pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

Cancer immunotherapy has gained significant momentum from recent clinical successes of checkpoint blockade inhibition. Massively parallel sequence analysis suggests a connection between mutational load and response to this class of therapy. Methods to identify which tumor-specific mutant peptides (neoantigens) can elicit anti-tumor T cell immunity are needed to improve predictions of checkpoint therapy response and to identify targets for vaccines and adoptive T cell therapies. Here, we present a flexible, streamlined computational workflow for identification of personalized Variant Antigens by Cancer Sequencing (pVAC-Seq) that integrates tumor mutation and expression data (DNA- and RNA-Seq). pVAC-Seq is available a

Life cycle inventory data for the Italian agri-food sector: background, sources and methodological aspects

AbstractPurposeFor the development of any life cycle assessment study, the practitioner frequently integrates primary data collected on-field, with background data taken from various life cycle inventory databases which are part of most commercial LCA software packages. However, such data is often not generally applicable to all product systems since, especially concerning the agri-food sector, available datasets may not be fully representative of the site specificity of the food product under examination. In this context, the present work investigates the background, sources and methodological aspects that characterise the most known commercial databases containing agri-food data, with a focus on four agri-food supply chains (olive oil, wine, wheat products and citrus fruit), which represent an important asset for the Italian food sector.MethodsSpecifically, the paper entails a review of currently available LCI databases and their datasets with a twofold scope: firstly, to understand how agri-food data is modelled in these databases for a coherent and consistent representation of regional scenarios and to verify whether they are also suitable for the Italian context and, secondly, to identify and analyse useful and relevant methodological approaches implemented in the existing LCI databases when regional data are modelled.ResultsBased on the aforementioned review, it is possible to highlight some problems which may arise when developing an LCI pertaining to the four Italian agri-food supply chains, namely:1. The need for specific inventory datasets to tackle the specificities of agri-food product systems.2. The lack of datasets, within the existing DBs, related to the Italian context and to the abovementioned supply chains. In fact, at present, in the currently available LCI DBs, there are very few (or in some cases none) datasets related to Italian wine, olive oil, wheat-based products and citrus fruit. The few available datasets often contain some data related to the Italian context but also approximate data with that of product systems representing other countries.Furthermore, the present study allowed to identify and discuss the main aspects to be used as starting elements for modelling regional data to be included in a future Italian LCI database of the abovementioned four supply chains.ConclusionsThe results of the present study represent a starting point for the collection of data and its organisation, in order to develop an Italian LCI agri-food database with datasets which are representative of the regional specificities of four agri-food supply chains which play an important role in the Italian economy

Life cycle inventory data for the Italian agri-food sector: background, sources and methodological aspects

Purpose: For the development of any life cycle assessment study, the practitioner frequently integrates primary data collected on-field, with background data taken from various life cycle inventory databases which are part of most commercial LCA software packages. However, such data is often not generally applicable to all product systems since, especially concerning the agri-food sector, available datasets may not be fully representative of the site specificity of the food product under examination. In this context, the present work investigates the background, sources and methodological aspects that characterise the most known commercial databases containing agri-food data, with a focus on four agri-food supply chains (olive oil, wine, wheat products and citrus fruit), which represent an important asset for the Italian food sector. Methods: Specifically, the paper entails a review of currently available LCI databases and their datasets with a twofold scope: firstly, to understand how agri-food data is modelled in these databases for a coherent and consistent representation of regional scenarios and to verify whether they are also suitable for the Italian context and, secondly, to identify and analyse useful and relevant methodological approaches implemented in the existing LCI databases when regional data are modelled. Results: Based on the aforementioned review, it is possible to highlight some problems which may arise when developing an LCI pertaining to the four Italian agri-food supply chains, namely: 1. The need for specific inventory datasets to tackle the specificities of agri-food product systems. 2. The lack of datasets, within the existing DBs, related to the Italian context and to the abovementioned supply chains. In fact, at present, in the currently available LCI DBs, there are very few (or in some cases none) datasets related to Italian wine, olive oil, wheat-based products and citrus fruit. The few available datasets often contain some data related to the Italian context but also approximate data with that of product systems representing other countries. Furthermore, the present study allowed to identify and discuss the main aspects to be used as starting elements for modelling regional data to be included in a future Italian LCI database of the abovementioned four supply chains. Conclusions: The results of the present study represent a starting point for the collection of data and its organisation, in order to develop an Italian LCI agri-food database with datasets which are representative of the regional specificities of four agri-food supply chains which play an important role in the Italian economy

Laser-tissue photothermal interaction: a thermal infrared imaging study

A 2-D approach, based on Infrared (IR) imaging for monitoring and optimizing the photo-therapy in dermatology, is proposed. We studied the possibility to employ IR imaging in order to select the laser treatment parameters for each patient. A Pulsed Thermography (PT) model allowed to evaluate morphological information on the specific area to treat after a single laser pulse test. The data were elaborated through a 2-D numerical simulation, which described the tissue temperature profiles for different sets of laser parameters. Based on this approach, it was possible to select the laser parameters according to specific pathology, morphology and phototype in order to achieve the best performances in the phototherapy practice

Italian multicenter study on infection hazards during dental practice: control of environmental microbial contamination in public dental surgeries.

BACKGROUND: The present study assessed microbial contamination in Italian dental surgeries. METHODS: An evaluation of water, air and surface microbial contamination in 102 dental units was carried out in eight Italian cities. RESULTS: The findings showed water microbial contamination in all the dental surgeries; the proportion of water samples with microbial levels above those recommended decreased during working. With regard to Legionella spp., the proportion of positive samples was 33.3%. During work activity, the index of microbial air contamination (IMA) increased. The level of microbial accumulation on examined surfaces did not change over time. CONCLUSION: These findings confirm that some Italian dental surgeries show high biocontamination, as in other European Countries, which highlights the risk of occupational exposure and the need to apply effective measures to reduce microbial loads

Volterra Distortions, Spinning Strings, and Cosmic Defects

Cosmic strings, as topological spacetime defects, show striking resemblance to defects in solid continua: distortions, which can be classified into disclinations and dislocations, are line-like defects characterized by a delta function-valued curvature and torsion distribution giving rise to rotational and translational holonomy. We exploit this analogy and investigate how distortions can be adapted in a systematic manner from solid state systems to Einstein-Cartan gravity. As distortions are efficiently described within the framework of a SO(3) {\rlap{\supset}\times}} T(3) gauge theory of solid continua with line defects, we are led in a straightforward way to a Poincar\'e gauge approach to gravity which is a natural framework for introducing the notion of distorted spacetimes. Constructing all ten possible distorted spacetimes, we recover, inter alia, the well-known exterior spacetime of a spin-polarized cosmic string as a special case of such a geometry. In a second step, we search for matter distributions which, in Einstein-Cartan gravity, act as sources of distorted spacetimes. The resulting solutions, appropriately matched to the distorted vacua, are cylindrically symmetric and are interpreted as spin-polarized cosmic strings and cosmic dislocations.Comment: 24 pages, LaTeX, 9 eps figures; remarks on energy conditions added, discussion extended, version to be published in Class. Quantum Gra

Extended search for supernovalike neutrinos in NOvA coincident with LIGO/Virgo detections

A search is performed for supernovalike neutrino interactions coincident with 76 gravitational wave events detected by the LIGO/Virgo Collaboration. For 40 of these events, full readout of the time around the gravitational wave is available from the NOvA Far Detector. For these events, we set limits on the fluence of the sum of all neutrino flavors of F29(50) kpc at 90% C.L. Weaker limits are set for other gravitational wave events with partial Far Detector data and/or Near Detector data

Laser-Induced, Green and Biocompatible Paper-Based Devices for Circular Electronics

The growing usage and consumption of electronics-integrated items into the daily routine has raised concerns on the disposal and proper recycling of these components. Here, a fully sustainable and green technology for the fabrication of different electronics on fruit-waste derived paper substrate, is reported. The process relies on the carbonization of the topmost surface of different cellulose-based substrates, derived from apple-, kiwi-, and grape-based processes, by a CO2 laser. By optimizing the lasing parameters, electronic devices, such as capacitors, biosensors, and electrodes for food monitoring as well as heart and respiration activity analysis, are realized. Biocompatibility tests on fruit-based cellulose reveal no shortcoming for on-skin applications. The employment of such natural and plastic-free substrate allows twofold strategies for electronics recycling. As a first approach, device dissolution is achieved at room temperature within 40 days, revealing transient behavior in natural solution and leaving no harmful residuals. Alternatively, the cellulose-based electronics is reintroduced in nature, as possible support for plant seeding and growth or even soil amendment. These results demonstrate the realization of green, low-cost and circular electronics, with possible applications in smart agriculture and the Internet-of-Thing, with no waste creation and zero or even positive impact on the ecosystem

Sequential valproic acid/all-trans retinoic acid treatment reprograms differentiation in refractory and high risk acute myeloid leukemia.

Epigenetic alterations of chromatin due to aberrant histone deacetylase (HDAC) activity and transcriptional silencing of all-trans retinoic acid (ATRA) pathway are events linked to the pathogenesis of acute myeloid leukemia (AML) that can be targeted by specific treatments. A pilot study was carried out in eight refractory or high-risk AML patients not eligible for intensive therapy to assess the biological and therapeutic activities of the HDAC inhibitor valproic acid (VPA) used to remodel chromatin, followed by the addition of ATRA, to activate gene transcription and differentiation in leukemic cells. Hyperacetylation of histones H3 and H4 was detectable at therapeutic VPA serum levels (>or=50 microg/mL) in blood mononuclear cells from seven of eight patients. This correlated with myelomonocytic differentiation of leukemic cells as revealed by morphologic, cytochemical, immunophenotypic, and gene expression analyses. Differentiation of the leukemic clone was proven by fluorescence in situ hybridization analysis showing the cytogenetic lesion +8 or 7q- in differentiating cells. Hematologic improvement, according to established criteria for myelodysplastic syndromes, was observed in two cases. Stable disease and disease progression were observed in five and one cases, respectively. In conclusion, VPA-ATRA treatment is well tolerated and induces phenotypic changes of AML blasts through chromatin remodeling. Further studies are needed to evaluate whether VPA-ATRA treatment by reprogramming differentiation of the leukemic clone might improve the response to chemotherapy in leukemia patients