Patterns of contribution to citizen science biodiversity projects increase understanding of volunteers’ recording behaviour

The often opportunistic nature of biological recording via citizen science leads to taxonomic, spatial and temporal biases which add uncertainty to biodiversity estimates. However, such biases may also give valuable insight into volunteers’ recording behaviour. Using Greater London as a case-study we examined the composition of three citizen science datasets – from Greenspace Information for Greater London CIC, iSpot and iRecord - with respect to recorder contribution and spatial and taxonomic biases, i.e. when, where and what volunteers record. We found most volunteers contributed few records and were active for just one day. Each dataset had its own taxonomic and spatial signature suggesting that volunteers’ personal recording preferences may attract them towards particular schemes. There were also patterns across datasets: species’ abundance and ease of identification were positively associated with number of records, as was plant height. We found clear hotspots of recording activity, the 10 most popular sites containing open water. We note that biases are accrued as part of the recording process (e.g. species’ detectability) as well as from volunteer preferences. An increased understanding of volunteer behaviour gained from analysing the composition of records could thus enhance the fit between volunteers’ interests and the needs of scientific projects

From the kilns to the fair: producing building materials at Faragola and Canusium (northern Apulia, Italy)

Faragola and Canusium potters used Ca-rich clays—widely available nearby—for the production of build- ing materials. The clayey materials were used as received, before being fired in the local kilns at temperatures between 600 and ~1000 ° C. No technological distinctions were made in relation to the type of object to be produced (tile, brick, etc). The investigated productions are compositionally distinguish- able from both coarse wares for cooking and fine table ware produced in the same archaeological sites. A fine clayey ma- terial, very similar to that used for table ware, was supplied for the production of these building materials, which are chemi- cally, mineralogically and petrographically very similar among themselves. Hence, the Faragola and Canusium bricks and tiles cannot be easily discriminated but the presence/ absence of volcanites and volcanic glass represents an effec- tive discriminating factor, able to indicate areas of different supplies within two main deposits: the Pleistocene marine and alluvial terraced deposits, typical of northern Apulia

Ki67 nuclei detection and ki67-index estimation: A novel automatic approach based on human vision modeling

Background: The protein ki67 (pki67) is a marker of tumor aggressiveness, and its expression has been proven to be useful in the prognostic and predictive evaluation of several types of tumors. To numerically quantify the pki67 presence in cancerous tissue areas, pathologists generally analyze histochemical images to count the number of tumor nuclei marked for pki67. This allows estimating the ki67-index, that is the percentage of tumor nuclei positive for pki67 over all the tumor nuclei. Given the high image resolution and dimensions, its estimation by expert clinicians is particularly laborious and time consuming. Though automatic cell counting techniques have been presented so far, the problem is still open. Results: In this paper we present a novel automatic approach for the estimations of the ki67-index. The method starts by exploiting the STRESS algorithm to produce a color enhanced image where all pixels belonging to nuclei are easily identified by thresholding, and then separated into positive (i.e. pixels belonging to nuclei marked for pki67) and negative by a binary classification tree. Next, positive and negative nuclei pixels are processed separately by two multiscale procedures identifying isolated nuclei and separating adjoining nuclei. The multiscale procedures exploit two Bayesian classification trees to recognize positive and negative nuclei-shaped regions. Conclusions: The evaluation of the computed results, both through experts' visual assessments and through the comparison of the computed indexes with those of experts, proved that the prototype is promising, so that experts believe in its potential as a tool to be exploited in the clinical practice as a valid aid for clinicians estimating the ki67-index. The MATLAB source code is open source for research purposes

Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction

Methods for phenotype and outcome prediction are largely based on inductive supervised models that use selected biomarkers to make predictions, without explicitly considering the functional relationships between individuals. We introduce a novel network-based approach named Patient-Net (P-Net) in which biomolecular profiles of patients are modeled in a graph-structured space that represents gene expression relationships between patients. Then a kernel-based semi-supervised transductive algorithm is applied to the graph to explore the overall topology of the graph and to predict the phenotype/clinical outcome of patients. Experimental tests involving several publicly available datasets of patients afflicted with pancreatic, breast, colon and colorectal cancer show that our proposed method is competitive with state-of-the-art supervised and semi-supervised predictive systems. Importantly, P-Net also provides interpretable models that can be easily visualized to gain clues about the relationships between patients, and to formulate hypotheses about their stratification

Whole-genome analysis uncovers recurrent IKZF1 inactivation and aberrant cell adhesion in blastic plasmacytoid dendritic cell neoplasm

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and highly aggressive hematological malignancy with a poorly understood pathobiology and no effective therapeutic options. Despite a few recurrent genetic defects (eg, single nucleotide changes, indels, large chromosomal aberrations) have been identified in BPDCN, none are disease-specific, and more importantly, none explain its genesis or clinical behavior. In this study, we performed the first high resolution whole-genome analysis of BPDCN with a special focus on structural genomic alterations by using whole-genome sequencing and RNA sequencing. Our study, the first to characterize the landscape of genomic rearrangements and copy number alterations of BPDCN at nucleotide-level resolution, revealed that IKZF1, a gene encoding a transcription factor required for the differentiation of plasmacytoid dendritic cell precursors, is focally inactivated through recurrent structural alterations in this neoplasm. In concordance with the genomic data, transcriptome analysis revealed that conserved IKZF1 target genes display a loss-of-IKZF1 expression pattern. Furthermore, up-regulation of cellular processes responsible for cell-cell and cell-ECM interactions, which is a hallmark of IKZF1 deficiency, was prominent in BPDCN. Our findings suggest that IKZF1 inactivation plays a central role in the pathobiology of the disease, and consequently, therapeutic approaches directed at reestablishing the function of this gene might be beneficial for patients

Predictors and outcomes associated with the growth curves of self-efficacy beliefs in regard to anger and sadness regulation during adolescence: a longitudinal cross-cultural study

IntroductionThis longitudinal study examined unique and joint effects of parenting and negative emotionality in predicting the growth curves of adolescents’ self-efficacy beliefs about regulating two discrete negative emotions (anger and sadness) and the association of these growth curves with later maladjustment (i.e., internalizing and externalizing problems).MethodsParticipants were 285 children (T1: Mage = 10.57, SD = 0.68; 53.3% girls) and their parents (mothers N = 286; fathers N = 276) from Colombia and Italy. Parental warmth, harsh parenting, and internalizing and externalizing problems were measured in late childhood at T1, whereas early adolescents’ anger and sadness were measured at T2 (T2: Mage = 12.10, SD = 1.09). Adolescent self-efficacy beliefs about anger and sadness regulation were measured at five time-points from T2 to T6 (T6: Mage = 18.45, SD = 0.71), and internalizing and externalizing problems were measured again at T6.ResultsMulti-group latent growth curve models (with country as the grouping variable) demonstrated that in both countries there was on average a linear increase in self-efficacy about anger regulation and no change or variation in self-efficacy about sadness regulation. In both countries, for self-efficacy about anger regulation (a) T1 harsh parenting and T1 externalizing problems were negatively associated with the intercept, (b) T2 anger was negatively associated with the slope, and (c) the intercept and the slope were associated with lower T6 internalizing and externalizing problems, controlling for T1 problems. For self-efficacy about sadness regulation, (a) T1 internalizing problems were negatively associated with the intercept only in Italy, (b) T2 sadness was negatively associated with the intercept only in Colombia, and (c) the intercept negatively predicted T6 internalizing problems.DiscussionThis study advances knowledge of the normative development of self-efficacy beliefs about anger and sadness regulation during adolescence across two countries, highlighting the predictive value of pre-existing family and individual characteristics on this development and prediction by the development of self-efficacy beliefs on later adjustment

Glass groups, glass supply and recycling in late Roman Carthage

Carthage played an important role in maritime exchange networks during the Roman and late antique periods. One hundred ten glass fragments dating to the third to sixth centuries CE from a secondary deposit at the Yasmina Necropolis in Carthage have been analysed by electron microprobe analysis (EPMA) to characterise the supply of glass to the city. Detailed bivariate and multivariate data analysis identified different primary glass groups and revealed evidence of extensive recycling. Roman mixed antimony and manganese glasses with MnO contents in excess of 250 ppm were clearly the product of recycling, while iron, potassium and phosphorus oxides were frequent contaminants. Primary glass sources were discriminated using TiO2 as a proxy for heavy minerals (ilmenite/spinel), Al2O3 for feldspar and SiO2 for quartz in the glassmaking sands. It was thus possible to draw conclusions about the chronological and geographical attributions of the primary glass types. Throughout much of the period covered in this study, glassworkers in Carthage utilised glass from both Egyptian and Levantine sources. Based on their geochemical characteristics, we conclude that Roman antimony and Roman manganese glasses originated from Egypt and the Levant, respectively, and were more or less simultaneously worked at Carthage in the fourth century as attested by their mixed recycling (Roman Sb-Mn). In the later fourth and early fifth centuries, glasses from Egypt (HIMT) and the Levant (two Levantine I groups) continued to be imported to Carthage, although the Egyptian HIMT is less well represented at Yasmina than in many other late antique glass assemblages. In contrast, in the later fifth and sixth centuries, glass seems to have been almost exclusively sourced from Egypt in the form of a manganese-decolourised glass originally described and characterised by Foy and colleagues (2003). Hence, the Yasmina assemblage testifies to significant fluctuations in the supply of glass to Carthage that require further attention