to determine construct validity; Spearman's rank correlation measured interobserver reliability; and Cronbach's alpha was used to assess internal consistency. RESULTS: Performance evaluations were completed on nine experts and 38 trainees (14 intermediate, 24 novice). Experts demonstrated superior performance compared to intermediates and novices overall and in all individual domains (p < 0.0001). In comparing intermediates and novices, the overall performance difference trended toward significance (p = 0.0505), while the individual domains of efficiency and autonomy were significantly different between groups (p = 0.0280 and 0.0425, respectively). Interobserver reliability between expert ratings was confirmed with a strong correlation observed (r = 0.857, 95 % CI [0.691, 0.941]). Experts and participant scoring showed less agreement (r = 0.435, 95 % CI [0.121, 0.689] and r = 0.422, 95 % CI [0.081, 0.0672]). Internal consistency was excellent for experts and participants (α = 0.96, 0.98, 0.93). CONCLUSIONS: In an independent cohort, GEARS was able to differentiate between different robotic skill levels, demonstrating excellent construct validity. As a standardized assessment tool, GEARS maintained consistency and reliability for an in vivo robotic surgical task and may be applied for skills evaluation in a broad range of robotic procedures.

Skin simulators for dermatological procedures.

BACKGROUND: A variety of skin simulators are available on which to practice procedures; however, choice of a suboptimal substitute compromises realism and productive practice. OBJECTIVE: Skin simulators for basic dermatological procedures are reviewed. METHODS: The authors' anecdotal experience with various skin simulators for different procedures is shared. RESULTS: The following simulators are suggested:  an unripe banana for elliptical excision, pork belly for undermining, pork belly for simple interrupted and buried suture, capped needle on a human shoulder for intramuscular injection, ripe tomato or hotdog with skin for intradermal injection, eggplant for shave biopsy, pork belly for punch biopsy, plastic tape over a dark surface for cryosurgery, and beef liver for electrosurgery.  Flaps are best practiced with foam sandwiched between foam tape or artificial anatomical models created specifically for this purpose. LIMITATIONS: The utility of one simulator over another was not compared in a controlled study. CONCLUSION: Efficient, realistic skin simulators are readily available for practice, which should enhance the safety of the practitioner and improve outcomes of novices.

Defining the role of CD2 in disease progression and overall survival among patients with completely resected stage-II to -III cutaneous melanoma.

BACKGROUND: Accurate assessment of prognosis remains clinically challenging in stage II to III cutaneous melanoma. Studies have implicated CD2 in immune surveillance, T-cell activation, and antitumor immunity, but its role in melanoma progression warrants further investigation. OBJECTIVE: We sought to investigate the prognostic role of CD2 in primary cutaneous melanoma. METHODS: Patients with American Joint Committee on Cancer stage II and III cutaneous melanoma were identified by retrospective review of dermatopathology databases from 2001 to 2010 at Mount Sinai Medical Center and Geisinger Medical Center. Additional patients were provided by New York University Medical Center based on retrospective review and tissue availability. Immunohistochemistry was performed on tumors from 90 patients with known recurrence status and documented follow-up. RESULTS: Primary tumors from patients who developed recurrent disease had fewer CD2(+) cells (P = .0003). In multivariable analyses including standard clinicopathologic predictors, CD2 was an independent predictor of disease recurrence (P = .008) and overall survival (P = .007). CD2 count correlated with characterization of tumor-infiltrating lymphocytes (P = .0004). Among the intermediate prognosis group of patients with nonbrisk tumor-infiltrating lymphocytes, CD2 count was predictive of disease recurrence (P = .0006) and overall survival (P = .0318). LIMITATIONS: Our retrospective design may have resulted in incomplete representation of patients lacking documented follow-up. CONCLUSIONS: CD2 may be an independent predictor of disease recurrence and overall survival among patients with primary cutaneous melanoma.

Cantharidin: a comprehensive review of the clinical literature.

BACKGROUND: Cantharidin is a topical vesicant that causes intraepidermal acantholysis with clinical application that includes the removal of warts, molluscum contagiosum (MC), calluses, and acquired perforating dermatoses. OBJECTIVE: To provide a comprehensive literature review of the efficacy and safety of cantharidin in the management of various cutaneous conditions. METHODS: A PubMed search was conducted using the term "cantharidin" combined with "warts", "plantar warts", "verruca vulgaris", "periungal", "subungual", "topical treatment", "topical therapy for warts", molluscum contagiosum", "perforating collagenosis," and "acantholysis." RESULTS: A total of 749 articles were identified and 37 articles met inclusion criteria for this review. The majority of studies show that cantharidin is an effective and safe treatment for removal of warts and MC. Several studies also show potential novel applications of cantharidin in acquired perforating dermatosis, acute herpes zoster, and leishmaniasis. Adverse effects are generally mild but common and should be monitored, particularly in the pediatric population. LIMITATIONS: There is a paucity of high-powered clinical studies involving the use of cantharidin. CONCLUSION: Topical cantharidin is a safe and effective treatment for warts, molluscum contagiosum, and callus removal, with promising uses in perforating dermatoses and leishmaniasis.

Nutritional Status and Physical Exercise Are Associated with Cognitive Function in Chinese Community-Dwelling Older Adults: The Role of Happiness.

We aim to assess the relationship between nutrition status, physical exercise, and cognitive function and particularly examine how happiness modifies and mediates the relationship, among 699 seniors aged 60 and above in Shanghai, China. Linear regression models were used to validate the effects of nutrition and exercise on cognitive function and to test their interaction effects with happiness. When the interactions were significant, stratified analyses in sub-groups were conducted. Mediation effects of happiness were examined using two-step causal mediation models. We confirmed that better nutrition (p < 0.001) and exercise (p = 0.009) were significantly associated with less cognitive decline. Furthermore, the effects of nutrition and exercise on cognitive decline were significant in the unhappy (happiness < 20) (p < 0.001) and younger (age < 74) sub-groups (p = 0.015). Happiness partially mediated 11.5% of the negative association of cognitive decline with nutrition (p = 0.015) and 23.0% of that with exercise (p = 0.017). This study suggests that happiness moderates and partially mediates the effects of exercise and nutrition on cognitive status. The beneficial effects of exercise and nutrition were stronger in less happy or younger seniors. Future intervention studies are required to confirm this path relationship.

Cardiovascular Risk Stratification of Patients Undergoing Hematopoietic Stem Cell Transplantation: The CARE-BMT Risk Score.

BACKGROUND: Evidence guiding the pre-hematopoietic stem cell transplantation (HSCT) cardiovascular evaluation is limited. We sought to derive and validate a pre-HSCT score for the cardiovascular risk stratification of HSCT candidates. METHODS AND RESULTS: We leveraged the CARE-BMT (Cardiovascular Registry in Bone Marrow Transplantation) study, a contemporary multicenter observational study of adult patients who underwent autologous or allogeneic HSCT between 2008 and 2019 (N=2435; mean age at transplant of 55 years; 4.9% Black). We identified the subset of variables most predictive of post-HSCT cardiovascular events, defined as a composite of cardiovascular death, myocardial infarction, heart failure, stroke, atrial fibrillation or flutter, and sustained ventricular tachycardia. We then developed a point-based risk score using the hazard ratios obtained from Cox proportional hazards modeling. The score was externally validated in a separate cohort of 919 HSCT recipients (mean age at transplant 54 years; 20.4% Black). The risk score included age, transplant type, race, coronary artery disease, heart failure, peripheral artery disease, creatinine, triglycerides, and prior anthracycline dose. Risk scores were grouped as low-, intermediate-, and high-risk, with the 5-year cumulative incidence of cardiovascular events being 4.0%, 10.3%, and 22.4%, respectively. The area under the receiver operating curves for predicting cardiovascular events at 100 days, 5 and 10 years post-HSCT were 0.65 (95% CI, 0.59-0.70), 0.73 (95% CI, 0.69-0.76), and 0.76 (95% CI, 0.69-0.81), respectively. The model performed equally well in autologous and allogeneic recipients, as well as in the validation cohort. CONCLUSIONS: The CARE-BMT risk score is easy to calculate and could help guide referrals of high-risk HSCT recipients to cardiovascular specialists before transplant and guide long-term monitoring.