Cytoscape.js 2023 update: a graph theory library for visualization and analysis

SUMMARY

Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. This update describes new features and enhancements introduced over many new versions from 2015 to 2022.

AVAILABILITY AND IMPLEMENTATION

Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Prevalence of cardiac amyloidosis among cardiac- and non-cardiac patients undergoing echocardiography at a large university echo lab in Germany: a cohort study

Background

Cardiac amyloidosis (CA) is a progressive infiltrative cardiomyopathy that leads to severe heart failure and, once clinically relevant, poses a high mortality risk. Epidemiological data for CA are still sparse and heterogeneous, but urgently needed since novel therapies against ATTR-CA are now available.

Aim

We aimed to assess minimum prevalence rates of CA among cardiac and non-cardiac patients undergoing routine echocardiography in an echo lab of a large university clinic serving all medical specialities in central Germany.

Methods

We established a retro- and prospective database based on suspicious findings in echocardiography for all echocardiographic exams over an 8.5 year period (03/2013 and 09/2021). During this time, 41,375 patients underwent at least one echo exam. Indication for echos were mixed, and consisted of non-cardiac and cardiac patients with acute and chronic illnesses as well as screening exams (e.g. before major surgery or chemotherapy). Suspicious echocardiography were retrospectively analysed whether they underwent further diagnostic or if it remained an unproven suspicion (figure). All echos of suspicious cases were comprehensively re-analysed regarding novel surrogate parameters and indices for CA. Various clinical and laboratory parameters were collected.

Results

The mean age of the cohort of 41,375 patients was 65.1±15.8 years for the first or only echo examination with a slightly unbalanced gender distribution (45% female). The age distribution is shown in the table. While 128 patients were suspected, the diagnosis was falsified in 16 patients and proven in 47 patients (light chain n=16, ATTR n=31; figure). A substantial proportion of patients with suspicious echo received no further diagnostic work-up (N=65). Over the given time frame of 101 months, the prevalence of suspicious echocardiograms was 1 per 323 patients (or 31 per 10,000). The proven cases had a prevalence of 1 per 880 patients (or 11.3 per 10,000). Since ATTR-CA is a disease of the elderly, we saw a vanishingly small number of cases in persons younger than 70 years (table), whereas 90% of all CA patients were older than 70 years. At timing of diagnosis, AL-CA patients were almost 10 years younger compared to diagnosis of ATTR-CA (69.1±8.4 years vs. 77.4±8.5 years). In patients older than 80 years, the prevalence rate of ATTR-CA peaked with 22.6 cases per 10.000 patients (0.23%). The prevalence rate of ATTR-CA was roughly twice as high compared to AL-CA.

Conclusion

For the first time, an estimation of minimum prevalence rates for CA for a defined volume of echocardiograms in an all-comers population is provided. In a mixed population of a hospital of maximum care CA prevalence rate is much higher than expected. Awareness for this “rare” disease is needed, since routine echo exams can prompt suspicion in clinically silent or so far unrecognized CA cases.

Funding Acknowledgement

Type of funding sources: None.

Adding troponin to echocardiography improves preoperative abscess detection in infective endocarditis. A REMOVE Trial analysis

Background

Detection of cardiac abscess in patients with infective endocarditis (IE) is important for surgical planning and decision-making. While transesophageal echocardiography (TEE) is the method of choice for abscess detection, in many cases uncertainty remains. Since IE abscesses often affect ventricular muscle, biomarker release may be a helpful adjunct for abscess detection.

Purpose

We assessed the accuracy of TEE and the value of combining it with preoperative measurement of cardiac Troponin (cTn) in the diagnosis of abscess, using surgical inspection as a reference.

Methods

Data collected in the electronic clinical report form for patients included in the prospective, multicenter, randomized, controlled trial (REMOVE Trial) were analyzed. Continuous variables are presented as median (25th–75th percentile) and categorical data as absolute and relative frequencies. The diagnostic performance of TEE was identified by comparing preoperative TEE findings with intraoperative findings. The concordance rate is expressed as a percentage. Receiver operating characteristic (ROC) curve was used to assess the ability of cTn to predict the presence of abscess intraoperatively. Area under curve (AUC) with 95% confidence interval as well as sensitivity and specificity are provided as measures of accuracy. Youden index was used to estimate an optimal cut-off value for cTn.

Results

Among the 282 patients included, 84 had abscesses detected intraoperatively. The sensitivity and specificity of TEE to detect abscess were 58.3% and 86.4%, respectively. cTn-I and cTn-T were measured preoperatively in 113 and 96 patients, respectively. Median cTn-I in patients with abscess was 132 pg/ml (interquartile range (IQR): 54–1528) vs 53 pg/ml (IQR: 17–250) in patients without abscess, p=0.002. Median cTn-T in patients with abscess was 941 pg/ml (IQR: 387–1527) vs 697 pg/ml (IQR: 282–1423) in patients without abscess, p=0.353. The incidence of recent preoperative myocardial infarction was not different between patients with or without abscess (7.1% vs 5.6%, respectively, p=0.593). The AUC for predicting abscess was 0.69 (95% CI: 0.57 to 0.80, p=0.002) and 0.56 (95% CI: 0.43 to 0.69, p=0.353) for preoperative cTn-I and cTn-T, respectively. Optimal cut-offs according to the Youden index are 38 pg/ml for cTn-I and 1632 pg/ml for cTn-T. By adding preoperative cTn-I or cTn-T to the TEE findings, the AUC increased to 0.82 (95% CI: 0.73 to 0.91, p<0.001) and 0.72 (95% CI: 0.59 to 00.84, p=0.001), respectively.

Conclusion

The results suggest that using TEE alone is a poor method for abscess detection in IE. Adding preoperative troponin values to TEE findings significantly improved IE abscess detection.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): The Federal Ministry of Education and Research (BMBF), Germany

Prognostic relevance of mitral regurgitation at different follow-up timepoints after transcatheter aortic valve implantation (TAVI): implications for therapeutic decision making?

Background

Transcatheter aortic valve implantation (TAVI) has developed rapidly in the last decade and is now recommended as state-of-the-art treatment for elderly patients suffering from severe symptomatic degenerative aortic stenosis (AS). The extent of mitral regurgitation (MR) following TAVI is likely to be of prognostic relevance. This raises the question whether treating MR following TAVI improves outcome of patients with significant MR.

Purpose

The current study was aimed to elucidate the prognostic value of MR at different follow-up (FU) timepoints after TAVI in a prospective real-world single-center registry study.

Methods

A total of 445 patients with severe AS, which were treated by transfemoral TAVI, were included and a wide range of clinical, laboratory, functional and imaging parameters were prospectively assessed. Mortality was recorded at 30 days, 1 year and 2 years after TAVI. Complete FU data including echocardiography were available at 6 to 8 weeks (n=334) as well as 6 months (n=235) after TAVI.

Results

All patients (mean age: 78.7±7.3 years, 52% female, mean STS score: 5±3.9%) were successfully treated by transfemoral TAVI using balloon- or self-expanding prostheses and showed mortality rates of 3.6% after 30 days, 16.4% after 1 year and 22.6% after 2 years. Moderate or severe (relevant) MR was detectable in 39% of the patients at baseline, in 27% of patients after 6 weeks (p=0.001) and in 28% of patients after 6 months (p=0.036, compared to baseline). Multivariate analysis identified independent predictors of 2-year mortality: clinical frailty scale and PAPsys at 6 to 8 weeks post-TAVI as well as BNP and relevant MR 6 months post TAVI. Among those parameters, MR after 6 months was the strongest predictor of long-term mortality (OR 3.192, CI 0.971–10.487, p=0.056). Kaplan-Meier survival analysis displayed significantly worse 2-year survival rates in patients suffering from relevant MR at 6 months (12.1% versus 4.8%, p=0.042).

Conclusions

Taken together, this real-life single-center experience underlines the prognostic value of relevant MR 6 months after TAVI with respect to long-term survival. Interestingly, MR was not predictive at the 6 to 8 weeks FU suggesting that early remodeling includes MR with prognostic relevance in those patients. Whether MR treatment, e.g., by transcatheter edge-to-edge repair, will improve patient outcomes post-TAVI has to be tested in prospective trials.

Funding Acknowledgement

Type of funding sources: None.

Tricuspid regurgitation and atrial fibrillation at baseline independently predict two-year survival after transcatheter aortic valve implantation (TAVI)

Background

Transcatheter aortic valve implantation (TAVI) is the accepted state-of-the-art treatment for elderly patients suffering from severe symptomatic aortic stenosis (AS). Co-morbidities at baseline are of great impact not only for individual peri-procedural risk stratification but also for the determination of long-term prognosis. The latter is of certain clinical interest, since a variety of co-existing disorders can be effectively treated in addition to TAVI.

Purpose

The current study aimed to elucidate the prognostic value of a wide range of baseline characteristics and co-morbidities with respect to long-term survival of TAVI patients in a prospective real-world single-center registry study.

Methods

A total of 445 patients with severe AS, which were treated by transfemoral TAVI, were included. A wide range of clinical, laboratory, functional and imaging parameters were prospectively assessed at baseline prior to TAVI. Mortality was recorded at 30 days, 1 year and 2 years after TAVI.

Results

The mean age of patients in this typical TAVI cohort was 78.7±7.3 years, 52% were female and the mean STS score was 5±3.9%. The mortality rates were as follows: 3.6% after 30 days, 16.4% after 1 and 22.6% after 2 years. Multivariate analysis could identify the following independent predictors of 2-year mortality assessed at baseline: sex, age, AS entity other than high-gradient, atrial fibrillation (Afib), renal function, relevant TR, systolic pulmonary artery pressure (PAPsys) and six-minute walk distance (SMWD). Among those, the strongest predictive value could be shown for Afib (OR 2.505, CI 1.509–4.157, p<0.001) and TR (OR 2.179, CI 1.105–4.299, p=0.025). Kaplan-Meier survival analysis displayed significantly worse 2-year survival rates in patients suffering from relevant TR (31.6% versus 17.4%, p<0.001) and Afib (29.4% versus 14.8%, p<0.001).

Conclusions

Taken together, the results of the current study demonstrate the prognostic value of cardiovascular co-morbidities assessed prior to TAVI. We identified relevant TR and Afib as the strongest independent predictors of long-term mortality in our cohort. Since both conditions are effectively treatable, special emphasis should be placed on the question, which patient might benefit from treatment, e.g., by transcatheter edge-to-edge repair of TR or rhythm control, in addition to TAVI.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): Else Kröner-Fresenius-Stiftung, Research Program “Else Kröner-Forschungskolleg AntiAge”

High-Temperature Majorana Zero Modes

We employ analytical and numerical approaches to show that unpaired Majorana zero modes can occur in cores of Abrikosov vortices at the interface between a three-dimensional topological insulator, such as Bi_{2}Se_{3}, and a twisted bilayer of high-T_{c} cuprate superconductor, such as Bi_{2}Sr_{2}CaCu_{2}O_{8+δ}. When the twist angle is close to 45° the latter has been predicted to form a fully gapped topological superconductor up to temperatures approaching its native T_{c}≃90  K. Majorana zero modes in these structures will persist up to unprecedented high temperatures and, depending on the quality of the interface, may be protected by gaps with larger magnitudes than other candidate systems.

Author-sourced capture of pathway knowledge in computable form using Biofactoid

Making the knowledge contained in scientific papers machine-readable and formally computable would allow researchers to take full advantage of this information by enabling integration with other knowledge sources to support data analysis and interpretation. Here we describe Biofactoid, a web-based platform that allows scientists to specify networks of interactions between genes, their products, and chemical compounds, and then translates this information into a representation suitable for computational analysis, search and discovery. We also report the results of a pilot study to encourage the wide adoption of Biofactoid by the scientific community.

Doxorubicin induced cardiotoxicity is mediated by increased CerS2 expression and ceramide accumulation in vitro and in vivo

Background

Doxorubicin (Dox) is a chemotherapeutic drug with cardiotoxicity as a severe side effect. Interestingly, Dox increases the expression of ceramide synthase 2 (CerS2) and increases long- chain ceramide levels with proinflammatory effects.

Aim

The purpose of our study was to identify the role of increased long- chain ceramides synthesized by CerS2 in Dox mediated cardiotoxicity in vitro and in vivo.

Methods

We incubated HL-1 cells (murine cardiomyocytes) with 0.7 μM Dox for 24h. In parallel cells were pretreated with fumonisin B (100 μM, 4h, FuB) to reduce Dox effects. We generated CerS2 ko mice and treated them with Dox and also generated doxycycline- inducible CerS2 mice. Expression of genes and proteins were measured with immunofluorescence (IF), western blot (WB) or qPCR. Ceramide levels were determined with mass spectrometry. Cellular staining was assessed by confocal laser scanning microscopy. Mitochondrial viability and activity were detected using seahorse analyzer.

Results

Protein expression measurement showed increased CerS2 level in vitro (2.4±0.32, p=0.03 for WB, 2.2±0.10, p<0.001 for IF). Coherently, very long chain ceramides were increased with the highest peak for C16:0 (1.9±0.04, p<0.001). FuB pretreatment reduced most ceramides to normal levels. Dox increased mRNA level of TNFα (6.0±0.48, p<0.001), IL-6 (4.6±0.37, p<0.001), IL-1β (46.2±0.59, p=0.05) and BNP (4.7±0.46, p=0.03). FuB reduced IL-1β (20.1±0.23, p=0.002) and BNP (2.3±0.05, p=0.01) expression. Dox reduced mitochondria fusion related genes MFN1 (0.7±0.18, p=0.02) and MFN2 (0.3±0.37, p=0.01) and increased mitochondria fission related genes Mff (1.5±0.22) and FIS1 (1.5±0.18). FuB returned Mff and FIS1 expression to normal levels. Mitochondrial ATP production was reduced with Dox (0.3±0.19, p<0.001) and was slightly improved with FuB (0.5±0.12, p<0.001). Dox led to increased cleaved Casp3/Casp3 ratio (64.9±0.61, p=0.04). In vivo CerS2 overexpression showed comparable results as well as increased fibrosis.

Conclusion

Our data show that Dox mediated cardiotoxicity is in part mediated by CerS2 and ceramides. CerS2 could be a valuable drug target for treatment of chemotherapy- associated cardiomyopathies.

Funding Acknowledgement

Type of funding sources: None. Immunofluorescence HL-1

Crucial role of extra-domain A containing fibronectin for the development of pulmonary hypertension and associated right heart failure

Background

Pulmonary vascular and right ventricular myocardial remodelling are unique phenomena in PH progression. Both processes are accompanied by an abundant re-expression of the extra-domain A of fibronectin (ED-A+ Fn) therefore qualifying as promising biomarker or even therapeutic target. Nevertheless, its functional role in PH pathogenesis remains unclear until now. Objective: The purpose of our study was to analyse the development of PH and RHF in a mouse model of monocrotaline (MCT)-induced PH comparing C57BL/6 ED-A+ Fn knockout (KO) and wild-type (WT) mice.

Methods

PH was induced by subcutaneous injection of a single dose of MCT (60 mg/kg body weight). Subgroups were additionally treated with the dual endothelin receptor antagonist Macitentan (MAC, 15mg/kg body weight per day from day 14 to 28). There were 6 experimental groups: sham-treated control WT mice (WTco, n=4); MCT induced PH WT mice (WTPH, n=6); MCT induced PH WT mice treated with MAC (WTPH_MAC, n=6); sham-treated control KO mice (KOco, n=4); MCT induced PH KO mice (KOPH, n=6); MCT induced PH KO mice treated with MAC (KOPH_MAC, n=6). Between day 26 and 28, transthoracic echocardiography and right heart catheterization were performed. Both, lung and cardiac tissue samples were subjected to histological analyses.

Results

Right heart catheterization revealed significantly increased RVPsys values in WTPH (87.0±16.4mmHg) compared to WTco (36.1±9.4mmHg; p=0.034) animals, which showed, at least in trend, a diminution in the WTPH_MAC group (67.1±20.9mmHg; p=n.s.). There was a non-significant increase in RVPsys in the KOPH (55.6±14.9mmHg) compared to KOco mice (37.2±5.6mmHg; p=n.s.) without any differences compared to the KOPH_MAC group (60.9±14.0mmHg; p=n.s.). When comparing the WTPH and the KOPH group, RVPsys was significantly lower in the KO animals (p=0.014), while there were no differences between the WTPH_MAC and the KOPH_MAC group (p=n.s.). Echocardiographic evaluation including surrogate parameters of right ventricular (RV) overload and failure were significantly altered in WTPH compared to WTco animals (p<0.05) and could not be shown to be relevantly improved in the WTPH_MAC group (p=n.s.). The majority of echocardiographic parameters did not significantly differ between the KOPH and the KOco group (p=n.s.). Lung tissue analysis revealed significant alterations in both, the WTPH and the KOPH group, each compared to the corresponding control (p<0.05). The level of lung tissue damage was significantly decreased in KOPH compared to WTPH mice (p<0.05). In RV, the amount of interstitial fibrosis was increased in the WTPH (p=0.009) but not in the KOPH group (p=n.s.), each compared to the corresponding controls.

Conclusions

The findings of the current study underline the hypothesis that ED-A+ Fn is a key player in the pathogenesis of PH and associated RHF. Thus, it might represent a promising therapeutic target, e.g., by the administration of neutralizing antibodies.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): University Hospital Jena

Inhibition of ceramide synthesis improves the outcome in ischemia/reperfusion injury using human-induced pluripotent stem cell derived cardiomyocyte

Introduction and aim

Ceramides are proven to be biologically active in apoptosis, inflammation, mitochondrial dysfunction, and as a second messenger in various signaling pathways1. However, the data linking the role of ceramides in ischemia/reperfusion injury (I/R injury) are lacking. We aimed to establish an I/R injury model using human-induced pluripotent stem cell (hiPSC)-derived cardiomyocyte (CM) and to evaluate ceramide levels, ceramide synthesis pathway, and outcome of CM with inhibition of ceramide synthesis during I/R injury.

Methods

HiPSC technology has been used to generate functional human CMs to elucidate the underlying mechanisms of the pathophysiology of the human heart.

Results

In our model, we observed an increase of mRNA levels of genes regulating ceramide synthesis after 6 h of ischemia followed by 16 h reperfusion, such as SPTLC1 (1.1±0.08 vs 1.0, p=0.2), CerS2 (1.6±0.3 vs 1.0, p<0.001), CerS4 (1.3±0.1 vs 1.0, p=0.02), CerS5 (1.3±0.1 vs 1.0, p=0.03), and SMPD (1.6±0.1 vs 1.0, p=0.008) compared to control. Also, both long- and very long-chain ceramide species levels measured with mass spectrometry were increased significantly after 6 h ischemia followed by 16 h reperfusion compared to control (C14:0: 1,1±0.3 pmol/million cells vs 0,3±0,2 pmol/ million cells, p=0.02 and C24:1: 26,3±7,1 pmol/ million cells vs 9,6±3,4 pmol/ million cells, p=0.02).

Inhibition of ceramide synthesis with Fumonisin B1 (FB1) significantly increased the viability after 6h of ischemia followed by 16 h of reperfusion compared to CMs incubated without inhibitors (32.2%±1.5% vs 26.9%±2.6%, p=0.04). Interestingly, we identified two mechanisms with which the viability improves after incubation with ceramide inhibitor. The first mechanism observed could be the restoration of both intracellular calcium baseline (control 29±1.2, I/R 55±5.7 and I/R with FB1 35.6±2.5, p<0,001) and peak (control 45.1±5.6, I/R 94.3±5.7 and I/R with FB1 56.5±7.5, p<0,001) levels to nearly the same levels as observed in control samples. A possible cause of increased calcium oscillations after 6 h of ischemia followed by 3 h of reperfusion in the first place could be an upregulation of the RyR2 levels detected by qPCR (2.5±0.4 vs control 1.0, p=0.008). The second mechanism of improving viability in I/R injury could be a decrease of generation of reactive oxygen species (ROS) detected by MitoSOX dye after incubation with FB1 inhibitor to nearly the same levels as observed in control (control 22±5.1, I/R 33.8±5.8 and I/R with FB1 30.7±5.9, p=0,06).

Conclusion

We conclude that ceramides have important implications in either mediating or causing injury and their inhibition improves the outcome of I/R injury by decreasing ROS generation and improving calcium oscillations.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): Jena University Hospital, Clinic for Internal Medicine 1Interdisciplinary Center for Clinical Research Jena

Kynurenine as a potential biomarker in detecting reduced muscle endurance: metabolomic profiling of patients with heart failure and exercise intolerance

Aims

Reduced muscle endurance (RME) in patients with HFpEF and HFrEF is associated with structural and metabolic changes in skeletal muscle. We investigated the role of kynurenine (Kyn) as a potential marker in detecting RME. Additionally, we described the likely distorted metabolic pathways in serum in patients with RME and both preserved (HFpEF) and reduced (HFrEF) ejection fraction.

Methods

Fifty-five participants were prospectively recruited (17 HFpEF, 18 HFrEF outpatients and 20 healthy controls, HC). All participants underwent echocardiography, CPET, isokinetic muscle function tests. Quantification of metabolites in serum was performed using liquid chromatography tandem mass spectrometry.

Results

In a linear regression, Kyn was an independent predictor for RME after adjusting for alanine, glutamate, ornithine, spermine and short-chain-ACs (B: −8.2 per 1μM increase, 95% CI: −13.01, −3.30, p=0.001). Kyn showed 83% sensitivity and 70% specificity (area under the curve 0.83) in detecting RME. Patients with RME and HFpEF showed reduced levels of long-chain-, medium-chain-, medium-/long-chain-ACs ratios and alanine (p<0.05). In patients with RME and HFrEF we observed reduced concentrations of AAs (p<0.05). Compared to HC, patients with HFpEF and HFrEF had reduced amino acid (AA)-concentrations except for branched-chain and aromatic AAs, and higher concentrations of acylcarnitines (ACs) and Kyn (p<0.05).

Conclusions

Kyn shows high potential as biomarker for detecting RME. RME was associated with impaired fatty acid oxidation rates in HFpEF patients and with reduced concentrations of AAs in those with HFrEF.

Funding Acknowledgement

Type of funding sources: None.

The impact of establishing a regional infective endocarditis (IE) network on pre-operative IE-related complications and on post-operative outcome

Background

Infective endocarditis (IE) requires a high degree of suspicion and advanced level of multidisciplinary management. In 2015, the European guidelines recommended the formation of an endocarditis-team (ET) for optimal treatment of IE. In 2011, we already established an ET within the hospital that was only consulted on demand for certain patients. Since 2015, ET has been increasingly involved in the management of almost all patients with IE. In addition, we established in 2015 a statewide endocarditis- (E) network for the referring hospitals.

Purpose

We investigated the effect of E-network on reducing referral latency and pre-operative IE-related complications. We also investigated the adherence to the ET management recommendations in our hospital and its impact on post-operative stroke and mortality.

Methods

We retrospectively analyzed data from patients operated for IE in our center between 01/2007 and 03/2018. We conducted univariate analysis using Chi-square or Fisher's exact test, Multivariate logistic regression models for in-hospital mortality and post-operative stroke, and Kaplan-Meier estimate of 5-years survival.

Results

Among 630 patients operated for IE in our center, 409 (65%) underwent surgery in the 1st era before 12/2014. S. aureus IE was more frequent in the second era (34% vs 25%, p<0.001). The median time from the onset of symptoms to referral in the 2nd era was halved compared to the first one [7 days (IQR 2–19) vs 15 days (IQR 6–35)]. Patients in the 2nd era were admitted with less IE-related complications, i.e. less preoperative stroke (14% vs 27%, p<0.001), less heart failure (45% vs 69%, p<0.001) less cardiac abscesses (24% vs 34%, p=0.018), less acute renal insufficiency requiring hemodialysis (8% vs 14%, p=0.026). The lack of ET management recommendations was an independent predictor for in-hospital mortality (adjusted OR: 2.13, 95% CI: 1.27–3.53, p=0.004) and post-operative stroke (adjusted OR: 2.23, 95% CI: 1.12–4.39, p=0.02), and was associated with worse 5-years survival (59% compared to 40%, log rank<0.001).

Conclusion

Endocarditis-network led to earlier referral of patients, which resulted in less IE-related complications on admission. Lack of ET management recommendations was an independent predictor for post-operative stroke, in-hospital mortality and was associated with worse 5-years survival.

Funding Acknowledgement

Type of funding sources: None. Figure 1Figure 2

Surveilling and Tracking COVID-19 Patients Using a Portable Quantum Dot Smartphone Device

The ability to rapidly diagnose, track, and disseminate information for SARS-CoV-2 is critical to minimize its spread. Here, we engineered a portable smartphone-based quantum barcode serological assay device for real-time surveillance of patients infected with SARS-CoV-2. Our device achieved a clinical sensitivity of 90% and specificity of 100% for SARS-CoV-2, as compared to 34% and 100%, respectively, for lateral flow assays in a head-to-head comparison. The lateral flow assay misdiagnosed ∼2 out of 3 SARS-CoV-2 positive patients. Our quantum dot barcode device has ∼3 times greater clinical sensitivity because it is ∼140 times more analytically sensitive than lateral flow assays. Our device can diagnose SARS-CoV-2 at different sampling dates and infectious severity. We developed a databasing app to provide instantaneous results to inform patients, physicians, and public health agencies. This assay and device enable real-time surveillance of SARS-CoV-2 seroprevalence and potential immunity.

Robotic and laparoscopic liver resection-comparative experiences at a high-volume German academic center

Purpose

Minimally invasive liver surgery (MILS) is a feasible and safe procedure for benign and malignant tumors. There has been an ongoing debate on whether conventional laparoscopic liver resection (LLR) or robotic liver resection (RLR) is superior and if one approach should be favored over the other. We started using LLR in 2010, and introduced RLR in 2013. In the present paper, we report on our experiences with these two techniques as early adopters in Germany.

Methods

The data of patients who underwent MILS between 2010 and 2020 were collected prospectively in the Magdeburg Registry for Minimally Invasive Liver Surgery (MD-MILS). A retrospective analysis was performed regarding patient demographics, tumor characteristics, and perioperative parameters.

Results

We identified 155 patients fulfilling the inclusion criteria. Of these, 111 (71.6%) underwent LLR and 44 (29.4%) received RLR. After excluding cystic lesions, 113 cases were used for the analysis of perioperative parameters. Resected specimens were significantly bigger in the RLR vs. the LLR group (405 g vs. 169 g, p = 0.002); in addition, the tumor diameter was significantly larger in the RLR vs. the LLR group (5.6 cm vs. 3.7 cm, p = 0.001). Hence, the amount of major liver resections (three or more segments) was significantly higher in the RLR vs. the LLR group (39.0% vs. 16.7%, p = 0.005). The mean operative time was significantly longer in the RLR vs. the LLR group (331 min vs. 181 min, p = 0.0001). The postoperative hospital stay was significantly longer in the RLR vs. the LLR group (13.4 vs. LLR 8.7 days, p = 0.03). The R0 resection rate for solid tumors was higher in the RLR vs. the LLR group but without statistical significance (93.8% vs. 87.9%, p = 0.48). The postoperative morbidity ≥ Clavien-Dindo grade 3 was 5.6% in the LLR vs. 17.1% in the RLR group (p = 0.1). No patient died in the RLR but two patients (2.8%) died in the LLR group, 30 and 90 days after surgery (p = 0.53).

Conclusion

Minimally invasive liver surgery is safe and feasible. Robotic and laparoscopic liver surgery shows similar and adequate perioperative oncological results for selected patients. RLR might be advantageous for more advanced and technically challenging procedures.

A novel echocardiographic-derived classification after LAA closure can accurately predict incomplete ostial closure and significant peri-device leaks

Background

The assessment of residual peri-device leaks (PDL) after percutaneous left atrial appendage closure (LAAC) remains crucial in the post-procedural management. Clinical significance of PDL is still poorly understood and echocardiographic recognition of PDL remains challenging. This study aimed to verify a novel proposed echocardiographic classification for prediction of clinically significant PDL following LAAC.

Methods

We retrospectively evaluated our echocardiographic data of 72 patients who underwent percutaneous LAAC at the University Hospital Jena between September 2015 - 2018. All echo images were transferred to a workstation for offline analysis by two independent investigators. Total number of studies was 127. We proposed a morphological classification of LAA devices (Fig. 1A-C) based on the amount of echodensity and luceny inside the devices into three types: type A: homogenous echodensity in 0, 45, 90 and 135°; indicating completely thrombosed device, type B with inhomogeneous echo-lucencies (<50% of device) and type C: partially thrombosed device with echo-lucencies >50% of total, which we labeled “ice-cream cone” sign. Each type was then matched to the degree of PDL and other clinical and paraclinical parameters.

Results

Tab.1 shows patient's characteristics. PDL was found in 21% of patients. Four patients showed regression of PDL after 160 days. Patients with type C had the most percentage of PDL in three types at 6 months follow-up (type A: 7%, type B: 33%, type C 100%, p<0.001). Device size in patients with type C was largest in three types (type A: 25.9±3.6mm, type B: 25.8±3.4mm, type C 29.8±3.0mm, type A vs. B, p=0.018; type B vs. C, p=0.007). Mean compression rate after 45 days was 21±9.3% in type A vs. 14±7.4% in type C (p=0.022). Ice cream sign showed a sensitivity of 53.1%, specificity of 100% and positive predictive value of 100% for prediction of PDL.

Conclusion

Our data demonstrate that: 1) This novel classification irrespective of anticoagulation regimen, can accurately discriminate among various degrees of PDL, in such that type C or “ice cream sign” has a very high positive predictive value for PDL (100%). 2) Type A, the ideal type, is associated with smaller landing zones and a higher compression rate.

Funding Acknowledgement

Type of funding source: None

Relevant correlation of Galectin-3 with a novel morphological classification system for LAA closure – the end of echocardiographic follow up after occluder implantation?

Introduction

Echocardiographic detection of residual peri-device leakage (PDL) after percutaneous left atrial appendage closure (LAAC) remains crucial. Significance of PDL and cardiac tissue remodeling after LAAC are still poorly understood but might have diagnostic implications. This study aims to characterize and verify if a novel echocardiographic classification system to asses the success of LAAC in combination with quantifiable biomarkers of cardiovascular tissue remodeling can help in the prediction of PDL.

Methods

Patients eligible for LAAC were included. Serum levels of the cardiac remodeling marker Galectin-3 were determined before device implantation (baseline), 45 days (45d) and 6 months (6M) after LAAC using ELISAs. Transesophageal echocardiography (TEE) was carried out to assess success of the LAAC procedure. All echo images were retrospectively evaluated by two independent investigators. Based on the amount of echodensity and luceny inside the devices after LAAC, three types can be distinguished that grade the degree of closure of the LAA. Type A has complete homogenous echodensity in 0, 45, 90 and 135°, indicating completely thrombosed device. Type B shows inhomogeneous echo-lucencies (<50% of device). Type C describes a partially thrombosed device with echo-lucencies >50%. Novel classification according to Hamadanchi, Jena, Germany (Fig. 1).

Results

We included 44 patients (characteristics listed in Table 1). Complete LAAC (without any residual flow) was achieved in 64% (28 patients) after 45 days and in 80% (35 patients) after 6 months. Mean PDL diameter was 3.5±1.5mm. Type A showed the lowest rate of PDL after 45d (Type A: 22% vs. Type B: 33% vs. Type C: 88%; p=0.007) and after 6M (Type A: 12% vs. Type B: 28% vs. Type C: 100%; p=0.002). Galectin-3 levels did not show a relevant difference regarding the type of AF at baseline (paroxysmal AF: 11.7±5.4 ng/ml vs. permanent AF: 12.1±6.3 ng/ml; p=0.45). We observed a significant increase and distribution of serum levels of Galectin-3 [ng/ml] after 45 days among the three types (Baseline: 13.1±5.8; 45d: 16.3±7.2 (Type A) vs. 19.2±8.6 (Type B) vs. 25.8±9.4 (Type C); p=0.031) followed after 6 months by a drop of Galectin-3 for type A and B toward and below baseline levels (6M: 8.9±3.1 (Type A) vs. 12.4±5.5 (Type B)) whereas type C persisted in showing elevated Galectin-3 levels compared to all other types (6M: 17.5±4.5 (Type C); p<0.001), Fig. 2. Correlation analysis shows a significant negative correlation trend between Galectin-3 and mean PDL diameter (−0.51; p=0.016) after 45 days and a relevant positive correlation after 6 months (0.58; p=0.017).

Conclusion

After LAAC, Galectin-3 levels are elevated, as a marker of myocardial fibrosis in the LAA. Depending on the degree of closure of the LAA, Galectin-3 decreases to the baseline level or stays elevated in case of relevant PDL and could therefore be considered as a new biomarker for closure success.

Funding Acknowledgement

Type of funding source: None

Dynamics of Galectin-3 serum levels after percutaneous occlusion of the left atrial appendage: a new surrogate parameter for successful LAA closure?

Introduction

Left atrial cardiac tissue remodeling following left atrial appendage closure (LAAC) is a scientifically neglected phenomenon until now but might have impact on functional outcome of patients suffering from atrial fibrillation (AF). Thus, our study is focused on quantification of key biomarkers reflecting fibrosis development as a major component within cardiovascular tissue remodeling.

Methods

Patients (CHA2DS2VASC score ≥1, HASBLED score ≥3) with bleeding complications under anticoagulation therapy and therefore eligible for LAAC were included in the present study. Serum levels of biomarkers of cardiac fibrosis and remodeling (Galectin-3, ST2/IL-2, ST2/IL-1, B domain containing Tenascin-C (B+ Tn-C), C domain containing Tenascin- C (C+ Tn-C)) were determined before device implantation (baseline), 45 days (45d) and 6 months (6M) after LAAC using commercially available ELISAs. To quantify functional outcome, all patients performed a 6-minutes walk test (6- MWT). Transesophageal echocardiography (TEE) was carried out to assess success of the LAAC procedure regarding peri-device leakage (PDL).

Results

We included 33 patients (age: 73.5±6.7 years; 21 men (64%) and 12 women (36%); BMI: 29.1±5.1 kg/m2; CHA2DS2VASC score: 4.2±1.2; left ventricular ejection fraction: 61.1±9.3%; mean occluder size: 25.9±3.9 mm; type of AF: 46% paroxysmal (15 patients), 55% permanent (18 patients)). Complete LAAC (without any residual low) was achieved in 60% (19 patients) after 45 days and in 87% (29 patients) after 6 months. At baseline, Galectin-3 levels did not show a relevant difference regarding the type of AF (paroxysmal AF: 14.7±5.4 ng/ml vs. permanent AF: 13.1±6.3 ng/ml; p=0.45). We observed a significant increase of serum levels of Galectin-3 [ng/ml] after 45 days vs. baseline (baseline: 13.3±5.8 vs. 45d: 18.3±10.6; p=0.005) with a return to baseline levels after 6 months (baseline: 13.3±5.8 vs. 6M: 12.5±5.4; p=0.28). Compared to patients with successful LAAC, patients with PDL had a trend towards higher levels of Galectin-3 after 6 months (11.3±5.5 ng/ml vs. 16.1±4.1 ng/ml, p=0.09). Measurements of other fibrosis markers were statistically not significantly different. The walking distance measured by the 6-MWT increased significantly from 298.5±89.5 meters at baseline to 335.5±95.1 meters (p=0.04) after 45d and remained significantly elevated after 6M (346.7±122.7 meters; p=0.02).

Conclusion

The implantation of an LAA occluder device is accompanied by significantly increased circulating levels of the fibrosis biomarker Galectin-3 after 45 days in patients with AF. The regression in serum levels after 6 months probably reflects a successful fibrotic remodeling in the left atrial appendage over time and might be used as surrogate parameter for LAAC success. Increased and stable exercise tolerance after 45 days can be observed.

Funding Acknowledgement

Type of funding source: None

Generation of an iPSC line (UMGWi001-B) from a patient with Floating-Harbor Syndrome (FLHS) carrying a heterozygous SRCAP mutation (p.Arg2444)

Floating-Harbor syndrome (FLHS) is a rare genetic disease caused by mutations in the SRCAP gene. Here, we generated an induced pluripotent stem cell line from gingival fibroblasts of a male patient with a heterozygous mutation in exon 34 of the SRCAP gene (c.7330C > T, p.Arg2444*). The iPSC colonies have an atypical morphology with diffuse borders and disintegrate quickly upon touch. Still, the cell line expresses pluripotency markers and differentiates into three germ layers. The cell line can be used as patient-specific disease model and help elucidate the molecular mechanisms involving SRCAP in the context of FLHS.

Pericarditis as a cardiac manifestation of acute leptospirosis

Leptospirosis is an infectious disease with an increasing incidence worldwide. The clinical presentation is unspecific and ranges from an asymptomatic clinical course to an acute fulminant disease. The current case report describes a 32-year-old male patient who presented with ST segment elevation in the electrocardiogram about 14 days after cross-country running. Pericarditis was diagnosed and linked to an acute leptospirosis that was serologically confirmed.

A falciform ligament flap surface sealing technique for laparoscopic and robotic-assisted liver surgery

Whether sealing the hepatic resection surface after liver surgery decreases morbidity is still unclear. Nevertheless, various methods and materials are currently in use for this procedure. Here, we describe our experience with a simple technique using a mobilized falciform ligament flap in minimally invasive liver surgery (MILS). We retrospectively analyzed the charts from 46 patients who received minor MILS between 2011 and 2019 from the same surgical team in a university hospital setting in Germany. Twenty-four patients underwent laparoscopic liver resection, and 22 patients received robotic-assisted liver resection. Sixteen patients in the laparoscopic group and fourteen in the robotic group received a falciform ligament flap (FLF) to cover the resection surface after liver surgery. Our cohort was thus divided into two groups: laparoscopic and robotic patients with (MILS + FLF) and without an FLF (MILS-FLF). Twenty-eight patients (60.9%) in our cohort were male. The overall mean age was 56.8 years (SD 16.8). The mean operating time was 249 min in the MILS + FLF group vs. 235 min in the MILS-FLF group (p = 0.682). The mean blood loss was 301 ml in the MILS + FLF group vs. 318 ml in the MILS-FLF group (p = 0.859). Overall morbidity was 3.3% in the MILS + FLF group vs. 18.8% in the MILS-FLF group (p = 0.114). One patient in the MILS-FLF group (overall 2.2%), who underwent robotic liver surgery, developed bile leakage, but this did not occur in the MILS + FLF group. Covering the resection surface of the liver after minor minimally invasive liver resection with an FLF is a simple and cost-effective technique that does not prolong surgical time or negatively affect other perioperative parameters. In fact, it is a safe add-on step during MILS that may reduce postoperative morbidity. Further studies with larger cohorts will be needed to substantiate our proof of concept and results.

A system to measure seat-human interaction parameters which might be comfort relevant

In this paper a measurement tool is described and tested to evaluate the characteristics of different elements of a seat. Many studies report a relationship between discomfort and pressure distribution, but it is unknown what exactly is happening in the interaction. The purpose of this study is to present a measuring device, which records the comfort relevant seat parameters pressure and elongation while loading a seat. The results of the study, including the repeatability, reproducibility and detectability show that the measurement method is appropriate for our purpose, although the reproducibility has to be improved by operator experience or by a more intuitive assembling of the measurement setup. An application example illustrates that the interaction of the seat components highly affect the resulting comfort relevant parameters. The question is whether this objectively recorded differences are also experienced by seat occupants, which is interesting to study in future research.

Predicting patient outcomes in psychiatric hospitals with routine data: a machine learning approach

BACKGROUND

A common problem in machine learning applications is availability of data at the point of decision making. The aim of the present study was to use routine data readily available at admission to predict aspects relevant to the organization of psychiatric hospital care. A further aim was to compare the results of a machine learning approach with those obtained through a traditional method and those obtained through a naive baseline classifier.

METHODS

The study included consecutively discharged patients between 1st of January 2017 and 31st of December 2018 from nine psychiatric hospitals in Hesse, Germany. We compared the predictive performance achieved by stochastic gradient boosting (GBM) with multiple logistic regression and a naive baseline classifier. We tested the performance of our final models on unseen patients from another calendar year and from different hospitals.

RESULTS

The study included 45,388 inpatient episodes. The models' performance, as measured by the area under the Receiver Operating Characteristic curve, varied strongly between the predicted outcomes, with relatively high performance in the prediction of coercive treatment (area under the curve: 0.83) and 1:1 observations (0.80) and relatively poor performance in the prediction of short length of stay (0.69) and non-response to treatment (0.65). The GBM performed slightly better than logistic regression. Both approaches were substantially better than a naive prediction based solely on basic diagnostic grouping.

CONCLUSION

The present study has shown that administrative routine data can be used to predict aspects relevant to the organisation of psychiatric hospital care. Future research should investigate the predictive performance that is necessary to provide effective assistance in clinical practice for the benefit of both staff and patients.

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g. metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (i) tools to search this comprehensive resource, (ii) a download site offering integrated bulk sets of pathway data (e.g. tables of interactions and gene sets), (iii) reusable software libraries for working with pathway information in several programming languages (Java, R, Python and Javascript) and (iv) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4794 detailed human biochemical processes (i.e. pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.