Miracle-dz/UniFAR-FTUs huggingface dataset:
Breast cancer intrinsic subtypes: a critical conception in bioinformatics

s Published MILIOLI, H.H. ; TISHCHENKO, I. ; RIVEROS, C. ; SAKOFF, J.; BERRETTA, R. ; MOSCATO, P. Consensus on breast cancer cell lines classification for an effective and efficient clinical decision-making. IMPAKT 2015 Breast Cancer Conference. Annals of Oncology 26 (suppl 3):iii32-iii33 (2015). doi: 10.1093/annonc/mdv121.08 MILIOLI, H.H. ; TISHCHENKO, I. ; RIVEROS, C. ; BERRETTA, R. ; MOSCATO, P. Molecular classification of basal-like breast cancer subtypes based on predictive survival markers. IMPAKT 2015 Breast Cancer Conference. Annals of Oncology. 26 (suppl 3):iii17-iii18 (2015). doi: 10.1093/annonc/mdv117.11 MILIOLI, H.H. , TISHCHENKO, I. , RIVEROS, C. , BERRETTA, R. & MOSCATO, P. (2015) Basal-like breast cancer subgroups uncovered by genomic and transcriptomic profiles and overall survival outcomes. Hunter Cancer Research Alliance Annual Symposium. Asia-Pacific Journal of Clinical Oncology 11(Suppl. 5):6-19 (2015). doi: 10.1111/ajco.12444 TISHCHENKO, I. , MILIOLI, H.H. , RIVEROS, C. & MOSCATO, P. How intrinsic are luminal breast cancer subtypes? Hunter Cancer Research Alliance Annual Symposium. Asia-Pacific Journal of Clinical Oncology 11(Suppl. 5):6-19 (2015). doi: 10.1111/ajco.12444 Bioinformatics in Breast Cancer XXV MILIOLI, H.H. , SANHUEZA, C. , BERRETTA, R. & MOSCATO, P. (2015) ABSTRACT P40 Breast Cancer Molecular Portraits of Intrinsic Subtypes and Integrative Clusters in the METABRIC Data Set. Hunter Cancer Research Alliance Annual Symposium. Asia-Pacific Journal of Clinical Oncology 12(Suppl. 6):13-34 (2016). doi: 10.1111/ajco.12618
An activation pathway governs cell wall polymerization by a bacterial morphogenic machine

Cell elongation in rod-shaped bacteria is mediated by the Rod system, a conserved morphogenic complex that spatially controls cell wall (CW) assembly. In Escherichia coli, alterations in a CW synthase component of the system called PBP2 were identified that overcome other inactivating defects. Rod system activity was stimulated in the suppressors in vivo, and purified synthase complexes with these changes showed more robust CW synthesis in vitro. Polymerization of the actin-like MreB component of the Rod system was also found to be enhanced in cells with the activated synthase. The results suggest an activation pathway governing Rod system function in which PBP2 conformation plays a central role in stimulating both CW glycan polymerization by its partner RodA and the formation of cytoskeletal filaments of MreB to orient CW assembly. An analogous activation pathway involving similar enzymatic components is likely responsible for controlling CW synthesis by the division machinery.
Characteristics and Motivations of Consumers of Direct Purchasing Channels and the Perceived Barriers to Alternative Food Purchase: A Cross-Sectional Study in the Ecuadorian Andes

Modern food systems generate social inequalities in the access to healthy food, but some families maintain behaviors that provide an alternative to these systems. Agroecological consumers (ACs) and non-agroecological direct market consumers (DMCs) are key actors in alternative food systems. We assessed the characteristics of ACs and DMCs using data from a representative sample of households in Ibarra, Quito and Riobamba (n = 2914). We also deepened the exploration of motivations for adopting these practices through mini-ethnographies with families who were identified as ACs or DMCs (n = 15). We found motivations related to personal health problems, food quality (e.g., taste, freshness), and safety (e.g., avoiding pesticides) to be key. Other motivations were price and community solidarity with farmers. Barriers included inconvenience, lack of awareness, and insecurity of market location. Using Chi-square tests, we found differences between ACs and DMCs on place of residence, education, employment, health, and diet. Controlling for socioeconomic and health variables using logistic regressions, we found DMC dietary habits to be similar to the remainder of the study population, except that they were less likely to eat processed foods less frequently (adjusted odds ratio (AOR) 0.6, 95% confidence interval 0.4–0.9). In contrast, ACs were more likely than the remainder of the study population to control their salt intake (3.2, 1.9–5.2) and have greater knowledge of nutrition labels (2.8, 1.7–4.6). They were more likely to eat traditional foods frequently (1.9, 1.1–3.3), fruit and vegetables daily (1.6, 1.0–2.8), and processed foods less frequently (2.7, 1.5–4.8). Hence, these two types of alternative food provisioning practices (AC and DMC) were adopted by different types of consumers, with heterogenous motivations and food consumption practices. These findings have implications for public health initiatives aiming to scale up the nutrition and ecological potential of alternative food systems.
Designing Novel and Engaging Interactions with and for Residents Living with Dementia and their Visitors

: This paper describes the interaction mechanism and content design of the “A Better Visit app” — a collection of touch screen tablet mini-games developed for people living with dementia and their visitors to create enjoyable shared experiences and spark social interaction between them. The published collection, available on the App Store and Google Play for tablet devices, is made up of eight different mini-games. The games were developed and refined over an 18-month co-design and observation process and matured to solutions that support easy to use games leading to meaningful interactions during the visit. Emphasis is placed on different sensory and creative experiences, skill development, and communication between the visitor and resident to live their relationship in the moment of time. The outcome are a specialised set of interaction mechanisms and recommendations developed to aid in the accessibility of the technology experience for people living with advanced dementia.
Soft sweeps and beyond: Understanding the patterns and probabilities of selection footprints under rapid adaptation

The tempo and mode of adaptive evolution determine how natural selection shapes patterns of genetic diversity in DNA polymorphism data. While slow mutation-limited adaptation leads to classical footprints of “hard” selective sweeps, these patterns are different when adaptation responds quickly to a novel selection pressure, acting either on standing genetic variation or on recurrent new mutation. In the past decade, corresponding footprints of “soft” selective sweeps have been described both in theoretical models and in empirical data. Here, we summarize the key theoretical concepts and contrast model predictions with observed patterns in Drosophila, humans, and microbes. Evidence in all cases shows that “soft” patterns of rapid adaptation are frequent. However, theory and data also point to a role of complex adaptive histories in rapid evolution. While existing theory allows for important implications on the tempo and mode of the adaptive process, complex footprints observed in data are, as yet, insufficiently covered by models. They call for in-depth empirical study and further model development.
Cytogenetic bioassays as tools to distinguish between toxic and non-toxic varieties of Jatropha curcas (Euphorbiaceae)

The tropical and subtropical naturalized physic nut ( Jatropha curcas L.), has been explored for biodiesel production in recent times. The oil is extracted from the seeds and, for the production to be feasible, utilization of the residual seed cake is crucial. Although the cake could be employed as a protein source in animal feed, it is rich in phorbol ester, which is toxic for animals. Therefore, breeding programs have been working to reduce or eliminate the phorbol ester content in physic nut. In this context, the present work aimed to evaluate the physic nut oil of toxic and non-toxic varieties (containing known or undetectable amounts of phorbol ester, respectively) with regards to phytotoxicity in a model experiment with Lactuca sativa L. For this, the percentage of germinated seeds was evaluated after 8, 16, 24, 36 and 48 hours of exposure to the treatments with toxic and non-toxic oil at concentrations of 22.5 %, 45 % and 67.5 % of emulsion (physic nut oil energetically mixed with distilled water). Root growth was determined after 48 hours of exposure and the germination speed index was obtained. The different stages of mitotic division as well as possible chromosomal and nuclear alterations were also recorded. The mitotic index was calculated as the number of dividing cells, as a fraction of the total number of cells, and the frequency of chromosome and nuclear alterations, expressed as the percentage of number of alterations divided by the total number of cells. Both varieties exhibited phytotoxicity, inducing significant reductions in percentage of germinated seeds (reduction of 98 %), germination speed index (reduction of 24.44) and root growth (reduction of 8.54 mm). In microscopic analysis, a mitodepressive effect was observed for both oils at the three concentrations used when compared to the negative control; however, it was possible to distinguish between the toxic and the non-toxic varieties based on the more expressive reduction of division promoted by the first, 2.19 %. Significant increments in the frequency of mitotic cells showing chromosome alterations as well, as the presence of condensed nuclei, were observed in the treated cells. However, these parameters were not significantly different from the control in the cells treated with both physic nut oils. In conclusion, the evaluation of root growth and cell division in the plant model L. sativa, can be proposed as an alternative to animal tests to distinguish the varieties with high and low phorbol ester concentration, thus contributing to the detection of toxicity in varieties used in breeding programs. Rev. Biol. Trop. 66(2): 495-502. Epub 2018 June 01.
Carotenoid-based plumage pigmentation and concentration as a function of sex and habitat type in the Yellow-breasted Boubou Laniarius atroflavus

The study of avian integumentary colouration can offer insight into dietary and metabolic processes as well as fitness in focal species. Yet, we know relatively less about the system of feather colouration in African birds in comparison to Europe, North America and the neotropics. In this study, we biochemically characterised and quantified the pigmentary basis for breast plumage colouration in the Yellow-breasted Boubou Laniarius atroflavus, a little-known Afromontane species restricted to the Nigerian–Cameroon Highlands. We also measured differences in carotenoid concentration and feather reflectance between sexes, and between birds inhabiting edge and riparian habitats. Six carotenoid pigments were recovered from the yellow feathers – canary xanthophyll A and B, a cis isomer of each, isoastaxanthin and an unidentified carotenoid. We determined that the yellow colour of the breast feathers is carotenoid-based, with the greater proportion as canary xanthophylls. The presence of the ketocarotenoid, isoastaxanthin, provides the basis for further studies into red, orange and yellow coloured congenerics. Males appeared to have higher feather pigment concentrations than females, and birds resident in the edge habitat appeared to have slightly higher feather pigment concentrations than those in the degraded riparian habitat. There was little indication of differences in feather reflectance between sexes and habitat types. However, low samples size restricted further differentiation. There is also the need for further studies on the dietary and metabolic pathways of feather colouration to better understand how ecological variation may shape pigment uptake, transport, synthesis and deposition in feathers.
Party preference representation

Political parties are key actors in electoral democracies: they organize the legislature, form governments, and citizens choose their representatives by voting for them. How citizens evaluate political parties and how well the parties that citizens evaluate positively perform thus provide useful tools to estimate the quality of representation from the individual’s perspective. We propose a measure that can be used to assess party preference representation at both the individual and aggregate levels, both in government and in parliament. We calculate the measure for over 160,000 survey respondents following 111 legislative elections held in 38 countries. We find little evidence that the party preferences of different socio-economic groups are systematically over or underrepresented. However, we show that citizens on the right tend to have higher representation scores than their left-wing counterparts. We also find that whereas proportional systems do not produce higher levels of representation on average, they reduce variance in representation across citizens.
Unraveling The Mechanisms Behind Chinese Outbound Tourist Shopping: A Social Practice Perspective

Chinese outbound tourist shopping is a prominent phenomenon in many destinations, but the mechanisms behind it have rarely been addressed. This study draws upon social practice theory to examine why shopping dominates the tourist experience of Chinese travelers in Australia. Thirty-two semistructured interviews were conducted to identify key social and consumption practices that lead to the dominance of Chinese outbound tourist shopping. The study argues that the shopping practices of Chinese tourists result from a combination of Chinese consumerism and guanxi maintenance under the condition of outbound travel. This study contributes to a holistic understanding of Chinese outbound tourist shopping by revealing how it is embedded in broader consumption practices in China.
Pest categorisation of naturally‐spreading psorosis

Abstract The EFSA Panel on Plant Health performed a pest categorisation of naturally‐spreading psorosis of citrus for the European Union. Naturally‐spreading psorosis is poorly defined, because the status of both the disease and its causal agent(s) is uncertain. However, Citrus psorosis virus (CPsV) is a well‐ characterised Ophiovirus that is systematically associated with the psorosis disease and therefore considered to be its causal agent. Efficient diagnostics are available for CPsV. It is present in at least three EU MS. Naturally‐spreading psorosis is currently regulated by Directive 2000/29/EC, while CPsV is not explicitly mentioned in this Directive. CPsV has the potential to enter, establish and spread in the EU territory. However, the main pathway for entry is closed by the existing legislation so that entry is only possible through minor alternative pathways. Plants for planting are the major means of spread while there are uncertainties on the existence and efficiency of a natural spread mechanism. CPsV introduction and spread in the EU would have negative consequences on the EU citrus industry. Of the criteria evaluated by EFSA to qualify as a Union quarantine pest or as a Union regulated non‐quarantine pest (RNQP), Naturally‐spreading psorosis does not meet the criterion of being a well characterised pest or disease. As it is not explicitly mentioned in the legislation, it is unclear whether CPsV meets the criterion of being currently regulated or under official control. It meets, however, all the RNQP criteria. The key uncertainties of this categorisation concern: (1) the causal role of CPsV in the psorosis disease as well as elements of its biology and epidemiology, (2) the exact nature of the Naturally‐spreading psorosis syndrome and the identity of its causal agent and, consequently, (3) whether CPsV should be considered as being covered by the current legislation.
Effect of Moisture on the Thermal Conductivity of Cellulose and Aramid Paper Impregnated with Various Dielectric Liquids

This paper presents the effect of the impact of moisture in paper insulation used as insulation of transformer windings on its thermal conductivity. Various types of paper (cellulose and aramid) and impregnated (mineral oil, synthetic ester, and natural ester) were tested. The impact of paper and impregnated types on the changes in thermal conductivity of paper insulation caused by an increase in moisture were analyzed. A linear equation, describing the changes in thermal conductivity due to moisture, for various types of paper and impregnated, was developed. The results of measuring the thermal conductivity of paper insulation depending on the temperature are presented. The aim of the study is to develop an experimental database to better understand the heat transport inside transformers to assess aging and optimize their performance.
Partial migration by large ungulates: characteristics of seasonal moose Alces alces ranges in northern Sweden

We studied seasonal migration of individually radio-collared moose Alces alces in a partially migrant population in northern Sweden. First, to investigate habitat selection at the level of individuals, we examined use vs availability of habitat characteristics within seasonal ranges. Second, to investigate what habitat characteristics migrants use to select these seasonal ranges, we contrasted the characteristics of summer and winter ranges of individual migrants. Third, to investigate why some moose migrate whereas others do not, we contrasted the snow conditions and the composition of the vegetation in the seasonal ranges of 36 migrant and 30 resident moose. At the level of habitat selection within a range, moose selected areas which had less mire, clear-cut and field habitats, as well as less snow. At the level of the entire range, migrants and residents had rather similar range compositions and differed only in migrants having less field habitats in their winter ranges; the proportion of Scots pine Pinus sylvestris stands, Norway spruce Picea abies stands, mire, deciduous, and clear-cut forest habitats did not differ, nor was there a difference in snow depth. Similarly, within the group of migrants, we detected no differences in habitat composition or snow depth between the summer ranges they just left, and the winter ranges they moved to. Snow quality (as indexed by the depths to which moose sank) did not differ between the two seasonal ranges of migrants, but calves sank less deeply in ranges of migrants than in ranges of residents, suggesting that snow quality may play a role in the selection of ranges by moose or their decision to migrate/remain resident. Thus, habitat composition and snow depth were important at lower levels of habitat selection, but differences among home ranges were not dramatic. The observation that snow quality differed significantly between ranges of residents and migrants suggests that future studies of migration might profitably investigate snow quality.
GEOMETRICAL CALIBRATION FOR THE PANROVER: A STEREO OMNIDIRECTIONAL SYSTEM FOR PLANETARY ROVER

Abstract. A novel panoramic stereo imaging system is proposed in this paper. The system is able to carry out a 360° stereoscopic vision, useful for rover autonomous-driving, and capture simultaneously a high-resolution stereo scene. The core of the concept is a novel "bifocal panoramic lens" (BPL) based on hyper hemispheric model (Pernechele et al. 2016). This BPL is able to record a panoramic field of view (FoV) and, simultaneously, an area (belonging to the panoramic FoV) with a given degree of magnification by using a unique image sensor. This strategy makes possible to avoid rotational mechanisms. Using two BPLs settled in a vertical baseline (system called PANROVER) allows the monitoring of the surrounding environment in stereoscopic (3D) mode and, simultaneously, capturing an high-resolution stereoscopic images to analyse scientific cases, making it a new paradigm in the planetary rovers framework. Differently from the majority of the Mars systems which are based on rotational mechanisms for the acquisition of the panoramic images (mosaicked on ground), the PANROVER does not contain any moving components and can rescue a hi-rate stereo images of the context panorama. Scope of this work is the geometric calibration of the panoramic acquisition system by the omnidirectional calibration methods (Scaramuzza et al. 2006) based on Zhang calibration grid. The procedures are applied in order to obtain well rectified synchronized stereo images to be available for 3D reconstruction. We applied a Zhang chess boards based approach even during STC/SIMBIO-SYS stereo camera calibration (Simioni et al. 2014, 2017). In this case the target of the calibration will be the stereo heads (the BPLs) of the PANROVER with the scope of extracting the intrinsic parameters of the optical systems. Differently by previous pipelines, using the same data bench the estimate of the extrinsic parameters is performed.
An epithelial-mesenchymal-amoeboid transition gene signature reveals molecular subtypes of breast cancer progression and metastasis

Cancer cells within a tumor are known to display varying degrees of metastatic propensity but the molecular basis underlying such heterogeneity remains unclear. We analyzed genome-wide gene expression data obtained from primary tumors of lymph node-negative breast cancer patients using a novel metastasis biology-based Epithelial-Mesenchymal-Amoeboid Transition (EMAT) gene signature, and identified molecularly distinct subtypes associated with distinct prognostic profiles. EMAT subtype status improved prognosis accuracy of clinical parameters and statistically outperformed traditional breast cancer intrinsic subtypes. Additionally, analysis of 3D spheroids from an in vitro isogenic model of breast cancer progression reveals that EMAT subtypes display progression from premalignant to malignant and pre-invasive to invasive cancer. EMAT classification is a biologically informed method to assess metastasis risk in early stage, lymph node-negative breast cancer patients and appears to molecularly reconcile conflicting paradigms of breast cancer metastasis.
Combining Simulation and Machine Learning as Digital Twin for the Manufacturing of Overmolded Thermoplastic Composites

The design and development of composite structures requires precise and robust manufacturing processes. Composite materials such as fiber reinforced thermoplastics (FRTP) provide a good balance between manufacturing time, mechanical performance and weight. In this contribution, we investigate the process combination of thermoforming FRTP sheets (organo sheets) and injection overmolding of short FRTP for automotive structures. The limiting factor in those structures is the bond strength between the organo sheet and the overmolded thermoplastic. Within this process chain, even small deviations of the process settings (e.g., temperature) can lead to significant defects in the structure. A cyber physical production system based framework for a digital twin combining simulation and machine learning is presented. Based on parametric Finite-Element-Method (FEM) studies, training data for machine learning methods are generated and a FEM surrogate is developed. A comparison of different data-driven methods yields information on the estimation accuracy of task-specific data-driven methods. Finally, in accordance with experimental cross tension tests, the investigated FEM surrogate model is able to predict the interface bond strength quality in dependence of the process settings. The visualization into different quality domains qualifies the presented approach as decision support.