Logic based methods for SNPs tagging and reconstruction

SNPs are positions of the DNA sequences where the differences among individuals are embedded. The knowledge of such SNPs is crucial for disease association studies, but even if the number of such positions is low (about 1% of the entire sequence), the cost to extract the complete information is actually very high. Recent studies have shown that DNA sequences are structured into blocks of positions, that are conserved during evolution, where there is strong correlation among values (alleles) of different loci. To reduce the cost of extracting SNPs information, the block structure of the DNA has suggested to limit the process to a subset of SNPs, the so-called Tag SNPs, that are able to maintain the most of the information contained in the whole sequence. In this paper, we apply a technique for feature selection based on integer programming to the problem of Tag SNP selection. Moreover, to test the quality of our approach, we consider also the problem of SNPs reconstruction, i.e. the problem of deriving unknown SNPs from the value of Tag SNPs and propose two reconstruction methods, one based on a majority vote and the other on a machine learning approach. We test our algorithm on two public data sets of different nature, providing results that are, when comparable, in line with the related literature. One of the interesting aspects of the proposed method is to be found in its capability to deal simultaneously with very large SNPs sets, and, in addition, to provide highly informative reconstruction rules in the form of logic formulas.     

Improving search results with data mining in a thematic search engine

The problem of obtaining relevant results in web searching has been tackled with several approaches. Although very effective techniques are currently used by the most popular search engines when no a priori knowledge on the user's desires beside the search keywords is available, in different settings it is conceivable to design search methods that operate on a thematic database of web pages that refer to a common body of knowledge or to specific sets of users. We have considered such premises to design and develop a search method that deploys data mining and optimization techniques to provide a more significant and restricted set of pages as the final result of a user search. We adopt a vectorization method based on search context and user profile to apply clustering techniques that are then refined by a specially designed genetic algorithm. In this paper we describe the method, its implementation, the algorithms applied, and discuss some experiments that has been run on test sets of web pages.     

On the Efficacy of ZnO Nanostructures against SARS-CoV-2

In 2019, the new coronavirus disease (COVID-19), related to the severe acute respiratory syndrome coronavirus (SARS-CoV-2), started spreading around the word, giving rise to the world pandemic we are still facing. Since then, many strategies for the prevention and control of COVID-19 have been studied and implemented. In addition to pharmacological treatments and vaccines, it is mandatory to ensure the cleaning and disinfection of the skin and inanimate surfaces, especially in those contexts where the contagion could spread quickly, such as hospitals and clinical laboratories, schools, transport, and public places in general. Here, we report the efficacy of ZnO nanoparticles (ZnONPs) against SARS-CoV-2. NPs were produced using an ecofriendly method and fully characterized; their antiviral activity was tested in vitro against SARS-CoV-2, showing a decrease in viral load between 70% and 90%, as a function of the material’s composition. Application of these nano-antimicrobials as coatings for commonly touched surfaces is envisaged.     

The I-meter, a distributor unit for the OPERA RPC HV system

The OPERA RPC HV system has been implemented using custom current measurement/distribution systems developed by the LNF Electronics Workshop.

Each system features eight inputs and 24 outputs (1–3 modularity). The current on each channel is measured with 100 pA sensitivity and 3% accuracy in the 1 nA– range.

In the paper we describe the measurement circuit as well as the results of the tests we have carried out to qualify the system.     

The calibration of slow neutron polarised beam instruments

A new procedure for calibrating the efficiencies of the polarisation sensitive components in slow neutron polarised beam instruments is described. The measurement of one “flipping ratio” and two “shim ratios” allows the effective polarisation, the spin flipping efficiency, and a depolarising shim efficiency to be determined unambiguously. Results of its application to the calibration of a neutron time-of-flight polarised beam reflectometer are presented.     

Histotypic in vitro reorganization of dissociated cells from mouse fetal gonads

Cell suspensions obtained from the testes of 13.5-14.5 day post coitum (dpc) mouse embryos reaggregate in cord-like structures following in vitro culture for 24 h on a reconstituted basement membrane (Matrigel). Ovarian cells of the same fetal age or cell suspensions from sex indifferent gonadal ridges (11.5 dpc embryos) form an organized cell network but not cord-like structures. Antibodies directed against laminin or against the alpha 6 subunit of its integrin receptor prevent such morphogenetic processes. The addition of 5 micrograms/ml cycloheximide, cytochalasin B or tunicamycin also inhibits the phenomenon. Interestingly, compounds that increase intracellular cyclic AMP (cAMP) (dbcAMP, forskolin and isobutyl-1-methylxanthine) induce embryonic testicular cells to organize into structures similar to those assembled by ovarian or sex indifferent cell suspensions. These findings offer a simple in vitro model for studying some aspects of early gonad development and provide novel experimental evidence that cell motility and cell-cell adhesion, possibly regulated by cAMP dependent mechanisms, are likely to play an important role in gonad morphogenesis.     

Controlled Micro/Nanodome Formation in Proton‐Irradiated Bulk Transition‐Metal Dichalcogenides

At the few‐atom‐thick limit, transition‐metal dichalcogenides (TMDs) exhibit strongly interconnected structural and optoelectronic properties. The possibility to tailor the latter by controlling the former is expected to have a great impact on applied and fundamental research. As shown here, proton irradiation deeply affects the surface morphology of bulk TMD crystals. Protons penetrate the top layer, resulting in the production and progressive accumulation of molecular hydrogen in the first interlayer region. This leads to the blistering of one‐monolayer thick domes, which stud the crystal surface and locally turn the dark bulk material into an efficient light emitter. The domes are stable (>2‐year lifetime) and robust, and host strong, complex strain fields. Lithographic techniques provide a means to engineer the formation process so that the domes can be produced with well‐ordered positions and sizes tunable from the nanometer to the micrometer scale, with important prospects for so far unattainable applications.     

Vascular-confined multi-passage discoidal nanoconstructs for the low-dose docetaxel inhibition of triple-negative breast cancer growth

Taxane efficacy in triple negative breast cancer(TNBC)is limited by insufficient tumor accumulation and severe off-target effects.Nanomedicines offer a unique opportunity to enhance the anti-cancer potency of this drug.Here,1,000 nm×400 nm discoidal polymeric nanoconstructs(DPN)encapsulating docetaxel(DTXL)and the near infrared compound Iipid-Cy5 were engineered.DPN were obtained by filling multiple times cylindrical wells in a poly(vinyl alcohol)template with a polymer mixture comprising poly(lactic-co-glycolic acid)(PLGA)and poly(ethylene glycol)diacrylate(PEG-DA)chains together with therapeutic and imaging agents.The resulting“multi-passage”DPN exhibited higher DTXL loading,Iipid-Cy5 stability,and stiffness as compared to the conventional"single-passage"approach.Confocal microscopy confirmed that DTXL-DPN were not taken up by MDA-MB-231 cells but would rather sit next to the cell membrane and slowly release DTXL thereof.Empty DPN had no toxicity on TNBC cells,whereas DTXL-DPN presented a cytotoxic potential comparable to free DTXL(IC₅₀=2.6 nM±1.0 nM vs.7.0 nM±1.09 nM at 72 h).In orthotopic murine models,DPN accumulated in TNBC more efficiently than free-DTXL.With only 2 mg/kg DTXL,intravenously administered every 2 days for a total of 13 treatments,DTXL-DPN induced tumor regression and were associated to an overall 80%survival rate as opposed to a 30%survival rate for free-DTXL,at 120 days.All untreated mice succumbed before 90 days.Collectively,this data demonstrates that vascular confined multi-passage DPN,biomimicking the behavior of circulating platelets,can efficiently deliver chemotherapeutic molecules to malignant tissues and effectively treat orthotopic TNBC at minimal taxane doses.