A measure of interrater absolute agreement for ordinal categorical data

A measure of interrater absolute agreement for ordinal scales is proposed capitalizing on the dispersion index for ordinal variables proposed by Giuseppe Leti. The procedure allows to overcome the limits affecting traditional measures of interrater agreement in different fields of application. An unbiased estimator of the proposed measure is introduced and its sampling properties are investigated. In order to construct confidence intervals for interrater absolute agreement both asymptotic results and bootstrapping methods are used and their performance is evaluated. Simulated data are employed to demonstrate the accuracy and practical utility of the new procedure for assessing agreement. Finally, an application to a real case is provided

Involvement of the sigma factor sigma H in the regulation of a small heat shock protein gene in Lactobacillus plantarum WCFS1

The relative expression of the heat shock protein hsp18.55 gene was monitored in Lactobacillus plantarum ΔctsR and ΔftsH mutant strains. Transcription of the hsp18.55 gene was drastically repressed in the ΔctsR mutant of L. plantarum; conversely, significant transcriptional induction of the hsp18.55 gene was noted in the L. plantarum ΔftsH strain. Overall, these results suggest a possible regulation of the hsp18.55 gene by the alternative sigma H factor in L. plantarum. We also noted a similarity with the small heat shock gene (shs) locus of Lactobacillus brevis, which might indicate a possible evolutionary relationship

Sand supply from shoreface to foredunes: aeolian transport measurements and morphological evolution of a Tuscany beach stretch (Italy)

The coastal dunes are a highly dynamic sedimentary environment characterized by a continuous time-space readjustment in terms of morphology, shape and dimension. This is mainly due to the periodic fluctuation of the volume of sand available and by the force of the deflation processes, which are in turn driven by the interplay among pattern of vegetation cover, surface roughness and local-regional wind regime. The aim of our research is to quantify the deflation, transport and deposition of sands in a natural coastal field dune system located in the northern coast of Tuscany, Italy. The northern part of the investigated area is characterized by stable coastline condition while southwards strong erosive processes took place since 1800 year. Sedimentological data come from a series of sand collectors spaced along transects orthogonal to the coastline from the backshore to the semi stable dune field. The collectors were constructed of PVC pipe 100 x height 10 cm, with two openings 7 cm wide and 50 cm tall arranged on opposite sides of the tube. Opening willing to windward served for sand collection, and to leeward, covered with a metal wire 60μm opening. Collectors were buried along, until the base of the free window coincide with the surface of the ground about 1,5 m. The sand trapped within each collector was sampled every two hours for three consecutive times. In laboratory sand samples were weighed and subject to grain size analysis by means of mechanical sieves. The local winds parameters and their fluctuation with the time were acquired through a Meteorological mobile station. The station is equipped with three ammeters located to three different heights from ground surface: 40, 120 and 180 cm. A wireless sensor allows the constant output of data (each 5 sec) to a device. Temperature, and relative humidity value are furnished every 30 minutes. Analysis of data has evidenced the time-space fluctuation of sand volume in the two study area (stable area and under erosion). Basing on this methodological approach the time-space fluctuation of sand volume experienced by the two study areas (stable area and under erosion) has been estimated

Dorsal Scapular Artery Variations And Relationship To The Brachial Plexus, And A Related Thoracic Outlet Syndrome Case

Knowledge of the relationship of the dorsal scapular artery (DSA) with the brachial plexus is limited. We report a case of a variant DSA path, and revisit DSA origins and underinvestigated relationship with the plexus in cadavers. The DSA was examined in a male patient and 106 cadavers. In the case, we observed an unusual DSA compressing the lower plexus trunk, that resulted in intermittent radiating pain and paresthesia. In the cadavers, the DSA originated most commonly from the subclavian artery (71%), with 35% from the thyrocervical trunk. Nine sides of eight cadavers (seven females) had two DSA branches per side, with one branch from each origin. The most typical DSA path was a subclavian artery origin before passing between upper and middle brachial plexus trunks (40% of DSAs), versus between middle and lower trunks (23%), or inferior (4%) or superior to the plexus (1%). Following a thyrocervical trunk origin, the DSA passed most frequently superior to the plexus (23%), versus between middle and lower trunks (6%) or upper and middle trunks (4%). Bilateral symmetry in origin and path through the brachial plexus was observed in 13 of 35 females (37%) and 6 of 17males (35%), with the most common bilateral finding of a subclavian artery origin and a path between upper and middle trunks (17%). Variability in the relationship between DSA and trunks of the brachial plexus has surgical and clinical implications, such as diagnosis of thoracic outlet syndrome

A PM10 chemically characterised nation-wide dataset for Italy. Geographical influence on urban air pollution and source apportionment

: Urban textures of the Italian cities are peculiarly shaped by the local geography generating similarities among cities placed in different regions but comparable topographical districts. This suggested the following scientific question: can such different topographies generate significant differences on the PM10 chemical composition at Italian urban sites that share similar geography despite being in different regions? To investigate whether such communalities can be found and are applicable at Country-scale, we propose here a novel methodological approach. A dataset comprising season-averages of PM10 mass concentration and chemical composition data was built, covering the decade 2005-2016 and referring to urban sites only (21 cities). Statistical analyses, estimation of missing data, identification of latent clusters and source apportionment modelling by Positive Matrix Factorization (PMF) were performed on this unique dataset. The first original result is the demonstration that a dataset with atypical time resolution can be successfully exploited as an input matrix for PMF obtaining Country-scale representative chemical profiles, whose physical consistency has been assessed by different tests of modelling performance. Secondly, this dataset can be considered a reference repository of season averages of chemical species over the Italian territory and the chemical profiles obtained by PMF for urban Italian agglomerations could contribute to emission repositories. These findings indicate that our approach is powerful, and it could be further employed with datasets typically available in the air pollution monitoring networks

Time course of risk factors associated with mortality of 1260 critically ill patients with COVID-19 admitted to 24 Italian intensive care units

Purpose: To evaluate the daily values and trends over time of relevant clinical, ventilatory and laboratory parameters during the intensive care unit (ICU) stay and their association with outcome in critically ill patients with coronavirus disease 19 (COVID-19). Methods: In this retrospective–prospective multicentric study, we enrolled COVID-19 patients admitted to Italian ICUs from February 22 to May 31, 2020. Clinical data were daily recorded. The time course of 18 clinical parameters was evaluated by a polynomial maximum likelihood multilevel linear regression model, while a full joint modeling was fit to study the association with ICU outcome. Results: 1260 consecutive critically ill patients with COVID-19 admitted in 24 ICUs were enrolled. 78% were male with a median age of 63 [55–69] years. At ICU admission, the median ratio of arterial oxygen partial pressure to fractional inspired oxygen (PaO2/FiO2) was 122 [89–175] mmHg. 79% of patients underwent invasive mechanical ventilation. The overall mortality was 34%. Both the daily values and trends of respiratory system compliance, PaO2/FiO2, driving pressure, arterial carbon dioxide partial pressure, creatinine, C-reactive protein, ferritin, neutrophil, neutrophil–lymphocyte ratio, and platelets were associated with survival, while for lactate, pH, bilirubin, lymphocyte, and urea only the daily values were associated with survival. The trends of PaO2/FiO2, respiratory system compliance, driving pressure, creatinine, ferritin, and C-reactive protein showed a higher association with survival compared to the daily values. Conclusion: Daily values or trends over time of parameters associated with acute organ dysfunction, acid–base derangement, coagulation impairment, or systemic inflammation were associated with patient survival

Results of the first European Source Apportionment intercomparison for Receptor and Chemical Transport Models

In this study, the performance of the source apportionment model applications were evaluated by comparing the model results provided by 44 participants adopting a methodology based on performance indicators: z-scores and RMSEu, with pre-established acceptability criteria. Involving models based on completely different and independent input data, such as receptor models (RMs) and chemical transport models (CTMs), provided a unique opportunity to cross-validate them. In addition, comparing the modelled source chemical profiles, with those measured directly at the source contributed to corroborate the chemical profile of the tested model results. The most used RM was EPA- PMF5. RMs showed very good performance for the overall dataset (91% of z-scores accepted) and more difficulties are observed with SCE time series (72% of RMSEu accepted). Industry resulted the most problematic source for RMs due to the high variability among participants. Also the results obtained with CTMs were quite comparable to their ensemble reference using all models for the overall average (>92% of successful z-scores) while the comparability of the time series is more problematic (between 58% and 77% of the candidates’ RMSEu are accepted). In the CTM models a gap was observed between the sum of source contributions and the gravimetric PM10 mass likely due to PM underestimation in the base case. Interestingly, when only the tagged species CTM results were used in the reference, the differences between the two CTM approaches (brute force and tagged species) were evident. In this case the percentage of candidates passing the z-score and RMSEu tests were only 50% and 86%, respectively. CTMs showed good comparability with RMs for the overall dataset (83% of the z-scores accepted), more differences were observed when dealing with the time series of the single source categories. In this case the share of successful RMSEu was in the range 25% - 34%.JRC.C.5-Air and Climat

Comparison of PM10 concentrations and metal content in three different sites of the Venice Lagoon: An analysis of possible aerosol sources

The Venice Lagoon is exposed to atmospheric pollutants from industrial activities, thermoelectric power plants, petrochemical plants, incinerator, domestic heating, ship traffic, glass factories and vehicular emissions on the mainland. In 2005, construction began on the mobile dams (MOSE), one dam for each channel connecting the lagoon to the Adriatic Sea as a barrier against high tide. These construction works could represent an additional source of pollutants. PM10 samples were taken on random days between 2007 and 2010 at three different sites: Punta Sabbioni, Chioggia and Malamocco, located near the respective dam construction worksites. Chemical analyses of V, Cr, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, Sb, Tl and Pb in PM10 samples were performed by Inductively coupled plasmaquadrupole mass spectrometry (ICP-QMS) and results were used to identify the main aerosol sources. The correlation of measured data with meteorology, and source apportionment, failed to highlight a contribution specifically associated to the emissions of the MOSE construction works. The comparison of the measurements at the three sites showed a substantial homogeneity of metal concentrations in the area. Source apportionment with principal component analysis (PCA) and positive matrix factorization (PMF) showed that a four principal factors model could describe the sources of metals in PM10. Three of them were assigned to specific sources in the area and one was characterised as a source of mixed origin (anthropogenic and crustal). A specific anthropogenic source of PM10 rich in Ni and Cr, active at the Chioggia site, was also identified

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.Peer reviewe

Common variants at 12p11, 12q24, 9p21, 9q31.2 and in ZNF365 are associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers

Abstract Introduction Several common alleles have been shown to be associated with breast and/or ovarian cancer risk for BRCA1 and BRCA2 mutation carriers. Recent genome-wide association studies of breast cancer have identified eight additional breast cancer susceptibility loci: rs1011970 (9p21, CDKN2A/B), rs10995190 (ZNF365), rs704010 (ZMIZ1), rs2380205 (10p15), rs614367 (11q13), rs1292011 (12q24), rs10771399 (12p11 near PTHLH) and rs865686 (9q31.2). Methods To evaluate whether these single nucleotide polymorphisms (SNPs) are associated with breast cancer risk for BRCA1 and BRCA2 carriers, we genotyped these SNPs in 12,599 BRCA1 and 7,132 BRCA2 mutation carriers and analysed the associations with breast cancer risk within a retrospective likelihood framework. Results Only SNP rs10771399 near PTHLH was associated with breast cancer risk for BRCA1 mutation carriers (per-allele hazard ratio (HR) = 0.87, 95% CI: 0.81 to 0.94, P-trend = 3 × 10-4). The association was restricted to mutations proven or predicted to lead to absence of protein expression (HR = 0.82, 95% CI: 0.74 to 0.90, P-trend = 3.1 × 10-5, P-difference = 0.03). Four SNPs were associated with the risk of breast cancer for BRCA2 mutation carriers: rs10995190, P-trend = 0.015; rs1011970, P-trend = 0.048; rs865686, 2df-P = 0.007; rs1292011 2df-P = 0.03. rs10771399 (PTHLH) was predominantly associated with estrogen receptor (ER)-negative breast cancer for BRCA1 mutation carriers (HR = 0.81, 95% CI: 0.74 to 0.90, P-trend = 4 × 10-5) and there was marginal evidence of association with ER-negative breast cancer for BRCA2 mutation carriers (HR = 0.78, 95% CI: 0.62 to 1.00, P-trend = 0.049). Conclusions The present findings, in combination with previously identified modifiers of risk, will ultimately lead to more accurate risk prediction and an improved understanding of the disease etiology in BRCA1 and BRCA2 mutation carriers