Comparative survey of the relative impact of mRNA features on local ribosome profiling read density

Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise. We illustrate how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally. We show that a few parameters extracted with RUST are sufficient for predicting experimental densities with high accuracy. Importantly the application of RUST to 30 publicly available Ribo-seq data sets revealed a substantial variation in sequence determinants of ribosome footprint frequencies, questioning the reliability of Ribo-seq as an accurate representation of local ribosome densities without prior quality control. This emphasizes our incomplete understanding of how protocol parameters affect ribosome footprint densities.

Impact of single parameter changes on Ceph cloud storage performance

In a general purpose cloud system efficiencies are yet to be had from supporting diverse applications and their requirements within a storage system used for a private cloud. Supporting such diverse requirements poses a significant challenge in a storage system that supports fine grained configuration on a variety of parameters. This paper uses the Ceph distributed file system, and in particular its global parameters, to show how a single changed parameter can effect the performance for a range of access patterns when tested with an OpenStack cloud system.

Multi-objective optimization of material model parameters of an adhesive layer by using SPEA2

The usage of multi material structures in industry, especially in the automotive industry are increasing. To overcome the difficulties in joining these structures, adhesives have several benefits over traditional joining methods. Therefore, accurate simulations of the entire process of fracture including the adhesive layer is crucial. In this paper, material parameters of a previously developed meso mechanical finite element (FE) model of a thin adhesive layer are optimized using the Strength Pareto Evolutionary Algorithm (SPEA2). Objective functions are defined as the error between experimental data and simulation data. The experimental data is provided by previously performed experiments where an adhesive layer was loaded in monotonically increasing peel and shear. Two objective functions are dependent on 9 model parameters (decision variables) in total and are evaluated by running two FEsimulations, one is loading the adhesive layer in peel and the other in shear. The original study converted the two objective functions into one function that resulted in one optimal solution. In this study, however, a Pareto frontis obtained by employing the SPEA2 algorithm. Thus, more insight into the material model, objective functions, optimal solutions and decision space is acquired using the Pareto front. We compare the results and show good agreement with the experimental data.

Evaluation of the impact of nursing clinics in the rheumatology services

Nursing clinics in rheumatology (NCRs) are organisational care models that provide care centred within the scope of a nurse’s abilities. To analyse the impact of NCR in the rheumatology services, national multicenter observational prospective cohort studied 1-year follow-up, comparing patients attending rheumatology services with and without NCR. NCR was defined by the presence of: (1) office itself; (2) at least one dedicated nurse; and (3) its own appointment schedule. Variables included were (baseline, 6 and 12 months): (a) test to evaluate clinical activity of the disease, research and training, infrastructure of unit and resources of NCR and (b) tests to evaluate socio-demographics, work productivity (WPAI), use of services and treatments and quality of life. A total of 393 rheumatoid arthritis and ankylosing spondylitis patients were included: 181 NCR and 212 not NCR, corresponding to 39 units, 21 with NCR and 18 without NCR (age 53 + 11.8 vs 56 + 13.5 years). Statistically significant differences were found in patients attended in sites without NCR, at some of the visits (baseline, 6 or 12 months), for the following parameters: higher CRP level (5.9 mg/l ± 8.3 vs 4.8 mg/l ± 7.8; p < 0.005), global disease evaluation by the patient (3.6 ± 2.3 vs 3.1 ± 2.4), physician (2.9 ± 2.1 vs 2.3 ± 2.1; p < 0.05), use of primary care consultations (2.7 ± 5.4 vs 1.4 ± 2.3; p < 0.001) and worse work productivity. The presence of NCR in the rheumatology services contributes to improve some clinical outcomes, a lower frequency of primary care consultations and better work productivity of patients with rheumatic diseases.

Impact of salt reduction on biogenic amines, fatty acids, microbiota, texture and sensory profile in traditional blood dry-cured sausages

Meat industry needs to reduce salt in their products due to health issues. The present study evaluated the effect of salt reduction from 6% to 3% in two Portuguese traditional blood dry-cured sausages. Physicochemical and microbiological parameters, biogenic amines, fatty acids and texture profiles and sensory panel evaluations were considered. Differences due to salt reduction were perceptible in a faint decline of water activity, which slightly favoured microbial growth. Total biogenic amines content ranged from 88.86 to 796.68 mg kg 1 fresh matter, with higher amounts, particularly of cadaverine, histamine and tyramine, in low-salt products. Still, histamine and other vasoactive amines remained at low levels, thus not affecting consumers’ health. Regarding fatty acids, no significant differences were observed due to salt. However, texture profile analysis revealed lower resilience and cohesiveness in low-salt products, although no textural changes were observed by the sensory panel. Nevertheless, low-salt sausages were clearly preferred by panellists.

A non-ordinary state-based peridynamics formulation for thermoplastic fracture

In this study, a three-dimensional (3D) non-ordinary state-based peridynamics (NOSB-PD) formulation for thermomechanical brittle and ductile fracture is presented. The Johnson–Cook (JC) constitutive and damage model is used to taken into account plastic hardening, thermal softening and fracture. The for- mulation is validated by considering two benchmark examples: 1) The Taylor-bar impact and 2) the Kalthoff– Winkler tests. The results show good agreements between the numerical simulations and the experimental results.

Sensitivity analysis of parameters of a photovoltaic cell under different condition

A photovoltaic cell is a component which converts light energy into electrical energy. Different environmental parameters and internal parameters have a great impact on the output of the photovoltaic cell. To identify its characteristics and estimate the output, the well known Shockley diode equation is used. This equation contains all the parameters, as one environmental and different internal. The properties of these parameters were studied and their sensitivity have been analyzed through the use of an error function; this error function allows the study of the behaviour of the parameters and their characteristics against the output of the photovoltaic cell through the analysis of its curves giving the sensitivity of the different parameters to the output of the photovoltaic cell. Using these results the impact of the parameters of the photovoltaic cell has been clearly identified. White noise is included both with the ideal values and the simulation and the ideal value is imposed to get the real time environment flavor. This work analyses both systems with and without white noise.

Fracture Toughening and Self-Healing of Composite Laminates by Nanofibrous Mats Interleaving

Composite laminates present important advantages compared to conventional monolithic materials, mainly because for equal stiffness and strength they have a weight up to four times lower. However, due to their ply-by-ply nature, they are susceptible to delamination, whose propagation can bring the structure to a rapid catastrophic failure. In this thesis, in order to increase the service life of composite materials, two different approaches were explored: increase the intrinsic resistance of the material or confer to them the capability of self-repair. The delamination has been hindered through interleaving the composite laminates with polymeric nanofibers, which completed the hierarchical reinforcement scale of the composite. The manufacturing process for the integration of the nanofibrous mat in the laminate was optimized, resulting in an enhancement of mode I fracture toughness up to 250%. The effect of the geometrical dimensions of the nano-reinforcement on the architecture of the micro one (UD and woven laminates) was studied on mode I and II. Moreover, different polymeric materials were employed as nanofibrous reinforcement (Nylon 66 and polyvinylidene fluoride). The nano toughening mechanism was studied by micrograph analysis of the crack path and SEM analysis of the fracture surface. The fatigue behavior to the onset of the delamination and the crack growth rate for woven laminates interleaved with Nylon 66 nanofibers was investigated. Furthermore, the impact behavior of GLARE aluminum-glass epoxy laminates, toughened with Nylon 66 nanofibers was investigated. Finally, the possibility of confer to the composite material the capability of self-repair was explored. An extrinsic self-healing-system, based on core-shell nanofibers filled with a two-component epoxy system, was developed by co-electrospinning technique. The healing potential of the nano vascular system has been proved by microscope electron observation of the healing agent release as result of the vessels rupture and the crosslinking reaction was verified by thermal analysis.

The foodomics approach to investigate the impact of the matrix structure on food quality: applications of magnetic resonance spectroscopy, relaxometry and imaging

The aim of this thesis is to explore the possible influence of the food matrix on food quality attributes. Using nuclear magnetic resonance techniques, the matrix-dependent properties of different foods were studied and some useful indices were defined to classify food products based on the matrix behaviour when responding to processing phenomena. Correlations were found between fish freshness indices, assessed by certain geometric parameters linked to the morphology of the animal, i.e. a macroscopic structure, and the degradation of the product structure. The same foodomics approach was also applied to explore the protective effect of modified atmospheres on the stability of fish fillets, which are typically susceptible to oxidation of the polyunsaturated fatty acids incorporated in the meat matrix. Here, freshness is assessed by evaluating the time-dependent change in the fish metabolome, providing an established freshness index, and its relationship to lipid oxidation. In vitro digestion studies, focusing on food products with different matrixes, alone and in combination with other meal components (e.g. seasoning), were conducted to investigate possible interactions between enzymes and food, modulated by matrix structure, which influence digestibility. The interaction between water and the gelatinous matrix of the food, consisting of a network of protein gels incorporating fat droplets, was also studied by means of nuclear magnetic relaxometry, in order to create a prediction tool for the correct classification of authentic and counterfeit food products protected by a quality label. This is one of the first applications of an NMR method focusing on the supramolecular structure of the matrix, rather than the chemical composition, to assess food authenticity. The effect of innovative processing technologies, such as PEF applied to fruit products, has been assessed by magnetic resonance imaging, exploiting information associated with the rehydration kinetics exerted by a modified food structure.

Modelling of ORC components and systems for low-medium temperature heat recovery applications with reduced environmental impact

Although its great potential as low to medium temperature waste heat recovery (WHR) solution, the ORC technology presents open challenges that still prevent its diffusion in the market, which are different depending on the application and the size at stake. Focusing on the micro range power size and low temperature heat sources, the ORC technology is still not mature due to the lack of appropriate machines and working fluids. Considering instead the medium to large size, the technology is already available but the investment is still risky. The intention of this thesis is to address some of the topical themes in the ORC field, paying special attention in the development of reliable models based on realistic data and accounting for the off-design performance of the ORC system and of each of its components. Concerning the “Micro-generation” application, this work: i) explores the modelling methodology, the performance and the optimal parameters of reciprocating piston expanders; ii) investigates the performance of such expander and of the whole micro-ORC system when using Hydrofluorocarbons as working fluid or their new low GWP alternatives and mixtures; iii) analyzes the innovative ORC reversible architecture (conceived for the energy storage), its optimal regulation strategy and its potential when inserted in typical small industrial frameworks. Regarding the “Industrial WHR” sector, this thesis examines the WHR opportunity of ORCs, with a focus on the natural gas compressor stations application. This work provides information about all the possible parameters that can influence the optimal sizing, the performance and thus the feasibility of installing an ORC system. New WHR configurations are explored: i) a first one, relying on the replacement of a compressor prime mover with an ORC; ii) a second one, which consists in the use of a supercritical CO2 cycle as heat recovery system.

Monitoring of New Psychoactive Substances in the hair of patients with a history of addiction. Evaluation of the public health impact.

Introduction. The term New Psychoactive Substances (NPS) encompasses a broad category of drugs which have become available on the market in recent years and whose illicit use for recreational purposes has recently exploded. The analysis of NPS usually requires mass spectrometry based techniques. The aim of our study was to define the preva-lence of NPS consumption in patients with a history of drug addiction followed by Public Services for Pathological Addictions, with the purpose of highlighting the effective presence of NPS within the area of Bologna and evaluating their association with classical drugs of abuse (DOA). Materials and methods. Sustained by literature, a multi-analyte UHPLC-MS/MS method for the identification of 127 NPS (phenethylamines, arylcyclohexylamines, synthetic opioids, tryptamines, synthetic cannabinoids, synthetic cathinones, designer benzodiazepines) and 15 classic drugs of abuse (DOA) in hair samples was developed and validated according to International Guidelines [112]. Samples pretreatment consisted of washing steps and overnight incubation at 45°C in an acid mixture of methanol and water. After cooling, supernatant were injected into the chromatographic system coupled with a tandem mass spectrometry detector. Results. Successful validation was achieved for almost all of the compounds. The method met all the required technical parameters. LOQ was set from 4 to 80 pg/mg The developed method was applied to 107 cases (85 males and 22 females) of clinical interest. Out of 85 hair samples resulting positive to classical drugs of abuse, NPS were found in twelve (8 male and 4 female). Conclusion. The present methodology represents an easy, low cost, wide-panel method for the de-tection of 127 NPS and 15 DOA in hair samples. Such multi-analyte methods facilitates the study of the prevalence of drugs abused that will enable the competent control authorities to obtain evi-dence-based reports regarding the critical spread of the threat represented by NPS.

Development of a relationship between physical parameters of tsunami waves and tsunami intensity based on macroscopic effects and its application to the Italian tsunami database

Tsunamis are rare events. However, their impact can be devastating and it may extend to large geographical areas. For low-probability high-impact events like tsunamis, it is crucial to implement all possible actions to mitigate the risk. The tsunami hazard assessment is the result of a scientific process that integrates traditional geological methods, numerical modelling and the analysis of tsunami sources and historical records. For this reason, analysing past events and understanding how they interacted with the land is the only way to inform tsunami source and propagation models, and quantitatively test forecast models like hazard analyses. The primary objective of this thesis is to establish an explicit relationship between the macroscopic intensity, derived from historical descriptions, and the quantitative physical parameters measuring tsunami waves. This is done first by defining an approximate estimation method based on a simplified 1D physical onshore propagation model to convert the available observations into one reference physical metric. Wave height at the coast was chosen as the reference due to its stability and independence of inland effects. This method was then implemented for a set of well-known past events to build a homogeneous dataset with both macroseismic intensity and wave height. By performing an orthogonal regression, a direct and invertible empirical relationship could be established between the two parameters, accounting for their relevant uncertainties. The target relationship is extensively tested and finally applied to the Italian Tsunami Effect Database (ITED), providing a homogeneous estimation of the wave height for all existing tsunami observations in Italy. This provides the opportunity for meaningful comparison for models and simulations, as well as quantitatively testing tsunami hazard models for the Italian coasts and informing tsunami risk management initiatives.

The Clinical Impact Of Cerebellar Grey Matter Pathology In Multiple Sclerosis.

The cerebellum is an important site for cortical demyelination in multiple sclerosis, but the functional significance of this finding is not fully understood. To evaluate the clinical and cognitive impact of cerebellar grey-matter pathology in multiple sclerosis patients. Forty-two relapsing-remitting multiple sclerosis patients and 30 controls underwent clinical assessment including the Multiple Sclerosis Functional Composite, Expanded Disability Status Scale (EDSS) and cerebellar functional system (FS) score, and cognitive evaluation, including the Paced Auditory Serial Addition Test (PASAT) and the Symbol-Digit Modalities Test (SDMT). Magnetic resonance imaging was performed with a 3T scanner and variables of interest were: brain white-matter and cortical lesion load, cerebellar intracortical and leukocortical lesion volumes, and brain cortical and cerebellar white-matter and grey-matter volumes. After multivariate analysis high burden of cerebellar intracortical lesions was the only predictor for the EDSS (p<0.001), cerebellar FS (p = 0.002), arm function (p = 0.049), and for leg function (p<0.001). Patients with high burden of cerebellar leukocortical lesions had lower PASAT scores (p = 0.013), while patients with greater volumes of cerebellar intracortical lesions had worse SDMT scores (p = 0.015). Cerebellar grey-matter pathology is widely present and contributes to clinical dysfunction in relapsing-remitting multiple sclerosis patients, independently of brain grey-matter damage.

Beam-energy Dependence Of The Directed Flow Of Protons, Antiprotons, And Pions In Au+au Collisions.

Rapidity-odd directed flow (v1) measurements for charged pions, protons, and antiprotons near midrapidity (y=0) are reported in sNN=7.7, 11.5, 19.6, 27, 39, 62.4, and 200 GeV Au+Au collisions as recorded by the STAR detector at the Relativistic Heavy Ion Collider. At intermediate impact parameters, the proton and net-proton slope parameter dv1/dy|y=0 shows a minimum between 11.5 and 19.6 GeV. In addition, the net-proton dv1/dy|y=0 changes sign twice between 7.7 and 39 GeV. The proton and net-proton results qualitatively resemble predictions of a hydrodynamic model with a first-order phase transition from hadronic matter to deconfined matter, and differ from hadronic transport calculations.

Mechanisms Predisposing Penile Fracture And Long-term Outcomes On Erectile And Voiding Functions.

Purpose. To determine the mechanisms predisposing penile fracture as well as the rate of long-term penile deformity and erectile and voiding functions. Methods. All fractures were repaired on an emergency basis via subcoronal incision and absorbable suture with simultaneous repair of eventual urethral lesion. Patients' status before fracture and voiding and erectile functions at long term were assessed by periodic follow-up and phone call. Detailed history included cause, symptoms, and single-question self-report of erectile and voiding functions. Results. Among the 44 suspicious cases, 42 (95.4%) were confirmed, mean age was 34.5 years (range: 18-60), mean follow-up 59.3 months (range 9-155). Half presented the classical triad of audible crack, detumescence, and pain. Heterosexual intercourse was the most common cause (28 patients, 66.7%), followed by penile manipulation (6 patients, 14.3%), and homosexual intercourse (4 patients, 9.5%). Woman on top was the most common heterosexual position (n = 14, 50%), followed by doggy style (n = 8, 28.6%). Four patients (9.5%) maintained the cause unclear. Six (14.3%) patients had urethral injury and two (4.8%) had erectile dysfunction, treated by penile prosthesis and PDE-5i. No patient showed urethral fistula, voiding deterioration, penile nodule/curve or pain. Conclusions. Woman on top was the potentially riskiest sexual position (50%). Immediate surgical treatment warrants long-term very low morbidity.