Pattern recognition in stained HEp-2 cells: Where are we now?

Indirect Immunofluorescence (IIF) images are increasingly being used for the diagnosis of autoimmune diseases. However, the analysis of this kind of images has until now reached a comparatively low level of automation, if compared with other medical imaging techniques. The Special Issue on the Analysis and Recognition of Indirect Immunofluorescence Images of the Pattern Recognition journal aims at providing a comprehensive evaluation of the state of the art for the staining pattern classification problem, through the adoption of a common experimental protocol and the testing of all the methods on a publicly available dataset.     

Pheomelanin Effect on UVB Radiation-Induced Oxidation/Nitration of l-Tyrosine

Pheomelanin is a natural yellow-reddish sulfur-containing pigment derived from tyrosinase-catalyzed oxidation of tyrosine in presence of cysteine. Generally, the formation of melanin pigments is a protective response against the damaging effects of UV radiation in skin. However, pheomelanin, like other photosensitizing substances, can trigger, following exposure to UV radiation, photochemical reactions capable of modifying and damaging cellular components. The photoproperties of this natural pigment have been studied by analyzing pheomelanin effect on oxidation/nitration of tyrosine induced by UVB radiation at different pH values and in presence of iron ions. Photoproperties of pheomelanin can be modulated by various experimental conditions, ranging from the photoprotection to the triggering of potentially damaging photochemical reactions. The study of the photomodification of l-Tyrosine in the presence of the natural pigment pheomelanin has a special relevance, since this tyrosine oxidation/nitration pathway can potentially occur in vivo in tissues exposed to sunlight and play a role in the mechanisms of tissue damage induced by UV radiation.     

Deep Resequencing of 9 Candidate Genes Identifies a Role for ARAP1 and IGF2BP2 in Modulating Insulin Secretion Adjusted for Insulin Resistance in Obese Southern Europeans

Type 2 diabetes is characterized by impairment in insulin secretion, with an established genetic contribution. We aimed to evaluate common and low-frequency (1–5%) variants in nine genes strongly associated with insulin secretion by targeted sequencing in subjects selected from the extremes of insulin release measured by the disposition index. Collapsing data by gene and/or function, the association between disposition index and nonsense variants were significant, also after adjustment for confounding factors (OR = 0.25, 95% CI = 0.11–0.59, p = 0.001). Evaluating variants individually, three novel variants in ARAP1, IGF2BP2 and GCK, out of eight reaching significance singularly, remained associated after adjustment. Constructing a genetic risk model combining the effects of the three variants, only carriers of the ARAP1 and IGF2BP2 variants were significantly associated with a reduced probability to be in the lower, worst, extreme of insulin secretion (OR = 0.223, 95% CI = 0.105–0.473, p < 0.001). Observing a high number of normal glucose tolerance between carriers, a regression posthoc analysis was performed. Carriers of genetic risk model variants had higher probability to be normoglycemic, also after adjustment (OR = 2.411, 95% CI = 1.136–5.116, p = 0.022). Thus, in our southern European cohort, nonsense variants in all nine candidate genes showed association with better insulin secretion adjusted for insulin resistance, and we established the role of ARAP1 and IGF2BP2 in modulating insulin secretion.     

Diagnostic Accuracy of CT Texture Analysis in Adrenal Masses: A Systematic Review

Adrenal incidentalomas (AIs) are incidentally discovered adrenal neoplasms. Overt endocrine secretion (glucocorticoids, mineralocorticoids, and catecholamines) and malignancy (primary or metastatic disease) are assessed at baseline evaluation. Size, lipid content, and washout characterise benign AIs (respectively, <4 cm, <10 Hounsfield unit, and rapid release); nonetheless, 30% of adrenal lesions are not correctly indicated. Recently, image-based texture analysis from computed tomography (CT) may be useful to assess the behaviour of indeterminate adrenal lesions. We performed a systematic review to provide the state-of-the-art of texture analysis in patients with AI. We considered 9 papers (from 70 selected), with a median of 125 patients (range 20–356). Histological confirmation was the most used criteria to differentiate benign from the malignant adrenal mass. Unenhanced or contrast-enhanced data were available in all papers; TexRAD and PyRadiomics were the most used software. Four papers analysed the whole volume, and five considered a region of interest. Different texture features were reported, considering first- and second-order statistics. The pooled median area under the ROC curve in all studies was 0.85, depicting a high diagnostic accuracy, up to 93% in differentiating adrenal adenoma from adrenocortical carcinomas. Despite heterogeneous methodology, texture analysis is a promising diagnostic tool in the first assessment of patients with adrenal lesions.     

DNA barcoding as a new tool for food traceability

Food safety and quality are nowadays a major concern. Any case of food alteration, especially when reported by the media, has a great impact on public opinion. There is an increasing demand for the improvement of quality controls, hence addressing scientific research towards the development of reliable molecular tools for food analysis. DNA barcoding is a widely used molecular-based system, which can identify biological specimens, and is used for the identification of both raw materials and processed food. In this review the results of several researches are critically analyzed, in order to exploit the effectiveness of DNA barcoding in food traceability, and to delineate some best practices in the application of DNA barcoding throughout the industrial pipeline. The use of DNA barcoding for food safety and in the identification of commercial fraud is also discussed.     

Genetic analysis of detailed milk protein composition and coagulation properties in Simmental cattle

The objective of this study was to estimate genetic parameters for milk protein fraction contents, milk protein composition, and milk coagulation properties (MCP). Contents of α_S1-, α_S2-, β-, γ-, and κ-casein (CN), β-lactoglobulin (β-LG), and α-lactalbumin (α-LA) were measured by reversed-phase HPLC in individual milk samples of 2,167 Simmental cows. Milk protein composition was measured as percentage of each CN fraction in CN (α_S1-CN%, α_S2-CN%, β-CN%, γ-CN%, and κ-CN%) and as percentage of β-LG in whey protein (β-LG%). Rennet clotting time (RCT) and curd firmness (a₃₀) were measured by a computerized renneting meter. Heritabilities for contents of milk proteins ranged from 0.11 (α-LA) to 0.52 (κ-CN). Heritabilities for α_S1-CN%, κ-CN%, and β-CN% were similar and ranged from 0.63 to 0.69, whereas heritability of α_S2-CN%, γ-CN%, and β-LG% were 0.28, 0.18, and 0.34, respectively. Effects of CSN2-CSN3 haplotype and BLG genotype accounted for more than 80% of the genetic variance of α_S1-CN%, β-CN%, and κ-CN% and 50% of the genetic variance of β-LG%. The genetic correlations among the contents of CN fractions and between CN and whey protein fractions contents were generally low. When the data were adjusted for milk protein gene effects, the magnitude of the genetic correlations among the contents of milk protein fractions markedly increased, indicating that they undergo a common regulation. The proportion of β-CN in CN correlated negatively with κ-CN% (r = −0.44). The genetic relationships between CN and whey protein composition were trivial. Low milk pH correlated with favorable MCP. Genetically, contents and proportions of α_S1- and α_S2-CN in CN were positively correlated with RCT. The relative proportion of β-CN in CN exhibited a genetic correlation with RCT of −0.26. Both the content and the relative proportion of κ-CN in CN did not correlate with RCT. Weak curds were genetically associated with increased proportions in CN of α_S1- and α_S2-CN, decreased contents of β-CN and κ-CN, and decreased proportion of κ-CN in CN. Negligible effects on the estimated correlations between a₃₀ and κ-CN contents or proportion in CN were observed when the model accounted for milk protein gene effects. Increasing β-CN and κ-CN contents and relative proportions in CN and decreasing the content and proportions of α_S1-CN and α_S2-CN and milk pH through selective breeding exert favorable effects on MCP.     

Issues in the characterization of power quality instruments

This paper analyzes some issues related to the metrological characterization of instruments for power quality monitoring, in order to move a step toward the definition of a full performance verification protocol. This protocol should include not only the test situations reported in corresponding standards, but also an array of different voltage and current fluctuations – linked to common power quality issues – that may be encountered in actual power systems. This performance analysis is particularly interesting because it can be found that different power quality instruments, fully meeting characteristics prescribed in standard, still may significantly disagree in some actual measurements. This is due for the existence of unresolved technical and theoretical issues related to the metrological characterization through the classical approaches of these instruments. The aim of the discussion carried out in this paper is also the specification of requirements of a test system devoted to calibration and verification of a power quality monitor, such as it is done in type testing. After a preliminary discussion about technical and theoretical issues related to the performance analysis of these instruments, a proposal of test protocol definition, with reference to some power quality phenomena and based on the design of experiment, is presented.     

Seasonal changes of abiotic and biotic gradients downstream a multiple use reservoir in a Mediterranean River

The effect of regulated flow regimentation on hydrogeomorphological variables, autochthonous and allochthonous trophic sources and macroinvertebrates communities of the Mucone River, Calabria (Italy) were studied in May, August and November 2005 at three study sites. The first site (M1) was located close to the impoundment, the second one (M2) immediately upstream from the first permanent tributary (Cerreto stream) and the third one (M3) about 1 km downstream from the Cerreto confluence. Our results suggest that hydrogeomorphological gradients already exist in spring but their strongest development, with major consequences for the lotic biota, take place only with the beginning and ending of the dry season. Reduction of river width, shading due to well preserved riparian alder trees and marked sand deposition in November, were the variables negatively affecting epilithic microalgae biomass at site M1. These factors partially relieved at M2 site and became much less important at M3 resulting in the highest levels of autotrophic periphyton production. Coarse particulate organic matter accumulation exhibited an opposite trend due to the lack of discharge peaks at M1, whereas in November, litter fall removed most differences between stations. In May macrozoobenthic communities of the three stations were relatively similar (reophilous gatherer and scraper taxa). In November sand accumulation reduced spatial heterogeneity and habitats density close to the Cecita dam promoting settlement of shredder sand tolerant taxa (Plecoptera: Leuctridae) and a drop of community biodiversity. Flow reactivation, especially after Cerreto confluence, hindered sand accumulation, favoured autochthonous primary production and increased energy sources for macroinvertebrates. Copyright © 2010 John Wiley & Sons, Ltd.