A Robust Tucker3 Model for Compositional Data

Double counting is inherent to the output concept, therefore it is preferable to use manufacturing value added (MVA) instead to measure the manufacturing production. While the issue of double counting in production statistics is successfully addressed by using MVA, commodity exchange in trade data is still measured as output. The relevance of value added has increased in the recent years due to the unbundling of the production process, where different stages of value chain take place in different countries. We want to represent the export statistics through value added to output ratio using data from international statistical databases. The data sets considered are organized by country, commodity or activity and year (activities are classified according to the International Standard Industrial Classification of all economic activities (ISIC)) and thus they are three-way compositional data.\ud Different methods exist for analysis of multi-way data and we choose Tucker3 because it provides a compromise between parsimonious and flexible models. The Tucker3 method as most of the N-way methods is based on alternating least squares (ALS) which makes it vulnerable to the presence of outliers in the data. Even a single outliying data point can\ud strongly influence the resulting model and the conclusions based on it. A robust version of Tucker3 was presented by Pravdova et al. (2001) but it suffers from two main deficiencies. First of all the robust initialization of the algorithm is based on MCD which will not work in high dimensions. And secondly, the method is not suitable for applying on compositional data. We propose to select the initial subset using robust PCA and to transform the compositional data applying ilr transformation (Egozcue et al., 2003). Furthermore, since to our knowledge there is no readily available software for computing robust Tucker3 models, we provide\ud implementation of the proposed algorithm in R. The method is compared to its competitors both in terms of its efficiency and the computational effort needed

Joint Biplots for CoDa

Compositional data (CoDa) consist of vectors of positive values summing to a unit, or in general, to some fixed constant for all vectors. They appear as proportions, percentages, concentrations, absolute and relative frequencies. Sometimes, compositions arise from non-negative data (such as counts, area, weights, volume) that have been scaled by the total of the components because the analyst is not interested in the total sum of the vector. The multidimensional analysis of this kind of data requires a careful consideration because the sample space for CoDa is the simplex. The first consistent methodological proposal to deal with CoDa was proposed by Aitchison (1986) when he introduced the log-ratio approach. Basically, the idea that this approach conveys is to move from the simplex space to the real space by using log.ratio transformations, applying standard statistical methods, and finally, by means of an inverse log-ratio transformation, to interpret the results in the simplex space. Starting from this paper, pairwise, centered, additive and isometric log-ratio transformations, in short plr, clr, alr (Aitchison, 1986) and ilr respectively, are proposed in literature (Egozucue et al., 2003). In the context of dimension-reducing techniques, Aitchison (1983) proposed applying principal component analysis (PCA) after having applied a centered log-ratio (clr) transformation to CoDa. Aitchison and Greenacre (2002) suggested an adaptation of the biplot to CoDa. The biplot is a well established graphical aid in other branches of statistical analysis and can prove to be a useful exploratory and expository tool for compositions. In literature many papers on dimensional-reduction techniques for CoDa are proposed. Based on log-ratio strategy, Gallo (2012a, 2012b, 2013) recently proposed to use three-mode analysis of compositional data.\ud Starting from Gallo (2012b), we propose using of plr and clr joint biplots. Where in some cases the plr joint biplot is the only ones that show clearly the correlations

Very early onset and greater vulnerability in schizophrenia: A clinical and neuroimaging study

Although schizophrenia has been diagnosed in children, this group of disorders has received too little attention in the clinical and research literature. Preliminary data suggest that early onset schizophrenia (EOS) and very early onset schizophrenia (VEOS) tend to have a worse outcome than adult onset schizophrenia, and seem to be related to a greater familial vulnerability, due to genetic, psychosocial, and environmental factors. Recently, advanced neuroimaging techniques have revealed structural and functional brain abnormalities in some cerebral areas. This paper reports on a case diagnosed as VEOS, with premorbid year-long psychopathological history. The patient showed atypical proton magnetic resonance spectroscopy findings, and normal brain and spine computer tomography and brain magnetic resonance images

The Italian experience of the national registry of renal biopsies

The Italian experience of the national registry of renal biopsies.BackgroundAlthough several registries collecting data of patients with kidney diseases exist, there are only a few registries which specifically collect data relating to renal biopsy; one such registry is the Italian Registry of Renal Biopsies (IRRB). The aim of this study was to report on the relative frequency of nephropathies according to gender, age at time of biopsy, clinical presentation and renal function, based on the histologic diagnosis during the years 1996 to 2000.MethodsWe evaluated data relating to 14607 renal biopsies, provided by 128 renal units in Italy. Data entry was performed by using the Internet-based database directly (URL http://www.irrb.net). Clinical presentation was defined as urinary abnormalities (UA), nephrotic syndrome (NS), acute nephritic syndrome (ANS). Renal diseases were divided in four major categories: (1) primary glomerulonephritides (GN); (2) secondary GN; (3) tubulointerstitial nephropathies (TIN); and (4) vascular nephropathies (VN).ResultsPrimary GN, TIN, and VN were more frequent in males compared to females while secondary GN was more frequent in females. Diseases whose frequency was higher in males were IgA nephropathy (IgAN), benign nephroangiosclerosis (BNA), and acute tubular necrosis (ATN). A significantly higher frequency of immune-mediated secondary GN, as well as primary GN, including minimal change disease (MCD), focal segmental glomerulosclerosis (FSGS), and mesangiocapillary GN (MCGN), was shown in females. Primary and secondary GN, TIN, and VN were more frequent in the range 15 to 65 years of age. At the time of biopsy 77% of primary GN and 61% of secondary GN presented with normal renal function. Acute renal failure (ACR) was more present in TIN (52%), while chronic renal failure (CRF) was more frequent in VN (47%).ConclusionWe believe collection of data relating to renal biopsies in a national registry is a useful tool for nephrologists in that it meets one of the current challenges facing the clinical research enterprise. The availability of these data will allow epidemiologic studies in health care to answer the several open questions in both prevention and treatment of renal diseases

The impact of active HIV-1 replication on the physiological age-related decline of immature-transitional B-cells in HIV-1 infected children

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Standardization of canine meningioma grading: Validation of new guidelines for reproducible histopathologic criteria.

Canine meningiomas are currently graded using the human grading system. Recently published guidelines have adapted the human grading system for use in dogs. The goal of this study was to validate the new guidelines for canine meningiomas. To evaluate the inter-observer agreement, 5 veterinary surgical pathologists graded 158 canine meningiomas following the human grading system alone or with the new guidelines. The inter-observer agreement for histologic grade and each of the grading criteria (mitotic grade, invasion, spontaneous necrosis, macronucleoli, small cells, hypercellularity, pattern loss and anaplasia) was evaluated using the Fleiss kappa index. The diagnostic accuracy (sensitivity and specificity) was assessed by comparing the diagnoses obtained with the 2 grading systems with a consensus grade (considered the reference classification). The consensus histologic grade was obtained by agreement between 4 experienced veterinary neuropathologists following the guidelines. Compared with the human grading alone, the canine-specific guidelines increased the inter-observer agreement for: histologic grade (κ = 0.52); invasion (κ = 0.67); necrosis (κ = 0.62); small cells (κ = 0.36); pattern loss (κ = 0.49) and anaplasia (κ = 0.55). Mitotic grade agreement remained substantial (κ = 0.63). The guidelines improved the sensitivity in identifying grade 1 (95.6%) and the specificity in identifying grade 2 (96.2%) meningiomas. In conclusion, the new grading guidelines for canine meningiomas are associated with an overall improvement in the inter-observer agreement and higher diagnostic accuracy in diagnosing grade 1 and grade 2 meningiomas

Standardization of canine meningioma grading: Validation of new guidelines for reproducible histopathologic criteria

Canine meningiomas are currently graded using the human grading system. Recently published guidelines have adapted the human grading system for use in dogs. The goal of this study was to validate the new guidelines for canine meningiomas. To evaluate the inter‐observer agreement, 5 veterinary surgical pathologists graded 158 canine meningiomas following the human grading system alone or with the new guidelines. The inter‐observer agreement for histologic grade and each of the grading criteria (mitotic grade, invasion, spontaneous necrosis, macronucleoli, small cells, hypercellularity, pattern loss and anaplasia) was evaluated using the Fleiss kappa index. The diagnostic accuracy (sensitivity and specificity) was assessed by comparing the diagnoses obtained with the 2 grading systems with a consensus grade (considered the reference classification). The consensus histologic grade was obtained by agreement between 4 experienced veterinary neuropathologists following the guidelines. Compared with the human grading alone, the canine‐specific guidelines increased the inter‐observer agreement for: histologic grade (κ = 0.52); invasion (κ = 0.67); necrosis (κ = 0.62); small cells (κ = 0.36); pattern loss (κ = 0.49) and anaplasia (κ = 0.55). Mitotic grade agreement remained substantial (κ = 0.63). The guidelines improved the sensitivity in identifying grade 1 (95.6%) and the specificity in identifying grade 2 (96.2%) meningiomas. In conclusion, the new grading guidelines for canine meningiomas are associated with an overall improvement in the inter‐observer agreement and higher diagnostic accuracy in diagnosing grade 1 and grade 2 meningiomas

An update of the evolving epidemic of blaKPC carrying Klebsiella pneumoniae in Sicily, Italy, 2014: Emergence of multiple Non-ST258 Clones

Background: In Italy, Klebsiella pneumoniae carbapenemase producing K. pneumoniae (KPC-Kp) strains are highly endemic and KPC producing CC258 is reported as the widely predominating clone. In Palermo, Italy, previous reports have confirmed this pattern. However, recent preliminary findings suggest that an epidemiological change is likely ongoing towards a polyclonal KPC-Kp spread. Here we present the results of molecular typing of 94 carbapenem non susceptible K. pneumoniae isolates detected during 2014 in the three different hospitals in Palermo, Italy. Methods and Results: Ninety-four consecutive, non replicate carbapenem non susceptible isolates were identified in the three largest acute general hospitals in Palermo, Italy, in the six-month period March-August 2014. They were characterized by PCR for β-lactam, aminoglycoside and plasmid mediated fluoroquinolone resistance genetic determinants. The mgrB gene of the colistin resistant isolates was amplified and sequenced. Clonality was assessed by pulsed field gel electrophoresis and multilocus sequence typing. Eight non-CC258 sequence types (STs) were identified accounting for 60% of isolates. In particular, ST307 and ST273 accounted for 29% and 18% of isolates. CC258 isolates were more frequently susceptible to gentamicin and non-CC258 isolates to amikacin. Colistin non susceptibility was found in 42% of isolates. Modifications of mgrB were found in 32 isolates. Conclusions: Concurrent clonal expansion of some STs and lateral transmission of genetic resistance determinants are likely producing a thorough change of the KPC-Kp epidemiology in Palermo, Italy. In our setting mgrB inactivation proved to substantially contribute to colistin resistance. Our findings suggest the need to continuously monitor the KPC-Kp epidemiology and to assess by a nationwide survey the possible shifting towards a polyclonal epidemic

Inhibition of exosome biogenesis affects cell motility in heterogeneous sub-populations of paediatric-type diffuse high-grade gliomas

Background: Paediatric-type diffuse High-Grade Gliomas (PDHGG) are highly heterogeneous tumours which include distinct cell sub-populations co-existing within the same tumour mass. We have previously shown that primary patient-derived and optical barcoded single-cell-derived clones function as interconnected networks. Here, we investigated the role of exosomes as a route for inter-clonal communication mediating PDHGG migration and invasion. Results: A comprehensive characterisation of seven optical barcoded single-cell-derived clones obtained from two patient-derived cell lines was performed. These analyses highlighted extensive intra-tumour heterogeneity in terms of genetic and transcriptional profiles between clones as well as marked phenotypic differences including distinctive motility patterns. Live single-cell tracking analysis of 3D migration and invasion assays showed that the single-cell-derived clones display a higher speed and longer travelled distance when in co-culture compared to mono-culture conditions. To determine the role of exosomes in PDHGG inter-clonal cross-talks, we isolated exosomes released by different clones and characterised them in terms of marker expression, size and concentration. We demonstrated that exosomes are actively internalized by the cells and that the inhibition of their biogenesis, using the phospholipase inhibitor GW4689, significantly reduced the cell motility in mono-culture and more prominently when the cells from the clones were in co-culture. Analysis of the exosomal miRNAs, performed with a miRNome PCR panel, identified clone-specific miRNAs and a set of miRNA target genes involved in the regulation of cell motility/invasion/migration. These genes were found differentially expressed in co-culture versus mono-culture conditions and their expression levels were significantly modulated upon inhibition of exosome biogenesis. Conclusions: In conclusion, our study highlights for the first time a key role for exosomes in the inter-clonal communication in PDHGG and suggests that interfering with the exosome biogenesis pathway may be a valuable strategy to inhibit cell motility and dissemination for these specific diseases