Earth matter density uncertainty in atmospheric neutrino oscillations

That muon neutrinos $\nu_{\mu}$ oscillating into the mixture of tau neutrinos $\nu_{\tau}$ and sterile neutrinos $\nu_{s}$ has been studied to explain the atmospheric $\nu_{\mu}$ disappearance. In this scenario, the effect of Earth matter is a key to determine the fraction of $\nu_{s}$. Considering that the Earth matter density has uncertainty and this uncertainty has significant effects in some neutrino oscillation cases, such as the CP violation in very long baseline neutrino oscillations and the day-night asymmetry for solar neutrinos, we study the effects caused by this uncertainty in the above atmospheric $\nu_{\mu}$ oscillation scenario. We find that this uncertainty seems to have no significant effects and that the previous fitting results need not to be modified fortunately.Comment: 7 pages, 1 figure, to appear in Phys. Rev.

Deep Excavation Braced by Diaphragm Wall in Gdańsk (Poland)

Protection of deep excavation by cast in situ concrete diaphragm walls for Shopping Center in Gdansk (Poland) is described. The structure was designed as five-storey-building with three additional underground floors and founded on diaphragm walls. The excavation was made by “half-floor” method with temporary supports of floor in the form of steel columns. Static calculations of excavation bracing were carried out by PLAXIS numerical code for both design stage (for two calculation schemes: anchored and supported by floor ring) as well as after its construction (back analysis). The calculations served for an assessment of predicted wall displacements, deformations of soil surface around the excavation and internal forces in subsequent stages of the excavation deepening and for different working schemes (supports) of the construction. During construction works vertical displacements of the soil surface around the excavation and surrounding buildings as well as horizontal displacements of diaphragm walls were monitored and compared with the results of corresponding calculations. Some exemplary distributions of calculated and measured values of the wall and soil surface deformations are presented. Subsoil unloading effects and the range of impact zones on the vicinity are also analyzed

Ceramic/metal nanocomposites by lyophilization: Processing and HRTEM study

5 páginas, 8 figuras, 1 tabla.-- El pdf del artículo es el manuscrito de autor.This work describes a wet-processing route based on spray-freezing and subsequent lyophilization designed to obtain nanostructured ceramic/metal powders. Starting from the ceramic powder and the corresponding metal salt, a water-based suspension is sprayed on liquid nitrogen. The frozen powders are subsequently freeze-dried, calcined and reduced. The material was analyzed using X-ray diffraction analysis at all stages. High resolution transmission electron microscopy studies showed a uniform distribution of metal nanoparticles on the ceramic grain surfaces, good interfaces and high crystallinity, with an average metal particle size in the nanometric range.This work was supported by the Spanish Ministry of Science and Innovation (MICINN) under the project MAT2009-14542-C02 and the Government of the Principality of Asturias through PCTI and ERDF (European Regional Development Fund) 2007-2013 under project PC10-65. C.F. Gutierrez- Gonzalez acknowledges CSIC and ESF for the concession of a JAE-Doc 2009 grant. S. Agouram thanks the Spanish Ministry of Science and European Social Fund for financial support.Peer reviewe

Multilocus sequence types of invasive Corynebacterium diphtheriae isolated in the Rio de Janeiro urban area, Brazil

Invasive infections caused by Corynebacterium diphtheriae in vaccinated and non-vaccinated individuals have been reported increasingly. In this study we used multilocus sequence typing (MLST) to study genetic relationships between six invasive strains of this bacterium isolated solely in the urban area of Rio de Janeiro, Brazil, during a 10-year period. Of note, all the strains rendered negative results in PCR reactions for the tox gene, and four strains presented an atypical sucrose-fermenting ability. Five strains represented new sequence types. MLST results did not support the hypothesis that invasive (sucrose-positive) strains of C. diphtheriae are part of a single clonal complex. Instead, one of the main findings of the study was that such strains can be normally found in clonal complexes with strains related to non-invasive disease. Comparative analyses with C. diphtheriae isolated in different countries provided further information on the geographical circulation of some sequence types

Improved contact tracing using network analysis and spatial-temporal proximity

PURPOSE: Contact tracing is a crucial tool in infection prevention and control (IPC), which aims to identify outbreaks and prevent onward transmission. What constitutes a contact is typically based on strict binary criteria (i.e., being at a location at the same time). Missing data, indirect contacts and background sources can however substantially alter contact-tracing investigations. Here, we present StEP, a Spatial-temporal Epidemiological Proximity model that accounts for imperfect data by introducing a network-based notion of contact based on spatial-temporal proximity derived from background flows of patient movement. METHODS & MATERIALS: We showcase StEP by analysing outbreaks of multidrug-resistant bacteria and COVID-19 within a large hospital Trust in London (UK).StEP utilises spatial-temporal patient trajectories and the background hospital movement flows to recover enhanced contact networks. Firstly, we study a well-characterised outbreak of carbapenemase-producing Enterobacteriaceae (CPE) involving 116 hospitalised patients where genetic sequencing is used to learn model parameters. Secondly, our trained model is deployed in an unsupervised manner on three unseen outbreaks involving 867 patients of related CPE-types. Thirdly, we test application to an altogether novel pathogen by analysing a hospital outbreak of COVID-19 among 90 hospital patients, and demonstrate the power of StEP when characterising newly emerging diseases, even when there is a lack of sequencing data. RESULTS: In addition to recovering core contact structures, StEP identifies missing contacts that link seemingly unconnected infection clusters, revealing a larger extent of transmission than conventional methods. Via genomic analyses we confirm that the additional contacts detected through StEP lead to improved alignment to the plasmid phylogeny (the major outbreak driving force). Hence the StEP contact network is most aligned to the transmission structure. CONCLUSION: By considering spatial-temporal information in a continuous manner, StEP tackles several challenges associated with traditional contact-tracing. StEP allows both direct and indirect contacts as possible routes of disease transmission and is tuneable to a pathogen's epidemiological characteristics. Such flexible use of heterogeneous data in uncertain situations can significantly enhance IPC

Geotechnical problems relating to foundation pit behavior and design

Opisuju se primjeri dubokih građevnih jama u Gdanjsku. Kod građevina čiji su podzemni dijelovi u prenapučenoj mreži gradske infrastrukture pojavljuju se ograničenja u vezi s iskorištavanjem mogućih tehnologija građenja. Ujedno se postavljaju vrlo visoki zahtjevi glede projektiranja i ugradnje novih građevina s obzirom na njihov utjecaj na susjedne građevine. U radu je prikazano nekoliko slučajeva takve izgradnje s analizom osnovnih čimbenika i područja utjecaja novih građevina.Several examples of deep foundation pits in Gdanjsk are described. In case of structures with underground portions situated in midst of crowded municipal infrastructure systems, the choice of possible construction technologies is often quite limited. In addition, builders are faced with very high requirements regarding design and erection of new buildings due to influence they exert on neighboring structures. Some cases of such construction are presented, and basic factors and area of influence of such new structures, are analyzed

Adaptive filtering framework to remove nonspecific and low-efficiency reactions in multiplex digital PCR based on sigmoidal trends.

Real-time digital polymerase chain reaction (qdPCR) coupled with machine learning (ML) methods has shown the potential to unlock scientific breakthroughs, particularly in the field of molecular diagnostics for infectious diseases. One promising application of this emerging field explores single fluorescent channel PCR multiplex by extracting target-specific kinetic and thermodynamic information contained in amplification curves, also known as data-driven multiplexing. However, accurate target classification is compromised by the presence of undesired amplification events and not ideal reaction conditions. Therefore, here, we proposed a novel framework to identify and filter out nonspecific and low-efficient reactions from qdPCR data using outlier detection algorithms purely based on sigmoidal trends of amplification curves. As a proof-of-concept, this framework is implemented to improve the classification performance of the recently reported data-driven multiplexing method called amplification curve analysis (ACA), using available published data where the ACA is demonstrated to screen carbapenemase-producing organisms in clinical isolates. Furthermore, we developed a novel strategy, named adaptive mapping filter (AMF), to adjust the percentage of outliers removed according to the number of positive counts in qdPCR. From an overall total of 152,000 amplification events, 116,222 positive amplification reactions were evaluated before and after filtering by comparing against melting peak distribution, proving that abnormal amplification curves (outliers) are linked to shifted melting distribution or decreased PCR efficiency. The ACA was applied to assess classification performance before and after AMF, showing an improved sensitivity of 1.2% when using inliers compared to a decrement of 19.6% when using outliers (p-value < 0.0001), removing 53.5% of all wrong melting curves based only on the amplification shape. This work explores the correlation between the kinetics of amplification curves and the thermodynamics of melting curves, and it demonstrates that filtering out nonspecific or low-efficient reactions can significantly improve the classification accuracy for cutting-edge multiplexing methodologies

Rapid detection of mobilized colistin resistance using a nucleic acid based lab-on-a-chip diagnostic system

The increasing prevalence of antimicrobial resistance is a serious threat to global public health. One of the most concerning trends is the rapid spread of Carbapenemase-Producing Organisms (CPO), where colistin has become the last-resort antibiotic treatment. The emergence of colistin resistance, including the spread of mobilized colistin resistance (mcr) genes, raises the possibility of untreatable bacterial infections and motivates the development of improved diagnostics for the detection of colistin-resistant organisms. This work demonstrates a rapid response for detecting the most recently reported mcr gene, mcr−9, using a portable and affordable lab-on-a-chip (LoC) platform, offering a promising alternative to conventional laboratory-based instruments such as real-time PCR (qPCR). The platform combines semiconductor technology, for non-optical real-time DNA sensing, with a smartphone application for data acquisition, visualization and cloud connectivity. This technology is enabled by using loop-mediated isothermal amplification (LAMP) as the chemistry for targeted DNA detection, by virtue of its high sensitivity, specificity, yield, and manageable temperature requirements. Here, we have developed the first LAMP assay for mcr−9 - showing high sensitivity (down to 100 genomic copies/reaction) and high specificity (no cross-reactivity with other mcr variants). This assay is demonstrated through supporting a hospital investigation where we analyzed nucleic acids extracted from 128 carbapenemase-producing bacteria isolated from clinical and screening samples and found that 41 carried mcr−9 (validated using whole genome sequencing). Average positive detection times were 6.58 ± 0.42 min when performing the experiments on a conventional qPCR instrument (n = 41). For validating the translation of the LAMP assay onto a LoC platform, a subset of the samples were tested (n = 20), showing average detection times of 6.83 ± 0.92 min for positive isolates (n = 14). All experiments detected mcr−9 in under 10 min, and both platforms showed no statistically significant difference (p-value > 0.05). When sample preparation and throughput capabilities are integrated within this LoC platform, the adoption of this technology for the rapid detection and surveillance of antimicrobial resistance genes will decrease the turnaround time for DNA detection and resistotyping, improving diagnostic capabilities, patient outcomes, and the management of infectious diseases

CIRCULAR DICHROISM OF LIGHT-HARVESTING COMPLEXES FROM PURPLE PHOTOSYNTHETIC BACTERIA

The CD spectra of a range of antenna complexes from several different species of purple photosynthetic bacteria were recorded in the wavelength range of 190 to 930 nm. Analysis of the far UV CD (190 to 250 nm) showed that in each case except for the B800-850 from Chr. vinosum the secondary structure of the light-harvesting complexes contains a large amount of α-helix (50%) and very little 0-pleated sheet. This confirms the predictions of the group of Zuber of a high a-helical content based upon consideration of the primary structures of several antenna apoproteins. The CD spectra from the carotenoids and the bacteriochlorophylls show considerable variations depending upon the type of antenna complex. The different amplitude ratios in the CD spectrum for the bacteriochlorophyll Qy, Qx and Soret bands indicate not only different degrees of exciton coupling, but also a strong and variable hyperchromism (Scherz and Parson, 1984a, b)