IMAGE: A New Tool for the Prediction of Transcription Factor Binding Sites

IMAGE is an application tool, based on the vector quantization method, aiding the discovery of nucleotidic sequences corresponding to Transcription Factor binding sites. Starting from the knowledge of regulation regions of a number of co-expressed genes, the software is able to predict the occurrence of specific motifs of different lengths (starting from 6 base pairs) with a defined number of punctual mutations

Amplification ratio control system for copy number variation genotyping

We describe a generic design for ratiometric analysis suitable for determination of copy number variation (CNV) class of a gene. Following two initial sequence-specific PCR priming cycles, both ends of both amplicons (one test and one reference) in a duplex reaction, are all primed by the same universal primer (UP). Following each amplification denaturation step, the UP target and its reverse complement (UP′) in each strand form a hairpin. The bases immediately beyond the 3′-end of the UP and 5′ of UP′ are chosen such as not to base pair in the hairpin (otherwise priming is ablated). This hairpin creates a single constant environment for priming events and chaperones free 3′-ends of amplicon strands. The resultant ‘amplification ratio control system’ (ARCS) permits ratiometric representation of amplicons relative to the original template into PCR plateau phase. These advantages circumvent the need for real-time PCR for quantitation. Choice of different %(G+C) content for the target and reference amplicons allows liquid phase thermal melt discrimination and quantitation of amplicons. The design is generic, simple to set up and economical. Comparisons with real-time PCR and other techniques are made and CNV assays demonstrated for haptoglobin duplicon and ‘chemokine (C-C motif) ligand 3-like 1’ gene

Germline CDH1 deletions in hereditary diffuse gastric cancer families

Germline CDH1 point or small frameshift mutations can be identified in 30–50% of hereditary diffuse gastric cancer (HDGC) families. We hypothesized that CDH1 genomic rearrangements would be found in HDGC and identified 160 families with either two gastric cancers in first-degree relatives and with at least one diffuse gastric cancer (DGC) diagnosed before age 50, or three or more DGC in close relatives diagnosed at any age. Sixty-seven carried germline CDH1 point or small frameshift mutations. We screened germline DNA from the 93 mutation negative probands for large genomic rearrangements by Multiplex Ligation-Dependent Probe Amplification. Potential deletions were validated by RT–PCR and breakpoints cloned using a combination of oligo-CGH-arrays and long-range-PCR. In-silico analysis of the CDH1 locus was used to determine a potential mechanism for these rearrangements. Six of 93 (6.5%) previously described mutation negative HDGC probands, from low GC incidence populations (UK and North America), carried genomic deletions (UK and North America). Two families carried an identical deletion spanning 193 593 bp, encompassing the full CDH3 sequence and CDH1 exons 1 and 2. Other deletions affecting exons 1, 2, 15 and/or 16 were identified. The statistically significant over-representation of Alus around breakpoints indicates it as a likely mechanism for these deletions. When all mutations and deletions are considered, the overall frequency of CDH1 alterations in HDGC is ∼46% (73/160). CDH1 large deletions occur in 4% of HDGC families by mechanisms involving mainly non-allelic homologous recombination in Alu repeat sequences. As the finding of pathogenic CDH1 mutations is useful for management of HDGC families, screening for deletions should be offered to at-risk families

Smart cities, social media platforms and security: online content regulation as a site of controversy and conflict

Abstract Smart, technologically managed city-regions are one of the main characteristics of the contemporary world. Since the attack to the Charlie Hebdo offices, city-regions and social media digital technologies have increasingly been changing the definition of 'territory of security' and 'security governance'. What are the characteristics of the security architecture created by the interaction of smart city-regions and digital technologies? Drawing from Actor-Network theory and Science and Technology Studies, we provide an empirical account of the shape of this new territory, by presenting a study of the controversy concerning security and social media in UK, the role of cities in this changed security space, and how social sciences can help better understand and respond to the opportunities and threats of smart cities

Endovascular Abdominal Aortic Aneurysm Repair With Ovation Alto Stent Graft: Protocol for the ALTAIR (ALTo endogrAft Italian Registry) Study

Background: Since 2010, the Ovation Abdominal Stent Graft System has offered an innovative sealing option for abdominal aortic aneurysm (AAA) by including a sealing ring filled with polymer 13 mm from the renal arteries. In August 2020, the redesigned Ovation Alto, with a sealing ring 6 mm closer to the top of the fabric, received CE Mark approval. Objective: This registry study aims to evaluate intraoperative, perioperative, and postoperative results in patients treated by the Alto stent graft (Endologix Inc.) for elective AAA repair in a multicentric consecutive experience. Methods: All consecutive eligible patients submitted to endovascular aneurysm repair (EVAR) by Alto Endovascular AAA implantation will be included in this analysis. Patients will be submitted to EVAR procedures based on their own preferences, anatomical features, and operators experience. An estimated number of 300 patients submitted to EVAR with Alto stent graft should be enrolled. It is estimated that the inclusion period will be 24 months. The follow-up period is set to be 5 years. Full data sets and cross-sectional images of contrast-enhanced computed tomography scan performed before EVAR, at the first postoperative month, at 24 or 36 months, and at 5-year follow-up interval will be reported in the central database for a centralized core laboratory review of morphological changes. The primary endpoint of the study is to evaluate the technical and clinical success of EVAR with the Alto stent graft in short- (90-day), mid- (1-year), and long-term (5-year) follow-up periods. The following secondary endpoints will be also addressed: operative time; intraoperative radiation exposure; contrast medium usage; AAA sac shrinkage at 12-month and 5-year follow-up; any potential role of patients' baseline characteristics, valuated on preoperative computed tomography angiographic study, and of device configuration (number of component) in the primary endpoint. Results: The study is currently in the recruitment phase and the final patient is expected to be treated by the end of 2023 and then followed up for 5 years. A total of 300 patients will be recruited. Analyses will focus on primary and secondary endpoints. Updated results will be shared at 1- and 3-5-year follow-ups. Conclusions: The results from this registry study could validate the safety and effectiveness of the new design of the Ovation Alto Stent Graft. The technical modifications to the endograft could allow for accommodation of a more comprehensive range of anatomies on-label

Measurement of the light component (p+He) energy spectrum with the DAMPE space mission

The DArk Matter Particle Explorer (DAMPE) is a space-based particle detector launched in a Sun- synchronous orbit on December 17th, 2015 from the Jiuquan Satellite Launch Center, in China. It has been taking data very smoothly for more than 5 years. Science goals of the DAMPE mission include the study of the electron-positron energy spectrum, the study of galactic cosmic-rays, gamma-ray astronomy, and indirect dark matter search. Performing precise measurements of light elements in space, the most abundant components of cosmic radiation, is necessary to address major problems in galactic cosmic ray acceleration and propagation mechanisms. Selecting a combined proton and helium sample (instead of proton or helium alone) allows larger efficiency and purity, also minimizing systematic effects in the reconstruction of the energy spectrum, due to possible cross-contaminations. The use of looser analysis cuts allows collecting larger statistics thus extending the covered energy range and providing a link between direct and indirect cosmic- ray measurements. The measurement of the p+He energy spectrum up to ∼ 150 TeV will be presented, along with a discussion on the features of the spectrum and a comparison with other experimental results

Observations of Forbush Decreases of Cosmic-Ray Electrons and Positrons with the Dark Matter Particle Explorer

The Forbush decrease (FD) represents the rapid decrease of the intensities of charged particles accompanied with the coronal mass ejections or high-speed streams from coronal holes. It has been mainly explored with the ground-based neutron monitor network, which indirectly measures the integrated intensities of all species of cosmic rays by counting secondary neutrons produced from interaction between atmospheric atoms and cosmic rays. The space-based experiments can resolve the species of particles but the energy ranges are limited by the relatively small acceptances except for the most abundant particles like protons and helium. Therefore, the FD of cosmic-ray electrons and positrons have just been investigated by the PAMELA experiment in the low-energy range (<5 GeV) with limited statistics. In this paper, we study the FD event that occurred in 2017 September with the electron and positron data recorded by the Dark Matter Particle Explorer. The evolution of the FDs from 2 GeV to 20 GeV with a time resolution of 6 hr are given. We observe two solar energetic particle events in the time profile of the intensity of cosmic rays, the earlier, and weaker, one has not been shown in the neutron monitor data. Furthermore, both the amplitude and recovery time of fluxes of electrons and positrons show clear energy dependence, which is important in probing the disturbances of the interplanetary environment by the coronal mass ejections

Machine learning methods for helium flux analysis with DAMPE experiment

DAMPE is a space-borne experiment for the measurement of the cosmic-ray fluxes at energies up to around 100 TeV per nucleon. At energies above several tens of TeV, the electronics of DAMPE calorimeter would saturate, leaving certain bars with no energy recorded. It is also observed that at high energies the tracker and the scintillator detector that serve for the charge identification become heavily populated with back-splash tracks. Both effects interfere in precise measurements of the helium flux at highest energies. In the present contribution we discuss the application of machine learning techniques for the treatment of DAMPE data, to compensate the calorimeter energy lost by saturation and to identify helium events