Testing for equivalence: an intersection-union permutation solution

The notion of testing for equivalence of two treatments is widely used in clinical trials, pharmaceutical experiments,bioequivalence and quality control. It is essentially approached within the intersection-union (IU) principle. According to this principle the null hypothesis is stated as the set of effects lying outside a suitably established interval and the alternative as the set of effects lying inside that interval. The solutions provided in the literature are mostly based on likelihood techniques, which in turn are rather difficult to handle, except for cases lying within the regular exponential family and the invariance principle. The main goal of present paper is to go beyond most of the limitations of likelihood based methods, i.e. to work in a nonparametric setting within the permutation frame. To obtain practical solutions, a new IU permutation test is presented and discussed. A simple simulation study for evaluating its main properties, and three application examples are also presented.Comment: 21 pages, 2 figure

Treatment of a Severe Pediatric Lyell Syndrome with Amniotic Membrane: Case Report and Histological Findings

Background: Lyell Syndrome (TEN, Toxic epidermal necrolysis) represents a medical emergency particularly in pediatric patients in whom the massive skin damage can quickly lead to multi-organ dysfunction and death. Prompt restoration of the physiologic mucosal/cutaneous barrier is mandatory. The use of amniotic membranes has been described in the treatment of ophthalmic Lyell Syndrome, but its use has not yet been adopted for the management of larger cutaneous wounds. Study Hypothesis: Here we report the use of amniotic membranes in a pediatric case of severe Lyell Syndrome with complete skin surface, ocular and mucosal involvement with life threating presentation. Methods: A 7-year old female was admitted to our Burn Centre for severe cutaneous/mucosal exfoliation (100% Total body surface area, TBSA) as a result of an adverse reaction to ibuprofen administration. Supportive fluid administration, cardiac-pulmonary assistance and pain management were complemented by serial grafting of amniotic membranes on all affected areas to provide coverage of the exfoliated skin/mucosa. Biopsies were obtained to monitor histological skin changes. Results: The patient showed an excellent response to amniotic membrane treatment, with rapid restoration of mucosal and cutaneous layers in the grafted areas. This resulted in a decreased need for dressing changes, avoidance of additional surgeries and a reduced dependence on supportive therapy. Lower pain levels than usually expected led to a reduced need for narcotic pain medications and allowed for early physical rehabilitation and a short hospital stay. Histology confirmed evidence of topical immune-modulation in treated areas (reduction of inflammatory infiltrate). Conclusion: As we tested in numerously TEN and burn pediatric injuries Amniotic membranes with their regenerative and immune-modulatory effects may represent an life saving treatment even in the worst cases of pediatric Lyell syndrome

Heterogeneity in regional notification patterns and its impact on aggregate national case notification data: the example of measles in Italy

BACKGROUND: A monthly time series of measles case notifications exists for Italy from 1949 onwards, although its usefulness is seriously undermined by extensive under-reporting which varies strikingly between regions, giving rise to the possibility of significant distortions in epidemic patterns seen in aggregated national data. RESULTS: A corrected national time series is calculated using an algorithm based upon the approximate equality between births and measles cases; under-reporting estimates are presented for each Italian region, and poor levels of reporting in Southern Italy are confirmed. CONCLUSION: Although an order of magnitude larger, despite great heterogeneity between regions in under-reporting and in epidemic patterns, the shape of the corrected national time series remains close to that of the aggregated uncorrected data. This suggests such aggregate data may be quite robust to great heterogeneity in reporting and epidemic patterns at the regional level. The corrected data set maintains an epidemic pattern distinct from that of England and Wales

Metabarcoding protocol: Analysis of Bacteria (including Cyanobacteria) using the 16S rRNA gene and a DADA2 pipeline (Version 1)

This protocol has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) - Innovative Ecological Assessment and Water Management Strategy for the Protection of Ecosystem Services in Alpine Lakes and Rivers, Activity A.T1.3, Deliverable D.T1.3.2 – 1, https://www.alpine-space.eu/projects/eco-alpswater/en/hom

Metabarcoding protocol: Analysis of protists using the 18S rRNA gene and a DADA2 pipeline (Version 1)

This protocol has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) - Innovative Ecological Assessment and Water Management Strategy for the Protection of Ecosystem Services in Alpine Lakes and Rivers, Activity A.T1.3, Deliverable D.T1.3.2 – 2, https://www.alpine-space.eu/projects/eco-alpswater/en/hom

Plankton DNA extraction from Sterivex filter units

The objective of this protocol is to provide a reliable and replicable method for the DNA extraction of lake micro-plankton to be used for downstream DNA analysis. This protocol is one of those proposed by the Eco-AlpsWater consortium to promote the implementation of High Throughput Sequencing (HT S) of environmental DNA (eDNA) in the biomonitoring and ecological assessment of water bodies. The extraction is performed from samples filtered through Sterivex cartridges (Sterivex™ GP 0.22μm) and stored at -20°C, as described in the protocol dx.doi.org/10.17504/protocols.io.xn6fmhe, and with the use of the DNeasy® PowerWater Sterivex Kit (QIAGEN) with specific modifications adapted to plankton DNA extraction. The application proposed here, in the context of EcoAlpsWater, aims at comparing DNA inventories to traditional phytoplanktonic inventories and at characterizing more broadly the micro-planktonic diversity through eDNA analysis (including bacteria). This protocol is part of the deliverables provided by the WP1 of the Eco-AlpsWater project. All members of the EcoAlpsWater consortium (http://www.alpine-space.eu/projects/eco-alpswater/en/home) contributed to the optimization of this protocol

Comparison of different methods for SNP detection in grapevine

Single nucleotide polymorphisms (SNPs) are the most abundant of all markers, both in animal and plant genomes. In crops and tree species considerable investment has been recently made on this genomic technology. While large-scale characterisation of SNPs by high-throughput techniques is possible, such highthroughput platforms are not available to all plant breeding laboratories. This report compares alternative multi-purpose and affordable methods for SNP assay in grapevine (Vitis spp.). In particular, the efficiency, sensitivity and reliability of single-strand conformation polymorphism (SSCP) on both non-denaturant gels and fluorescence-based capillary electrophoresis are compared with minisequencing (single nucleotide extension reaction). The results indicate that when multiplexing in combination with minisequencing is a mid-throughput, reliable and flexible technique for the detection of SNPs and can therefore be used effectively to improve marker assisted breeding in grapevine.