Re-evaluation of single nucleotide variants and identification of structural variants in a cohort of 45 sudden unexplained death cases

Sudden unexplained death (SUD) takes up a considerable part in overall sudden death cases, especially in adolescents and young adults. During the past decade, many channelopathy- and cardiomyopathy-associated single nucleotide variants (SNVs) have been identified in SUD studies by means of postmortem molecular autopsy, yet the number of cases that remain inconclusive is still high. Recent studies had suggested that structural variants (SVs) might play an important role in SUD, but there is no consensus on the impact of SVs on inherited cardiac diseases. In this study, we searched for potentially pathogenic SVs in 244 genes associated with cardiac diseases. Whole-exome sequencing and appropriate data analysis were performed in 45 SUD cases. Re-analysis of the exome data according to the current ACMG guidelines identified 14 pathogenic or likely pathogenic variants in 10 (22.2%) out of the 45 SUD cases, whereof 2 (4.4%) individuals had variants with likely functional effects in the channelopathy-associated genes SCN5A and TRDN and 1 (2.2%) individual in the cardiomyopathy-associated gene DTNA. In addition, 18 structural variants (SVs) were identified in 15 out of the 45 individuals. Two SVs with likely functional impairment were found in the coding regions of PDSS2 and TRPM4 in 2 SUD cases (4.4%). Both were identified as heterozygous deletions, which were confirmed by multiplex ligation-dependent probe amplification. In conclusion, our findings support that SVs could contribute to the pathology of the sudden death event in some of the cases and therefore should be investigated on a routine basis in suspected SUD cases

Spectral element methods for predicting the die-swell of Newtonian and viscoelastic fluids

This thesis is concerned with the development of numerical methods for free surface problems. In particular, the die-swell problem is analyzed for Newtonian and viscoelastic fluids. For several materials comparisons with experiments are presented. The viscoelastic models explored are the Upper Convective Maxwell model, single and multi-mode Oldroyd B and the single and multi-mode eXtended Pom-Pom models. The numerical method employed is based on a spectral element method. The time marching scheme follows a pseudo-transient approach. Discretization in time is performed by means of the Operator-Integration FActor Splitting method of first and second order. The free surface evolves according to an Adams-Bashforth scheme of order three. Comparison with first and second order schemes are also presented for the Newtonian case. The viscoelastic scheme is uncoupled. The fully discretized constitutive equation is solved using a Bi-Conjugate Gradient Stabilized method, while the mass and momentum equations are solved simultaneously by means of the Conjugate Gradient method. Preconditioners are used to accelerate the inversion process. The die-swell of a Newtonian fluid is investigated. The physical interpretation of the phenomenon for Newtonian fluids is also revisited, with the goal of reanalyzing findings from the literature and enrich them by means of specifically addressed numerical simulations. The effect of inertia and surface tension are considered. Analysis of convergence is performed and comparison with available results are presented. Numerical simulations of viscoelastic die-swell are performed for the UCM, Oldroyd-B and XPP models. The effect of elasticity is analyzed through the stress fields, normal stress difference, pressure drops and swelling ratios. For the Oldroyd-B and XPP models, several materials are fully characterized for quantitative comparisons. For the XPP model, the effect of orientation and polydispersity on extrusion is discussed

Degradation of human mRNA transcripts over time as an indicator of the time since deposition (TsD) in biological crime scene traces

Knowledge about the age of a stain, also termed as time since deposition (TsD), would provide law-enforcing authorities with valuable information for the prosecution of criminal offenses. Yet, there is no reliable method for the inference / assessment of TsD available. The aim of this study was to gain further insight into the RNA degradation pattern of forensically relevant body fluids and to find candidate markers for TsD estimation. Blood, menstrual blood, saliva, semen and vaginal secretion samples were exposed to indoor (dark, room temperature) and outdoor (exposed to sun, wind, etc. but protected from rain) conditions for up to 1.5 years. Based on expression and degradation analyses, we were able to identify body fluid specific signatures and RNA degradation patterns. The indoor samples showed a marked drop in RNA integrity after 6 months, while the outdoor samples were difficult to interpret and therefore excluded for some of the analyses. Up to 4 weeks, indoor samples showed more stable and less degrading transcripts than outdoor samples. Stable transcripts tended to be significantly shorter than degrading ones or transcripts, which are neither degrading nor stable. We reinforced the body fluid specific and the housekeeping gene nature of previously reported markers. With an unbiased approach, we selected stable and degrading genes for each body fluid in the short term and assessed their integrity during extended storage. We identified several stable and degrading gene transcripts, which could be tested in a targeted assay to assess the TsD interval e.g. by analyzing the ratio of degrading vs stable transcripts. In conclusion, we were able to detect RNA degradation patterns in samples being aged up to 1.5 years and identified several candidate markers, which could be evaluated for TsD estimation

Potential use in the treatment of inflammatory disorders and obesity of selected wild edible plants from Calabria region (Southern Italy)

Abstract The potential role of plants and their metabolites has been recently considered in the search for new well-tolerated anti-arthritic and anti-obesity drugs. This study was designed to assess the potential effectiveness of the methanolic extracts from four wild edible species from Southern Italy, Asparagus officinalis L., Bellis perennis L., Daucus carota L. and Sambucus nigra L. All these plants have a history as anti-rheumatic or anti-arthritic remedies. The chemical constituents were identified through GC–MS and HPTLC analyses and the in vitro antioxidant activity was determined by means of DPPH, ABTS, FRAP-Ferrozine and β-carotene bleaching tests. To assess the anti-inflammatory and anti-arthritic potentials, the capacity to inhibit nitric oxide production in murine macrophage RAW 264.7 cells and protein denaturation was measured. The anti-obesity potential was determined by evaluating the ability of the sample to inhibit pancreatic lipase, a key enzyme for dietary fats absorption. The raw extract of D. carota showed the best inhibitory activity on NO production (IC50 = 45.1 ± 1.0 μg/mL), followed by B. perennis and A. officinalis (IC50 equal to 193.1 ± 3.2 μg/mL and 506.3 ± 5.1 μg/mL, respectively). D. carota induced also inhibitory effects against the heat-induced denaturation of bovine serum albumin (IC50 = 878.7 ± 19.09 μg/mL) and the best lipase inhibitory potential (IC50 = 1.63 ± 0.07 mg/mL). Our findings suggest that this species could be a potential effective therapeutic agent to treat inflammation and arthritis, supporting the traditional popular use of this plant

Agent-oriented Modeling and Simulation of IoT Networks

Internet of Things (IOT) networks are being continually developed in several domains, however no systematic processes for their modeling and simulation exist so far. In this paper, an agent-oriented approach to IoT networks modeling is proposed by exploiting the ACOSO model. Then, agent-modelled IOT networks of different scales are simulated through the Omnet++ simulation platform, with the goal of analyzing issues and bottlenecks at communication level

Analysis of Open Source Software Development Iterations by Means of Burst Detection Techniques

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Assessing time dependent changes in microbial composition of biological crime scene traces using microbial RNA markers

Current body fluid identification methods do not reveal any information about the time since deposition (TsD) of biological traces, even though determining the age of traces could be crucial for the investigative process. To determine the utility of microbial RNA markers for TsD estimation, we examined RNA sequencing data from five forensically relevant body fluids (blood, menstrual blood, saliva, semen, and vaginal secretion) over seven time points, ranging from fresh to 1.5 years. One set of samples was stored indoors while another was exposed to outdoor conditions. In outdoor samples, we observed a consistent compositional shift, occurring after 4 weeks: this shift was characterized by an overall increase in non-human eukaryotic RNA and an overall decrease in prokaryotic RNA. In depth analyses showed a high fraction of tree, grass and fungal signatures, which are characteristic for the environment the samples were exposed to. When examining the prokaryotic fraction in more detail, three bacterial phyla were found to exhibit the largest changes in abundance, namely Actinobacteria, Proteobacteria and Firmicutes. More detailed analyses at the order level were done using a Lasso regression analysis to find a predictive subset of bacterial taxa. We found 26 bacterial orders to be indicative of sample age. Indoor samples did not reveal such a clear compositional change at the domain level: eukaryotic and prokaryotic abundance remained relatively stable across the assessed time period. Nonetheless, a Lasso regression analysis identified 32 bacterial orders exhibiting clear changes over time, enabling the prediction of TsD. For both indoor and outdoor samples, a larger number (around 60%) of the bacterial orders identified as indicative of TsD are part of the Actinobacteria, Proteobacteria and Firmicutes. In summary, we found that the observed changes across time are not primarily due to changes associated with body fluid specific bacteria but mostly due to accumulation of bacteria from the environment. Orders of these environmental bacteria could be evaluated for TsD prediction, considering the location and environment of the crime scene. However, further studies are needed to verify these findings, determine the applicability across samples, replicates, donors, and other variables, and also to further assess the effect of different seasons and locations on the samples

Severe bloodstream infection due to KPC-producer e coli in a renal transplant recipient treated with the double-carbapenem regimen and analysis of in vitro synergy testing a case report

Transplant recipients are at high risk of infections caused by multidrug resistant microorganisms. Due to the limited thera- peutic options, innovative antimicrobial combinations against carbape- nem-resistant Enterobacteriaceae causing severe infections are necessary. A 61-year-old woman with a history of congenital solitary kidney underwent renal transplantation. The postoperative course was compli- cated by nosocomial pneumonia due to Stenotrophomonas maltophilia and pan-sensitive Escherichia coli, successfully treated with antimicrobial therapy. On postoperative day 22, diagnosis of surgical site infection and nosocomial pneumonia with concomitant bacteremia due to a Kle- bisella pneumoniae carbapenemase-producer E coli was made. The patient was treated with the double-carbapenem regimen (high dose of merope- nem plus ertapenem) and a potent synergistic and bactericidal activity of this un-conventional therapeutic strategy was observed in vitro. Despite a microbiological response with prompt negativity of blood cultures, the patient faced a worse outcome because of severe hemorrhagic shock. The double-carbapenem regimen might be considered as a rescue therapy in those subjects, including transplant recipients, in whom previous antimicrobial combinations failed or when colistin use might be discouraged. Performing in vitro synergy testing should be strongly encouraged in cases of infections caused by pan-drug resistant strains, especially in high-risk patients

Gram-negative septic thrombosis in critically ill patients: A retrospective case-control study

Background: Data on septic thrombosis caused by Gram-negative bacilli (GN-ST) in intensive care unit (ICU) patients are currently limited. Methods: The aim of this retrospective case–control study (matched 1:3) performed over a 15-month period on ICU patients with bacteraemia, associated (cases) or not (controls) with GN-ST, was to assess 30-day mortality and clinical/microbiological features of GN-ST. Results: During the study period, 16 patients with GN-ST and 48 controls were analyzed. Polytrauma was the cause of ICU admission in 12 (75%) cases and 22 (46%) controls (p = 0.019). In no case of septic thrombosis was surgical debridement performed. The site of venous thrombosis was more frequently in the lower limbs, associated with bone fracture in nine out of 12 (75%) cases. The median duration of bacteraemia (22 days vs 1 day; p 72 h was significantly associated with GN-ST (area under the curve (AUC) 0.95, sensitivity 0.996 and specificity 0.810; p < 0.001). Finally, 30-day mortality was 20% in cases and 67% in controls (p < 0.001). Conclusions: Critically ill patients with GN-ST showed specific clinical features. Despite delayed bacteraemia clearance, targeted antibiotic therapy plus anticoagulation usually provided clinical improvement and a low 30-day mortality rate

Dark current spectroscopy of transition metals in CMOS image sensors

We have investigated the effects of deliberate heavymetals contamination on dark current and image defects in CMOS Image Sensors (CIS). Analysis of dark current in these imager dice has revealed different behaviors among most important 3d metals present in the process line. We have implanted directly in 3 Mega array pixels the following metals: Cr, V, Cu, Ni, Fe, Ti, Mo, W, Al and Zn. Analyzing the dark current "spectrum" as obtained for fixed integration periods of time by means of standard image-Testing equipment, these impurities can be identified and detected with a sensitivity of ∼ 109 traps/cm3 or higher