Near optimal solutions to least-squares problems with stochastic uncertainty

In this paper, we consider least-squares (LS) problems where the regression data is affected by parametric stochastic uncertainty. In this setting, we study the problem of minimizing the expected value with respect to the uncertainty of the LS residual. For general nonlinear dependence of the data on the uncertain parameters, determining an exact solution to this problem is known to be computationally prohibitive. Here, we follow a probabilistic approach, and determine a probable near optimal solution by minimizing the empirical mean of the residual. Finite sample convergence of the proposed method is assessed using statistical learning methods. In particular, we prove that if one constructs the empirical approximation of the mean using a finite number N of samples, then the minimizer of this empirical approximation is, with high probability, an ε-suboptimal solution for the original problem. Moreover, this approximate solution can be efficiently determined numerically by a standard recursive algorithm. Comparisons with gradient algorithms for stochastic optimization are also discussed in the paper and several numerical examples illustrate the proposed methodology.     

Regulation of the proliferative potential of cord blood long-term culture-initiating cells (LTC-IC) by different stromal cell lines: implications for LTC-IC measurement

BACKGROUND AND OBJECTIVE: Long-term culture-initiating cells (LTC-IC) are the best available approximation to an in vitro assay of stem cells in humans although they still represent a heterogeneous population in terms of proliferative capacity and sensitivity to different growth factors. Human umbilical cord blood (CB) is rich in hemopoietic progenitor cells, as measured by clonogenic assays and contains stem cells capable of reconstituting the marrow after ablation in clinical transplantation. We evaluated the influence of culture conditions on the in vitro behavior of LTC-IC from CB. DESIGN AND METHODS: LTC-IC were evaluated in long-term cultures, comparing two types of murine stromal cell lines: M2-10B4 and M2-10B4 transfected with cDNAs for human G-CSF and IL-3. RESULTS: Two and five fold higher numbers of terminally differentiated cells were produced during nine weeks of culture of CB mononuclear or CD34+ cells respectively, in cultures containing a M2-10B4 IL-3 G-CSF cell line compared to cultures containing the parental cell line. Likewise, a higher number of colony-forming cells (CFC) were detected in the supernatant of cultures with the transfected cell line. In contrast, the number of CFC generated within the stromal layer, after 5 or 9 weeks of culture, was significantly higher in cultures on M2-10B4 cells than those on M2-10B4 IL-3 G-CSF. INTERPRETATION AND CONCLUSIONS: Our results show that the proliferative capacity of CB LTC-IC can be strongly influenced by culture conditions and that the frequency of LTC-IC estimated using these cell lines as stromal support is not identical.     

Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H BOX/ACA-motif snoRNPs and constitute a common bipartite structure

The eukaryotic nucleolus contains a large number of small nucleolar RNAs (snoRNAs) that are involved in preribosomal RNA (pre-rRNA) processing. The H box/ACA-motif (H/ACA) class of snoRNAs has recently been demonstrated to function as guide RNAs targeting specific uridines in the pre-rRNA for pseudouridine (psi) synthesis. To characterize the protein components of this class of snoRNPs, we have purified the snR42 and snR30 snoRNP complexes by anti-m3G-immunoaffinity and Mono-Q chromatography of Saccharomyces cerevisiae extracts. Sequence analysis of the individual polypeptides demonstrated that the three proteins Gar1p, Nhp2p, and Cbf5p are common to both the snR30 and snR42 complexes. Nhp2p is a highly basic protein that belongs to a family of putative RNA-binding proteins. Cbf5p has recently been demonstrated to be involved in ribosome biogenesis and also shows striking homology with known prokaryotic psi synthases. The presence of Cbf5p, a putative psi synthase in each H/ACA snoRNP suggests that this class of RNPs functions as individual modification enzymes. Immunoprecipitation studies using either anti-Cbf5p antibodies or a hemagglutinin-tagged Nhp2p demonstrated that both proteins are associated with all H/ACA-motif snoRNPs. In vivo depletion of Nhp2p results in a reduction in the steady-state levels of all H/ACA snoRNAs. Electron microscopy of purified snR42 and snR30 particles revealed that these two snoRNPs possess a similar bipartite structure that we propose to be a major structural determining principle for all H/ACA snoRNPs.     

Learning hierarchical probabilistic logic programs

Machine Learning - Probabilistic logic programming (PLP) combines logic programs and probabilities. Due to its expressiveness and simplicity, it has been considered as a powerful tool for learning...     

Complementary Effects of Carbamylated and Citrullinated LL37 in Autoimmunity and Inflammation in Systemic Lupus Erythematosus

LL37 acts as T-cell/B-cell autoantigen in Systemic lupus erythematosus (SLE) and psoriatic disease. Moreover, when bound to “self” nucleic acids, LL37 acts as “danger signal,” leading to type I interferon (IFN-I)/pro-inflammatory factors production. T-cell epitopes derived from citrullinated-LL37 act as better antigens than unmodified LL37 epitopes in SLE, at least in selected HLA-backgrounds, included the SLE-associated HLA-DRB1*1501/HLA-DRB5*0101 backgrounds. Remarkably, while “fully-citrullinated” LL37 acts as better T-cell-stimulator, it loses DNA-binding ability and the associated “adjuvant-like” properties. Since LL37 undergoes a further irreversible post-translational modification, carbamylation and antibodies to carbamylated self-proteins other than LL37 are present in SLE, here we addressed the involvement of carbamylated-LL37 in autoimmunity and inflammation in SLE. We detected carbamylated-LL37 in SLE-affected tissues. Most importantly, carbamylated-LL37-specific antibodies and CD4 T-cells circulate in SLE and both correlate with disease activity. In contrast to “fully citrullinated-LL37,” “fully carbamylated-LL37” maintains both innate and adaptive immune-cells’ stimulatory abilities: in complex with DNA, carbamylated-LL37 stimulates plasmacytoid dendritic cell IFN-α production and B-cell maturation into plasma cells. Thus, we report a further example of how different post-translational modifications of a self-antigen exert complementary effects that sustain autoimmunity and inflammation, respectively. These data also show that T/B-cell responses to carbamylated-LL37 represent novel SLE disease biomarkers.     

Evidence for a Negative Correlation between Human Reactive Enamine-Imine Intermediate Deaminase A (RIDA) Activity and Cell Proliferation Rate: Role of Lysine Succinylation of RIDA

Reactive intermediate deaminase (Rid) proteins are enzymes conserved in all domains of life. UK114, a mammalian member of RidA subfamily, has been firstly identified as a component of liver perchloric acid-soluble proteins (L-PSP). Although still poorly defined, several functions have been attributed to the mammalian protein UK114/RIDA, including the reactive intermediate deamination activity. The expression of UK114/RIDA has been observed in some tumors, arousing interest in this protein as an evaluable tumor marker. However, other studies reported a negative correlation between UK114/RIDA expression, tumor differentiation degree and cell proliferation. This work addressed the question of UK114/RIDA expression in human non-tumor HEK293 cell lines and in some human tumor cell lines. Here we reported that human RIDA (hRIDA) was expressed in all the analyzed cell line and subjected to lysine (K-)succinylation. In HEK293, hRIDA K-succinylation was negatively correlated to the cell proliferation rate and was under the control of SIRT5. Moreover, K-succinylation clearly altered hRIDA quantification by immunoblotting, explaining, at least in part, some discrepancies about RIDA expression reported in previous studies. We found that hRIDA was able to deaminate reactive enamine-imine intermediates and that K-succinylation drastically reduced deaminase activity. As predicted by in silico analysis, the observed reduction of deaminase activity has been related to the drastic alterations of hRIDA structure inferred by K-succinylation. The role of hRIDA and the importance of its K-succinylation in cell metabolism, especially in cancer biology, have been discussed.     

Cyclic Nigerosyl-Nigerose as Oxygen Nanocarrier to Protect Cellular Models from Hypoxia/Reoxygenation Injury: Implications from an In Vitro Model

Heart failure (HF) prevalence is increasing among the aging population, and the mortality rate remains unacceptably high despite improvements in therapy. Myocardial ischemia (MI) and, consequently, ischemia/reperfusion injury (IRI), are frequently the basis of HF development. Therefore, cardioprotective strategies to limit IRI are mandatory. Nanocarriers have been proposed as alternative therapy for cardiovascular disease. Controlled reoxygenation may be a promising strategy. Novel nanocarriers, such as cyclic nigerosyl-nigerose (CNN), can be innovative tools for oxygen delivery in a controlled manner. In this study we analyzed new CNN-based formulations as oxygen nanocarriers (O₂-CNN), and compared them with nitrogen CNN (N₂-CNN). These different CNN-based formulations were tested using two cellular models, namely, cardiomyoblasts (H9c2), and endothelial (HMEC) cell lines, at different concentrations. The effects on the growth curve during normoxia (21% O₂, 5% CO₂ and 74% N₂) and their protective effects during hypoxia (1% O₂, 5% CO₂ and 94% N₂) and reoxygenation (21% O₂, 5% CO₂ and 74% N₂) were studied. Neither O₂-CNN nor N₂-CNN has any effect on the growth curve during normoxia. However, O₂-CNN applied before hypoxia induces a 15–30% reduction in cell mortality after hypoxia/re-oxygenation when compared to N₂-CNN. O₂-CNN showed a marked efficacy in controlled oxygenation, which suggests an interesting potential for the future medical application of soluble nanocarrier systems for MI treatment.     

Design of Lu2O3-reinforced Cf/SiC-ZrB2-ZrC ultra-high temperature ceramic matrix composites: Wetting and interfacial reactivity by ZrSi2 based alloys

The wettability and infiltration of molten ZrSi₂ and ZrSi₂-Lu₂O₃ alloys into C_f/SiC and B₄C-infiltrated C_f/SiC composites were investigated to understand the interfacial interactions that occur during the development of C_f/SiC-ZrC and C_f/SiC-ZrB₂-ZrC-Lu₂O₃ materials. A significant evaporation of Si from the liquid affected the wetting behaviour of the alloy when tested in a vacuum at 1670 °C. The better wetting and spreading of the alloy over the surface was observed for the composites with lower overall porosity (12 %). On the other hand, the formation of an outer dense layer, followed up by the uniform infiltrated region up to ～ 1 mm was observed for the C_f/SiC with higher porosity (21 %). The infiltrated alloy reacted with SiC matrix to form ZrC or with B₄C-infiltrated SiC matrix to form ZrB₂-ZrC-SiC. The Lu₂O₃ particles were not wetted by the melt, and were pushed away of the reaction zone by the solidification front.     

An optimization framework for “build-or-buy” decisions in software architecture

Building a software architecture that meets functional requirements is a quite consolidated activity, whereas keeping high quality attributes is still an open challenge. In this paper we introduce an optimization framework that supports the decision whether to buy software components or to build them in-house upon designing a software architecture. We devise a non-linear cost/quality optimization model based on decision variables indicating the set of architectural components to buy and to build in order to minimize the software cost while keeping satisfactory values of quality attributes. From this point of view, our tool can be ideally embedded into a Cost Benefit Analysis Method to provide decision support to software architects. The novelty of our approach consists in building costs and quality attributes on a common set of decision variables related to software development. We start from a special case of the framework where the quality constraints are related to the delivery time and the product reliability, and the model solution also devises the amount of unit testing to be performed on built components. We generalize the framework formulation to represent a broader class of architectural cost-minimization problems under quality constraints, and discuss advantages and limitations of such approach.     

Outlier detection using default reasoning

Default logics are usually used to describe the regular behavior and normal properties of domain elements. In this paper we suggest, conversely, that the framework of default logics can be exploited for detecting outliers. Outliers are observations expressed by sets of literals that feature unexpected semantical characteristics. These sets of literals are selected among those explicitly embodied in the given knowledge base. Hence, essentially we perceive outlier detection as a knowledge discovery technique. This paper defines the notion of outlier in two related formalisms for specifying defaults: Reiter's default logic and extended disjunctive logic programs. For each of the two formalisms, we show that finding outliers is quite complex. Indeed, we prove that several versions of the outlier detection problem lie over the second level of the polynomial hierarchy. We believe that a thorough complexity analysis, as done here, is a useful preliminary step towards developing effective heuristics and exploring tractable subsets of outlier detection problems.