The use of digital images to evaluate the interobserver agreement on cervical smear readings in Italian cervical cancer screening

G. Tinacci, A. Biggeri, A. Pellegrini, M.P. Cariaggi, M.L. Schiboni and M. Confortini The use of digital images to evaluate the interobserver agreement on cervical smear readings in Italian cervical cancer screening Objective: The aim of this study was to measure interobserver agreement among cytologists on using a set of digital images. Methods: A set of 90 selected Papanicolaou‐stained cervical smears were digitalized and the digital images circulated among 117 readers, from laboratories spread across almost all Italian regions. Three representative fields of each smear were displayed at 20× and 40× magnification (overall six images for each case). The diagnoses made by the cytologists who provided the images were taken as target diagnoses. Results: The κ values were: very low for the categories atypical squamous cells of undetermined significance (ASC‐US), and atypical squamous cells – cannot exclude high‐grade squamous intraepithelial lesion (ASC‐H); poor for the categories atypical glandular cells (AGC), high‐grade squamous intraepithelial lesion (HSIL) and invasive cancer; and fair to good for the categories negative and low‐grade squamous intraepithelial lesion (LSIL). However, we found a cluster of 42 best concordant readers. The overall κ value and overall weighted κ with the target diagnosis for these 42 readers were 0.45 and 0.66, respectively. This finding is in contrast with the overall κ value and overall weighted κ for the other readers of 0.39 and 0.59, respectively. Conclusions: As this finding is an estimate of the accuracy of the readers, we can infer that it will be very important to reach this level of concordance for all the participating readers. Future effort will facilitate common experiences in order to improve the reproducibility of diagnostic criteria. Digital images could be the key to reach this aim.     

EFFECTS OF MORTALITY RISK AND GROWTH ON A MODEL OF REPRODUCTIVE EFFORT: WHY THE SHINE AND SCHWARZKOPF MODEL IS NOT GENERAL

Using data and reanalysis of a model published by Shine and Schwarzkopf (1992) we reject the two unsubstantiated assertions made by Shine et al. (1996) about modeling the evolution of reproductive effort in squamate reptiles: (1) mortality schedules do not affect predictions of the Shine and Schwarzkopf (1992) model; and (2) growth rates that would affect the predictions of the original model are biologically unreasonable. On the basis of these two points alone, we strongly reject Shine et al.'s (1996) claim that a critique by Niewiarowski and Dunham (1994) actually reinforces the original conclusions of Shine and Schwarzkopf (1992). Furthermore, results and data presented here are strong enough to severely circumscribe the generality of the Shine and Schwarzkopf (1992) model. Though we do not provide data or new analyses of the potential effects of offspring size variation, we reaffirm the position of Niewiarowski and Dunham (1994) that the sensitivity of the Shine and Schwarzkopf (1992) model to such effects should be explored before using it as a basis for structuring future research on the evolution of reproductive effort in squamate reptiles.     

Structural and functional measures of leaf-associated invertebrates and fungi as predictors of stream eutrophication

Eutrophication is a major threat to freshwater ecosystems worldwide that affects aquatic biota and compromises ecosystem functioning. In this study, we assessed the potential use of leaf decomposition and associated decomposer communities to predict stream eutrophication. Because leaf quality is expected to affect leaf decomposition, we used five leaf species, differing in their initial nitrogen concentration. Leaves of alder, chestnut, plane, oak and eucalyptus were placed in coarse-mesh bags and immersed in six streams along an eutrophication gradient to assess leaf decomposition and the structure of associated decomposer communities. A hump-shaped relationship was established between leaf decomposition and the eutrophication gradient for all leaf species, except for eucalyptus. Invertebrate biomass and density as well as fungal biomass and sporulation were lowest at the extremes of the gradient. Leaf-associated invertebrate and fungal assemblages were mainly structured by stream eutrophication. The percentage of shredders on leaves decreased, whereas the percentage of oligochaeta increased along the eutrophication gradient. The Iberian Biological Monitoring Working Party Index (IBMWP) applied to benthic invertebrates increased from oligotrophic to moderately eutrophic streams and then dropped sharply at highly and hypertrophic streams. Overall, leaf decomposition was a valuable tool to assess changes in stream water quality, and it allowed the discrimination of sites classified by the IBMWP within class I and class IV. Moreover, decomposition of most leaf species responded in a similar way to eutrophication when decomposition was normalized by the quality of leaves.     

Effects of grazing intensity and grazing exclusion on litter decomposition in the temperate steppe of Nei Mongol,China

Aims Grazing intensity and grazing exclusion affect ecosystem carbon cycling by changing the plant community and soil micro-environment in grassland ecosystems. The aims of this study were: 1) to determine the effects of grazing intensity and grazing exclusion on litter decomposition in the temperate grasslands of Nei Mongol; 2) to compare the difference between above-ground and below-ground litter decomposition; 3) to identify the effects of precipitation on litter production and decomposition. Methods We measured litter production, quality, decomposition rates and soil nutrient contents during the growing season in 2011 and 2012 in four plots, i.e. light grazing, heavy grazing, light grazing exclusion and heavy grazing exclusion. Quadrate surveys and litter bags were used to measure litter production and decomposition rates. All data were analyzed with ANOVA and Pearson’s correlation procedures in SPSS. Important findings Litter production and decomposition rates differed greatly among four plots. During the two years of our study, above-ground litter production and decomposition in heavy-grazing plots were faster than those in light-grazing plots. In the dry year, below-ground litter production and decomposition in light-grazing plots were faster than those in heavy-grazing plots, which is opposite to the findings in the wet year. Short-term grazing exclusion could promote litter production, and the exclusion of light-grazing could increase litter decomposition and nutrient cycling. In contrast, heavy-grazing exclusion decreased litter decomposition. Thus, grazing exclusion is beneficial to the restoration of the light-grazing grasslands, and more human management measures are needed during the restoration of heavy-grazing grasslands. Precipitation increased litter production and decomposition, and below-ground litter was more vulnerable to the inter-annual change of precipitation than above-ground litter. Compared to the light-grazing grasslands, heavy-grazing grasslands had higher sensitivity to precipitation. The above-ground litter decomposition was strongly positively correlated with the litter N content (R² = 0.489, p < 0.01) and strongly negatively correlated with the soil total N content (R² = 0.450, p < 0.01), but it was not significantly correlated with C:N and lignin:N. Below-ground litter decomposition was negatively correlated with the litter C (R² = 0.263, p < 0.01), C:N (R² = 0.349, p < 0.01) and cellulose content (R² = 0.460, p < 0.01). Our results will provide a theoretical basis for ecosystem restoration and the research of carbon cycling.     

Yeasts and yeast-like fungi in tap water and groundwater,and their transmission to household appliances

In the present study we describe the occurrence of fungi in 100 tap water and 16 groundwater samples from Slovenia. We used culture-dependent and culture-independent techniques. 28 fungal species belonging to 16 genera were isolated with selected culturing conditions, targeting human opportunistic yeasts and yeast-like fungi. Of special concern was the detection of Aureobasidium melanogenum, Exophiala dermatitidis, Rhinocladiella similis, Candida parapsilosis and Rhodotorula mucilaginosa. The DGGE analysis of ITS1 rDNA revealed from 6 to 16 bands hypothetically corresponding to different taxa, while pyrosequencing showed the presence of Aspergillus and Exophiala. According to the statistic machine learning methodology, the profile of fungi in water is determined by the concentration of calcium and magnesium ions and the presence of nitrate. Exophiala spp., C. parapsilosis and R. mucilaginosa are known as dominant contaminants of household appliances. It appears that they are transferred with water to dishwashers and washing machines, where they subsequently proliferate.     

RNA‐seq analysis reveals new candidate genes for drip loss in a Pietrain × Duroc × Landrace × Yorkshire population

Drip loss, one of the most important meat quality traits, is characterized by low heritability. To date, the genetic factors affecting the drip loss trait have not been clearly elucidated. The objective of this study was to identify critical candidate genes affecting drip loss. First, we generated a Pietrain × Duroc × Landrace × Yorkshire commercial pig population and obtained phenotypic values for the drip loss trait. Furthermore, we constructed two RNA libraries from pooled samples of longissimus dorsi muscles with the highest (H group) and lowest (L group) drip loss and identified the differentially expressed genes (DEGs) between these extreme phenotypes using RNA‐seq technology. In total, 25 883 genes were detected in the H and L group libraries, and none was specifically expressed in only one library. Comparative analysis of gene expression levels found that 150 genes were differentially expressed, of which 127 were upregulated and 23 were downregulated in the H group relative to the L group. In addition, 68 drip loss quantitative trait loci (QTL) overlapping with 63 DEGs were identified, and these QTL were distributed mainly on chromosomes 1, 2, 5 and 6. Interestingly, the triadin (TRDN) gene, which is involved in muscle contraction and fat deposition, and the myostatin (MSTN) gene, which has a role in muscle growth, were localized to more than two drip loss QTL, suggesting that both are critical candidate genes responsible for drip loss.     

Arsenic Bioaccumulation in Freshwater Fishes

The arsenic ambient water quality criterion (AWQC) for protection of human health via ingestion of aquatic organisms is currently 0.14 μ g/L. This AWQC is derived using a bioconcentration factor (BCF) of 44, which is a consumption-weighted average based on two data points for oysters and fish that was proposed by the U.S. Environmental Protection Agency in 1980 for broad application to freshwater and marine environments. This BCF is based on the assumption that bioaccumulation is a simple linear function of the exposure concentration. In the nearly quarter of a century since this BCF was promulgated, there have been additions to the arsenic bioaccumulation database and a broader scientific understanding of bioaccumulation mechanisms and how they can be applied to estimating tissue concentrations in aquatic organisms. From this database, we identified 12 studies of arsenic bioaccumulation in freshwater fishes in order to explore differences in laboratory-generated BCFs and field-generated bioaccumulation factors (BAFs) and to assess their relationship to arsenic concentrations in water. Our analysis indicates that arsenic concentrations in tissue and arsenic BAFs may be power functions of arsenic concentration in water. A power function indicates that the highest BCF values may occur at low background levels and may decrease as environmental concentrations increase above the ambient range.     

Influence of gestational maternal feed restriction on growth performance and meat quality of rabbit offsprings

The purpose of the present study was to evaluate the effect of feed restriction during pregnancy on reproductive performance of rabbit does and growth performance and meat quality of their offspring. A total of 26 primiparous non lactating does were equally divided into two treatment groups: the control group (C, n=13) that was fed ad libitum throughout gestation and the feed restricted group (R, n=13) that was fed to 75% of maintenance energy requirements from the 7^th to the 26^th day of gestation. Rabbit offsprings were weaned at 35 days of age and grown until the 72 days of age when they were slaughtered for meat quality assessment. Meat quality traits measured were pH₂₄, colour (L*, a*, b*), percentage of released water, cook loss, shear values and intramuscular fat. At kindling, R does produced smaller litter weights compared with those of does from group C, 447.8 and 591.4 g, respectively, and smaller individual kit birth weights, 56.2 and 71.5 g, respectively (P<0.05). Ratio of stillborn kits and mortality rate from parturition until weaning was higher (P<0.05) in the R group, 21.4% and 11.1%, respectively, in comparison with the C group, 8.1% and 3.5%, respectively. Litter size and gestation length were unaffected by maternal undernutrition. Kit birth weight treatment differences were eliminated at weaning because of compensatory growth (P>0.05). Performance and meat quality characteristics of fattening rabbits at 72 days of age were not influenced by gestational feed restriction of their mothers (P>0.05). Taking into consideration that, simultaneous gestation and lactation in rabbit does may be simulated by gestational feed restriction, results of the present study suggest that lactating does can support a simultaneous gestation without any adverse effect on the offsprings’ quantitative and qualitative performance at the expense of increased mortality rates at parturition and until weaning.     

Atlas versus range maps: robustness of chorological relationships to distribution data types in European mammals

Aim Chorological relationships describe the patterns of distributional overlap among species. In addition to revealing biogeographical structure, the resulting clusters of species with similar geographical distributions can serve as natural units in conservation planning. Here, we assess the extent to which temporal, methodological and taxonomical differences in the source of species’ distribution data can affect the relationships that are found. Location Western Europe. Methods We used two data sets – the Atlas of European mammals and polygon range maps from the IUCN Global Mammal Assessment – both as presence–absence data for UTM 50 km × 50 km squares. We performed pairwise comparisons among 156 species for each data set to build matrices of the similarity in distribution across species, using both Jaccard’s and Baroni‐Urbani & Buser’s indices. We then compared these similarity matrices (chorological relationships), as well as the species richness and occurrence patterns from the two data sets. Results As expected, range maps increased both the mean prevalence per species and mean species richness per grid cell in comparison to atlas data, reflecting the general view that these data types respectively over‐ and underestimate species occurrence. However, species richness and occurrence patterns in atlas and range map data were positively associated and, most importantly, the chorological relationships underlying the two data sets were highly similar. Main conclusions Despite many methodological, temporal and taxonomical differences between atlas data and range maps, the chorological relationships encountered between species were similar for both data sets. Chorological analyses can thus be robust to the data source used and provide a solid basis for analytical biogeographical studies, even over broad spatial scales.     

The role of protein quality control in mitochondrial protein homeostasis under oxidative stress

Mitochondria contribute significantly to the cellular production of ROS. The deleterious effects of increased ROS levels have been implicated in a wide variety of pathological reactions. Apart from a direct detoxification of ROS molecules, protein quality control mechanisms are thought to protect protein functions in the presence of elevated ROS levels. The reactivities of molecular chaperones and proteases remove damaged polypeptides, maintaining enzyme activities, thereby contributing to cellular survival both under normal and stress conditions. We characterized the impact of oxidative stress on mitochondrial protein homeostasis by performing a proteomic analysis of isolated yeast mitochondria, determining the changes in protein abundance after ROS treatments. We identified a set of mitochondrial proteins as substrates of ROS‐dependent proteolysis. Enzymes containing oxidation‐sensitive prosthetic groups like iron/sulfur clusters represented major targets of stress‐dependent degradation. We found that several proteins involved in ROS detoxification were also affected. We identified the ATP‐dependent protease Pim1/LON as a major factor in the degradation of ROS‐modified soluble polypeptides localized in the matrix compartment. As Pim1/LON expression was induced significantly under ROS treatment, we propose that this protease system performs a crucial protective function under oxidative stress conditions.