Network regression with predictive clustering trees

Network data describe entities represented by nodes, which may be connected with (related to) each other by edges. Many network datasets are characterized by a form of autocorrelation, where the value of a variable at a given node depends on the values of variables at the nodes it is connected with. This phenomenon is a direct violation of the assumption that data are independently and identically distributed. At the same time, it offers an unique opportunity to improve the performance of predictive models on network data, as inferences about one entity can be used to improve inferences about related entities. Regression inference in network data is a challenging task. While many approaches for network classification exist, there are very few approaches for network regression. In this paper, we propose a data mining algorithm, called NCLUS, that explicitly considers autocorrelation when building regression models from network data. The algorithm is based on the concept of predictive clustering trees (PCTs) that can be used for clustering, prediction and multi-target prediction, including multi-target regression and multi-target classification. We evaluate our approach on several real world problems of network regression, coming from the areas of social and spatial networks. Empirical results show that our algorithm performs better than PCTs learned by completely disregarding network information, as well as PCTs that are tailored for spatial data, but do not take autocorrelation into account, and a variety of other existing approaches.     

The Landscape of microRNAs in βCell: Between Phenotype Maintenance and Protection

Diabetes mellitus is a group of heterogeneous metabolic disorders characterized by chronic hyperglycaemia mainly due to pancreatic β cell death and/or dysfunction, caused by several types of stress such as glucotoxicity, lipotoxicity and inflammation. Different patho-physiological mechanisms driving β cell response to these stresses are tightly regulated by microRNAs (miRNAs), a class of negative regulators of gene expression, involved in pathogenic mechanisms occurring in diabetes and in its complications. In this review, we aim to shed light on the most important miRNAs regulating the maintenance and the robustness of β cell identity, as well as on those miRNAs involved in the pathogenesis of the two main forms of diabetes mellitus, i.e., type 1 and type 2 diabetes. Additionally, we acknowledge that the understanding of miRNAs-regulated molecular mechanisms is fundamental in order to develop specific and effective strategies based on miRNAs as therapeutic targets, employing innovative molecules.     

The GAUGAA Motif Is Responsible for the Binding between circSMARCA5 and SRSF1 and Related Downstream Effects on Glioblastoma Multiforme Cell Migration and Angiogenic Potential

Circular RNAs (circRNAs) are a large class of RNAs with regulatory functions within cells. We recently showed that circSMARCA5 is a tumor suppressor in glioblastoma multiforme (GBM) and acts as a decoy for Serine and Arginine Rich Splicing Factor 1 (SRSF1) through six predicted binding sites (BSs). Here we characterized RNA motifs functionally involved in the interaction between circSMARCA5 and SRSF1. Three different circSMARCA5 molecules (Mut1, Mut2, Mut3), each mutated in two predicted SRSF1 BSs at once, were obtained through PCR-based replacement of wild-type (WT) BS sequences and cloned in three independent pcDNA3 vectors. Mut1 significantly decreased its capability to interact with SRSF1 as compared to WT, based on the RNA immunoprecipitation assay. In silico analysis through the “Find Individual Motif Occurrences” (FIMO) algorithm showed GAUGAA as an experimentally validated SRSF1 binding motif significantly overrepresented within both predicted SRSF1 BSs mutated in Mut1 (q-value = 0.0011). U87MG and CAS-1, transfected with Mut1, significantly increased their migration with respect to controls transfected with WT, as revealed by the cell exclusion zone assay. Immortalized human brain microvascular endothelial cells (IM-HBMEC) exposed to conditioned medium (CM) harvested from U87MG and CAS-1 transfected with Mut1 significantly sprouted more than those treated with CM harvested from U87MG and CAS-1 transfected with WT, as shown by the tube formation assay. qRT-PCR showed that the intracellular pro- to anti-angiogenic Vascular Endothelial Growth Factor A (VEGFA) mRNA isoform ratio and the amount of total VEGFA mRNA secreted in CM significantly increased in Mut1-transfected CAS-1 as compared to controls transfected with WT. Our data suggest that GAUGAA is the RNA motif responsible for the interaction between circSMARCA5 and SRSF1 as well as for the circSMARCA5-mediated control of GBM cell migration and angiogenic potential.     

P16 and HPV Genotype Significance in HPV-Associated Cervical Cancer—A Large Cohort of Two Tertiary Referral Centers

The expression of p16 is a good surrogate of human papillomavirus (HPV) infection in HPV-associated cancers. The significance of p16 expression, HPV genotype and genera in the outcome of patients with HPV-associated cervical cancer (CC) is unclear. Our aim is to ascertain the prognostic significance of these factors. Data from 348 patients (median age: 47.5 years old) with CC, diagnosed in two referral centers, were retrospectively collected. Advanced disease (FIGO2018 IB2-IV) was present in 68% of patients. A single HPV genotype was identified in 82.8% of patients. The most common HPVs were HPV16 (69%) and HPV18 (14%). HPV genera reflected this distribution. HPV16 tumors presented at an earlier stage. P16 was negative in 18 cases (5.2%), 83.3% of which were squamous cell carcinomas. These cases occurred in older patients who tended to have advanced disease. In the univariate analysis, HPV16 (HR: 0.58; p = 0.0198), α-9 genera (HR: 0.37; p = 0.0106) and p16 overexpression (HR: 0.54; p = 0.032) were associated with better survival. HPV16 (HR: 0.63; p = 0.0174) and α-9 genera (HR: 0.57; p = 0.0286) were associated with less relapse. In the multivariate analysis, only the International Federation of Gynecology and Obstetrics (FIGO) stage retained an independent prognostic value. HPV16, α-9 genera and p16 overexpression were associated with better survival, although not as independent prognostic factors. Patients with p16-negative HPV-associated CC were older, presented with advanced disease and had worse prognosis.     

Syndecan-1 Depletion Has a Differential Impact on Hyaluronic Acid Metabolism and Tumor Cell Behavior in Luminal and Triple-Negative Breast Cancer Cells

Glycosaminoglycans (GAGs) and proteoglycans (PGs) are major components of the glycocalyx. The secreted GAG and CD44 ligand hyaluronic acid (HA), and the cell surface PG syndecan-1 (Sdc-1) modulate the expression and activity of cytokines, chemokines, growth factors, and adhesion molecules, acting as critical regulators of tumor cell behavior. Here, we studied the effect of Sdc-1 siRNA depletion and HA treatment on hallmark processes of cancer in breast cancer cell lines of different levels of aggressiveness. We analyzed HA synthesis, and parameters relevant to tumor progression, including the stem cell phenotype, Wnt signaling constituents, cell cycle progression and apoptosis, and angiogenic markers in luminal MCF-7 and triple-negative MDA-MB-231 cells. Sdc-1 knockdown enhanced HAS-2 synthesis and HA binding in MCF-7, but not in MDA-MB-231 cells. Sdc-1-depleted MDA-MB-231 cells showed a reduced CD24-/CD44+ population. Furthermore, Sdc-1 depletion was associated with survival signals in both cell lines, affecting cell cycle progression and apoptosis evasion. These changes were linked to the altered expression of KLF4, MSI2, and miR-10b and differential changes in Erk, Akt, and PTEN signaling. We conclude that Sdc-1 knockdown differentially affects HA metabolism in luminal and triple-negative breast cancer model cell lines and impacts the stem phenotype, cell survival, and angiogenic factors.     

Total content and dialyzable iron and zinc in foods from northern and Southern Mexico

Developing countries diets are based on a variety of plant foods that often are the main suppliers of important amounts of iron (Fe) and zinc (Zn). The objectives of this study were 1) to measure the total and dialyzable amounts of Fe and Zn in foods from Northern Mexico (Sonora) and from Southern Mexico (Oaxaca) and 2) to evaluate the effect of meat content of diets on the dialyzable amount of Fe and Zn. Methods to calculate the total dialyzable amount of Fe and Zn, were those of the AOAC and of Shen et al. Total Fe in e northern Mexican foods went from 0.78 +/- 0.0 to 11.59 +/- to 0.03 mg/ 100g (dry weight, DW); in southern Mexican foods the same micronutrient amounts were 0.86 +/- 0.18 to 8.8 +/- 0.57 mg/100 g (BS). Total Zn values were 0.91 +/- 0.00 to 13.58 +/- 0.05 mg/100 g (DW) in Sonora, and 0.64 +/- 0.18 to 20.80 +/- 0.33 mg/100 g (DW) in Oaxaca. In northern Mexico, foods dialyzable Fe had values from 0.1 +/- 0.04% to 10.6 +/- 0.36% and for Zn from 4.0 +/- 0.21% to 55.32 +/- 0.14%. Meanwhile, the range of values of dialyzable Fe for foods from Oaxaca were from 0.22 +/- 0.06% to 9.40 +/- 0.14% for and from 2.41 +/- 0.26% to 54.27 +/- 1.49% for dialyzable Zn. The average value for dialyzable Fe was higher in the foods that contained meat or meat products (p= 0.001).     

A low-cost real time virtual system for postural stability assessment at home

Background and objective

The degeneration of the balance control system in the elderly and in many pathologies requires measuring the equilibrium conditions very often. In clinical practice, equilibrium control is commonly evaluated by using a force platform (stabilometric platform) in a clinical environment.In this paper, we demonstrate how a simple movement analysis system, based on a 3D video camera and a 3D real time model reconstruction of the human body, can be used to collect information usually recorded by a physical stabilometric platform.

Methods

The algorithm used to reconstruct the human body model as a set of spheres is described and discussed. Moreover, experimental measurements and comparisons with data collected by a physical stabilometric platform are also reported. The measurements were collected on a set of 6 healthy subjects to whom a change in equilibrium condition was stimulated by performing an equilibrium task.

Results

The experimental results showed that more than 95% of data collected by the proposed method were not significantly different from those collected by the classic platform, thus confirming the usefulness of the proposed system.

Conclusions

The proposed virtual balance assessment system can be implemented at low cost (about 500$) and, for this reason, can be considered a home use medical device. On the contrary, astabilometric platform has a cost of about 10,000$ and requires periodical calibration. The proposed system does not require periodical calibration, as is necessary for stabilometric force platforms, and it is easy to use. In future, the proposed system with little integration can be used, besides being an emulator of a stabilometric platform, also to recognize and track, in real time, head, legs, arms and trunk, that is to collect information actually obtained by sophisticated optoelectronic systems.     

Broken probes: toward the design of worn media

This article describes the development and use of broken probes: prompted processes of degradation that produce unique identifiers with which to associate and retrieve digitally recorded histories. We offer our design and deployment of Broken Probes as a methodology for eliciting insights into how broken objects and acts of breakage may be given new life through their integration with ubiquitous computing technologies. Based on these developments, we introduce the genre of worn media—a variety of computational material with which to frame and critically examine the manifestation of wear among digital things. We end by discussing how the genre of worn media sensitizes designers and Ubicomp researchers to issues of incompleteness, impermanence, and imperfection to help account for the ethical, material, and historical terms of endurance in a digital age.