Standardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two popular command-line solutions, are increasingly adopted by users, complementing GUI-based platforms such as Galaxy. We report recent developments of the nf-core framework with the new Nextflow Domain-Specific Language (DSL2). An extensive library of modules and subworkflows enables research communities to adopt common standards progressively, as resources and needs allow. We present an overview of some of the research communities built around nf-core and showcase its adoption by six EuroFAANG farmed animal research consortia.

DNA variation analysis has become indispensable in many aspects of modern biomedicine, most prominently in the comparison of normal and tumor samples. Thousands of samples are collected in local sequencing efforts and public databases requiring highly scalable, portable, and automated workflows for streamlined processing. Here, we present nf-core/sarek 3, a well-established, comprehensive variant calling and annotation pipeline for germline and somatic samples. It is suitable for any genome with a known reference. We present a full rewrite of the original pipeline showing a significant reduction of storage requirements by using the CRAM format and runtime by increasing intra-sample parallelization. Both are leading to a 70% cost reduction in commercial clouds enabling users to do large-scale and cross-platform data analysis while keeping costs and CO 2 emissions low. The code is available at https://nf-co.re/sarek.

MOTIVATION:Machine learning has shown extensive growth in recent years and is now routinely applied to sensitive areas. To allow appropriate verification of predictive models before deployment, models must be deterministic. Solely fixing all random seeds is not sufficient for deterministic machine learning, as major machine learning libraries default to the usage of nondeterministic algorithms based on atomic operations.RESULTS:Various machine learning libraries released deterministic counterparts to the nondeterministic algorithms. We evaluated the effect of these algorithms on determinism and runtime. Based on these results, we formulated a set of requirements for deterministic machine learning and developed a new software solution, the mlf-core ecosystem, which aids machine learning projects to meet and keep these requirements. We applied mlf-core to develop deterministic models in various biomedical fields including a single-cell autoencoder with TensorFlow, a PyTorch-based U-Net model for liver-tumor segmentation in computed tomography scans, and a liver cancer classifier based on gene expression profiles with XGBoost.AVAILABILITY AND IMPLEMENTATION:The complete data together with the implementations of the mlf-core ecosystem and use case models are available at https://github.com/mlf-core.

OBJECTIVES:The plasma level of N-terminal pro-brain natriuretic peptide is regulated by sex hormones. It has been controversial whether N-terminal pro-brain natriuretic peptide is a prognosis marker for sepsis. The aim of this study is to examine the sex-dependent association of plasma N-terminal pro-brain natriuretic peptide with organ dysfunction and mortality of sepsis patients.DESIGN:In this retrospective study, the association between plasma N-terminal pro-brain natriuretic peptide concentration on the day of sepsis diagnosis and the degree of organ dysfunction, occurrence of septic shock, or 30-day mortality in both male and female patients was analyzed.SETTING:This study was conducted in the Sepsis Laboratory at the Huaihe Hospital of Henan University in China.PATIENTS:Diagnoses of sepsis, and septic shock, were based on the recently revised criteria (Sepsis 3.0). All sepsis patients (517) hospitalized in the respiratory ICU of the Huaihe Hospital from June 2016 to December 2019 were enrolled in this study.INTERVENTIONS:None.MEASUREMENTS AND MAIN RESULTS:No significant difference was found in the age, occurrence rate of septic shock, 30-day mortality, or degree of organ dysfunction between male and female patients. Median concentration of plasma N-terminal pro-brain Natriuretic peptide was higher by 93.48% in female than male patients. A significant association was found between N-terminal pro-brain natriuretic peptide and septic shock or 30-day mortality in female, but not in male patients of community- or hospital-acquired sepsis. N-terminal pro-brain natriuretic peptide levels correlated to functional deficiencies of the cardiac and nervous systems, only in female patients.CONCLUSIONS:The plasma N-terminal pro-brain natriuretic peptide level is a female-specific prognosis indicator of septic shock and mortality.

Chronic hypoxic stress induces epigenetic modifications mainly DNA methylation in cardiac fibroblasts, inactivating tumor suppressor genes (RASSF1A) and activating kinases (ERK1/2) leading to fibroblast proliferation and cardiac fibrosis. The Ras/ERK signaling pathway is an intracellular signal transduction critically involved in fibroblast proliferation. RASSF1A functions through its effect on downstream ERK1/2. The antioxidant enzyme, extracellular superoxide dismutase (EC-SOD), decreases oxidative stress from chronic hypoxia, but its effects on these epigenetic changes have not been fully explored. To test our hypothesis, we used an in-vitro model: wild-type C57B6 male mice (WT) and transgenic males with an extra copy of human hEC-SOD (TG). The studied animals were housed in hypoxia (10% O 2 ) for 21 days. The right ventricular tissue was studied for cardiac fibrosis markers using RT-PCR and Western blot analyses. Primary C57BL6 mouse cardiac fibroblast tissue culture was used to study the in-vitro model, the downstream effects of RASSF-1 expression and methylation, and its relation to ERK1/2. Our findings showed a significant increase in cardiac fibrosis markers: Collagen 1, alpha smooth muscle actin (ASMA), and SNAIL, in the WT hypoxic animals as compared to the TG hypoxic group ( p < 0.05). The expression of DNA methylation enzymes (DNMT 1&3b) was significantly increased in the WT hypoxic mice as compared to the hypoxic TG mice ( p < 0.001). RASSF1A expression was significantly lower and ERK1/2 was significantly higher in hypoxia WT compared to the hypoxic TG group ( p < 0.05). Use of SiRNA to block RASSF1A gene expression in murine cardiac fibroblast tissue culture led to increased fibroblast proliferation ( p < 0.05). Methylation of the RASSF1A promoter region was significantly reduced in the TG hypoxic group compared to the WT hypoxic group (0.59 vs. 0.75, respectively). Based on our findings, we can speculate that EC-SOD significantly attenuates RASSF1A gene methylation and can alleviate cardiac fibrosis induced by hypoxia.

This study shows ChAT-expressing T cells can induce vasodilation of the blood vessel in the coronary circulation and that this effect relies on a direct interaction between T cells and the coronary vascular endothelium. The study establishes a potential immunomodulatory role for T cells in the coronary circulation. The present findings offer an additional possibility that a deficiency of ChAT-expressing T cells could contribute to reduced coronary blood flow and ischemic events in the myocardium.

Background: It was recently shown that tetranectin (TN) concentration in the plasma of sepsis patients was significantly lower than healthy control and that exogenous TN reduced the mortality rate in septic mice. The aim of this study is to determine whether the reduction of plasma TN is a sepsis-specific host response and its impact on organ dysfunction in sepsis. Methods: The study was conducted in the Sepsis Laboratory at the Huaihe Hospital of Henan University in China. Thirty-seven healthy, 30 community-acquired pneumonia (CAP) and 363 sepsis with comorbid pneumonia (SWP) subjects were recruited. A murine model of polymicrobial sepsis was used to characterize the role of plasma TN in sepsis pathogenesis. Results: TN concentrations in plasma from both CAP and SWP subjects were lower than healthy controls, but not significantly different between male and female sepsis patients, before and after the occurrence or the resolution of sepsis. In addition, plasma TN was not associated with the occurrence of septic shock or sepsis mortality in both genders. On the other hand, plasma TN negatively correlated with liver injury indicators in moribund SWP subjects. In mice of polymicrobial sepsis, a significant decrease in plasma TN occurred within hours after the ligation and puncture of the cecum. Recombinant human TN induced significant reductions of tissue injury markers of liver, but not other organs. In addition, exogenous TN selectively reduced the level of receptor-interacting protein kinase 3 among a panel of cell death markers in septic mouse liver. Conclusions: The dramatic and persistent down-regulation of plasma TN is not a sepsis-specific host response, but contributes to liver injury in pneumonia-associated sepsis.

Connexin (Cx) family members form hemichannels (HCs) and gap junctions (GJs). Biological functions of Cx HCs have not been adequately characterized due to the inability to selectively target HCs or GJs. Recently, we developed a 6-mer peptide mimetic (P5) of the first extracellular loop of Cx43 and showed that it can block the permeability of HCs but not GJs formed by Cx43. In this study, we further characterized the HC blocking property of P5 and investigated the role of Cx HCs in acute lung injury (ALI). We found that P5 administration decreased HC permeability, in pulmonary microvascular endothelial cells, HepG2 cells, and even Cx43-deficient astrocytes, which express different sets of Cxs, suggesting that P5 is a broad spectrum Cx HC blocker. In addition, P5 reduced HC permeability of alveolar cells in vivo. Moreover, P5 decreased endotoxin-induced release, by vascular endothelial cells in vitro, of high mobility group box protein 1 (HMGB1), a critical mediator of acute lung injury (ALI), and reduced HMGB1 accumulation in bronchoalveolar lavage fluid (BALF) of mice subjected to intratracheal endotoxin instillation. Furthermore, P5 administration resulted in a significant decrease in the concentrations of ALT, AST, and LDH in the BALF, the accumulation of leukocytes in alveoli, and the mortality rate of mice subjected to ALI. Wright-Giemsa staining showed that P5 caused similar reductions of both neutrophils and monocytes in BALF of ALI mice. Together, these results suggest that Cx HCs mediate HMGB1 release, augment leukocyte recruitment, and contribute to ALI pathology.

OBJECTIVE:In patients with aneurysmal subarachnoid hemorrhage (aSAH), poor outcomes have been shown to be correlated with subsequent cerebral vasospasm (CV) and delayed cerebral ischemia (DCI). The identification of novel biomarkers may aid in the prediction of which patients are vulnerable to developing vasospasm, cerebral ischemia, and neurological deterioration. METHODS:In this prospective clinical study at North Shore University Hospital, patients with aSAH or normal pressure hydrocephalus (NPH) with external ventricular drains were enrolled. The concentration of macrophage migration inhibitory factor (MIF) in CSF was assessed for correlation with CV or DCI, the primary outcome measures. RESULTS:Twenty-five patients were enrolled in the aSAH group and 9 were enrolled in the NPH group. There was a significant increase in aggregate CSF MIF concentration in patients with aSAH versus those with NPH (24.4 ± 19.2 vs 2.3 ± 1.1 ng/ml, p < 0.0002). Incidence of the day of peak MIF concentration significantly correlated with the onset of clinical vasospasm (rho = 0.778, p < 0.0010). MIF concentrations were significantly elevated in patients with versus those without evidence of DCI (18.7 ± 4.93 vs 8.86 ± 1.28 ng/ml, respectively, p < 0.0025). There was a significant difference in MIF concentrations between patients with infection versus those without infection (16.43 ± 4.21 vs 8.5 ± 1.22 ng/ml, respectively, p < 0.0119). CONCLUSIONS:Preliminary evidence from this study suggests that CSF concentrations of MIF are correlated with CV and DCI. These results, however, could be confounded in the presence of clinical infection. A study with a larger patient sample size is necessary to corroborate these findings.

In the original version of this article, the name of the author "Kamesh Ayasolla" was incorrectly given as "Kamesh Ayyasola". This has now been corrected to "Kamesh Ayasolla" in both the PDF and HTML versions of the article.

Background There is a compelling unmet medical need for biomarker-based models to risk-stratify patients with acute respiratory distress syndrome. Effective stratification would optimize participant selection for clinical trial enrollment by focusing on those most likely to benefit from new interventions. Our objective was to develop a prognostic, biomarker-based model for predicting mortality in adult patients with acute respiratory distress syndrome. Methods This is a secondary analysis using a cohort of 252 mechanically ventilated subjects with the diagnosis of acute respiratory distress syndrome. Survival to day 7 with both day 0 (first day of presentation) and day 7 sample availability was required. Blood was collected for biomarker measurements at first presentation to the intensive care unit and on the seventh day. Biomarkers included cytokine-chemokines, dual-functioning cytozymes, and vascular injury markers. Logistic regression, latent class analysis, and classification and regression tree analysis were used to identify the plasma biomarkers most predictive of 28-day ARDS mortality. Results From eight biologically relevant biomarker candidates, six demonstrated an enhanced capacity to predict mortality at day 0. Latent-class analysis identified two biomarker-based phenotypes. Phenotype A exhibited significantly higher plasma levels of angiopoietin-2, macrophage migration inhibitory factor, interleukin-8, interleukin-1 receptor antagonist, interleukin-6, and extracellular nicotinamide phosphoribosyltransferase (eNAMPT) compared to phenotype B. Mortality at 28 days was significantly higher for phenotype A compared to phenotype B (32% vs 19%, p = 0.04). Conclusions An adult biomarker-based risk model reliably identifies ARDS subjects at risk of death within 28 days of hospitalization.

Massive pulmonary embolism, sepsis, and ALI are the other main causes of acute pulmonary arterial hypertension (PAH) in the adult patient population.Preexisting pulmonary vascular and lung diseases, including Interstitial lung disease, chronic obstructive pulmonary disease and obstructive sleep apnea are other leading causes of chronic PAH.Whatever the cause, the management of critically ill patients with hemodynamically significant pulmonary hypertension remains challenging, especially in the field, away from equipped ICU and tertiary medical centers.We developed an innovative therapeutic approach by stimulation vagal nerve (VNS) which can be used in modulation vascular tone.Our study aims was focused to treat acute and chronic PAH in different animal model using VNS approach.A rodent model with PAH induced by hypoxia (FiO2 10%) for 3 weeks only (mild form of PAH) or hypoxia and Sugen together (Chronic form of PAH), were used.Continuous monitoring of the vital signs: Heart rate, EKG, oxygen saturation, breathing rate and both right ventricular pressure (RVP) and systemic pressure; were recorded using a computerized hemodynamic recording system.Continuous monitoring/stimulation of vagal nerve activity was established using a stimulation module controlled by the Acknowledge software (Biopac Systems).Stimulation was delivered using different matching stimulation parameters (current intensity Amplitude, pulse width htz, pulsing frequency, and pulsing duration).Our data showed that by using specific electric stimulation with specific parameters, we were able to target specific nerve fiber which can induce smooth muscle relaxation of the pulmonary vascular bed, followed a subsequent drop of RVP.Analysis of the data using beat to beat analysis showed that specific target for certain vagal nerve fibers can induce relaxation of contracted pulmonary vascular tree and significant drop of RVP, without any significant or marked change in systemic pressure, heart rate or breathing pattern (no apnea).Similar data was obtained using different murine animal models with wide range of PH severity and with variable degree of pulmonary vascular remodeling induced by Hypoxia and Sugen.We did also able to define a specific pattern of VNS (with a safe margin), which can trigger the vascular smooth muscle relaxation with none or minimal systemic or unwanted side effects (including hypotension, apnea and bradycardia).In conclusion, VNS is an innovative therapeutic modality which can be used in alleviating pulmonary pressure in animal model with variable degree and severity of PAH.Pre-clinical experiment on large animal model is warranted Neuromodulation as a New Strategy in Management of Pulmonary Hypertension

Introduction: Assessment of frailty is essential for determining eligibility for advanced therapies (AT). Most programs use a subjective provider assessment (SPA) or “eye-ball” test. The Modified F...

Purpose Both macrophage migration inhibitory factor (MIF) and angiopoietin-2 (Ang-2) have been linked to poor outcomes in cardiogenic shock (CS). These proteins are rapidly released from intracellular storage and have profound effects on the cardiopulmonary vasculature. We describe the changes in plasma MIF and Ang-2 in patients with CS supported with VA ECMO. Methods All patients supported with VA ECMO for CS in our center were enrolled. Blood samples were drawn at the following time points: within 24 hrs of ECMO (baseline), at 72 hours, and on the day of the weaning study (4-12d). MIF and Ang-2 were measured using commercially available ELISA (R&D Systems Inc., Minneapolis, MN). Results Twenty-three ECMO patients were studied. At baseline, both MIF and Ang-2 were significantly elevated compared to controls (n=9) (455±514 vs 1.5±0.7 ng/mL, p<0.001, and 48±75 vs 3.3±0.7 ng/mL, p=0.009). Both MIF and Ang-2 decreased on ECMO (Figure 1). At 72 hours, there was a significant decrease in MIF compared with baseline (74±42 ng/mL, p=0.035). Similarly, Ang-2 levels had significantly decreased by the day of weaning (12±7 ng/mL, p=0.038). Five patients had durable recovery (no pharmacologic or mechanical support at 30d post explant). In these patients, baseline MIF levels were significantly lower than those without durable recovery (113±35 vs 555±547 ng/mL, p=0.004). Conclusion CS is associated with significant derangement of plasma MIF and Ang-2 that improves with circulatory support. Importantly, patients who recovered had lower levels of MIF at presentation. Further study of these mediators may identify novel targets for therapy in cardiogenic shock. Both macrophage migration inhibitory factor (MIF) and angiopoietin-2 (Ang-2) have been linked to poor outcomes in cardiogenic shock (CS). These proteins are rapidly released from intracellular storage and have profound effects on the cardiopulmonary vasculature. We describe the changes in plasma MIF and Ang-2 in patients with CS supported with VA ECMO. All patients supported with VA ECMO for CS in our center were enrolled. Blood samples were drawn at the following time points: within 24 hrs of ECMO (baseline), at 72 hours, and on the day of the weaning study (4-12d). MIF and Ang-2 were measured using commercially available ELISA (R&D Systems Inc., Minneapolis, MN). Twenty-three ECMO patients were studied. At baseline, both MIF and Ang-2 were significantly elevated compared to controls (n=9) (455±514 vs 1.5±0.7 ng/mL, p<0.001, and 48±75 vs 3.3±0.7 ng/mL, p=0.009). Both MIF and Ang-2 decreased on ECMO (Figure 1). At 72 hours, there was a significant decrease in MIF compared with baseline (74±42 ng/mL, p=0.035). Similarly, Ang-2 levels had significantly decreased by the day of weaning (12±7 ng/mL, p=0.038). Five patients had durable recovery (no pharmacologic or mechanical support at 30d post explant). In these patients, baseline MIF levels were significantly lower than those without durable recovery (113±35 vs 555±547 ng/mL, p=0.004). CS is associated with significant derangement of plasma MIF and Ang-2 that improves with circulatory support. Importantly, patients who recovered had lower levels of MIF at presentation. Further study of these mediators may identify novel targets for therapy in cardiogenic shock.