Immunosensors: Concepts and Structures for Fast and Accurate Sensing

Peer ReviewedPostprint (published version

Liquefaction Analysis for Rubber Dam and Review of Case Histories of Liquefaction of Gravels

A geotechnical investigation for the design and construction of an air-inflated rubber dam (for ground-water recharge) was performed, including evaluation of the liquefaction potential of the dam\u27s foundation. The dam, about 300 feet long and 13 feet high when fully inflated is located along Alameda Creek at the upper part of the alluvial fan near Fremont, California. The sediments at the site are generally sandy gravels and gravelly sands. In order to fully investigate the liquefaction potential of the gravelly soils, the soils themselves were studied, and case histories involving similar conditions were reviewed. These case histories indicate that, in all cases where liquefaction appears to have occurred, the gravelly soils were loose to very loose and at shallow to moderate depths. For most of the reported cases the gravelly soils contained significant quantities of fines, and it was the fine matrix which actually liquefied. There are also numerous cases where earthquake induced liquefaction of gravelly soils (loose to dense) did not occur, but which are not given adequate coverage in the literature. The results of percolation tests, SPT blow count data, and comparison of particle-size distributions with gravelly soils that liquefied in past events all indicate that the soils at the rubber dam site have a very low probability of liquefaction

Machine Learning Based Predictions of Dissolved Oxygen in a Small Coastal Embayment

Coastal dissolved oxygen (DO) concentrations have a profound impact on nearshore ecosystems and, in recent years, there has been an increased prevalance of low DO hypoxic events that negatively impact nearshore organisms. Even with advanced numerical models, accurate prediction of coastal DO variability is challenging and computationally expensive. Here, we apply machine learning techniques in order to reconstruct and predict nearshore DO concentrations in a small coastal embayment while using a comprehensive set of nearshore and offshore measurements and easily measured input (training) parameters. We show that both random forest regression (RFR) and support vector regression (SVR) models accurately reproduce both the offshore DO and nearshore DO with extremely high accuracy. In general, RFR consistently peformed slightly better than SVR, the latter of which was more difficult to tune and took longer to train. Although each of the nearshore datasets were able to accurately predict DO values using training data from the same site, the model only had moderate success when using training data from one site to predict DO at another site, which was likely due to the the complexities in the underlying dynamics across the sites. We also show that high accuracy can be achieved with relatively little training data, highlighting a potential application for correcting time series with missing DO data due to quality control or sensor issues. This work establishes the ability of machine learning models to accurately reproduce DO concentrations in both offshore and nearshore coastal waters, with important implications for the ability to detect and indirectly measure coastal hypoxic events in near real-time. Future work should explore the ability of machine learning models in order to accurately forecast hypoxic events

The preburning condition of Chalcolithic cremated human remains from the Perdigoes enclosures (Portugal)

The Iberian Chalcolithic displayed a remarkable variety of funerary practices, which has been related to interpopulation differences, intrapopulation social-cultural differences, and complex multistage funerary rituals. Perdigoes, a Chalcolithic set of ditched enclosures, reflects such diversity including a wide array of funerary practices. Among those practices is cremation, which, despite relatively rare, is represented in different structures in Perdigoes. One of these structures (Pit 40) presents an unparalleled high minimum number of individuals (n = 240), contrasting with nearby and coeval structures. In this study, we analyse heat-induced bone changes and other archaeothanatological variables to tentatively assess the preburning condition of the human remains. The results of Pit 40 are also compared with other comparable contexts to assess if this unique context presents further funerary differences relative to those other contexts in, for example, body processing. Our results suggest preferential cremation of fleshed human remains, but burning of at least a minority of skeletonised remains and deposition of possibly unburned remains also likely occurred. Body processing appears to be comparable with that of the cremation contexts of Perdigoes but contrasts with that of another nearby context (Dolmen of Olival da Pega 2b) in which burned bones were also found.Portuguese Foundation for Science and TechnologyPortuguese Foundation for Science and Technology [PEst-OE/SADG/UI0283/2013, POCI-01-0145-FEDER-016766, PTDC/EPH-ARQ/0798/2014, PTDC/IVC-ANT/1201/2014, SFRH/BPD/84268/2012]info:eu-repo/semantics/publishedVersio

Numerical taxonomy of moderately halophilic Gram-negative bacteria from hypersaline soils

A total of 132 moderately halophilic bacteria were isolated from hypersaline soils with a C1- content between 2-36 and 12.72% (w/v) located near Alicante (S.E. Spain) and examined for 98 phenotypic characteristics including their response to cytological, physiological, biochemical and nutritional tests. They were submitted to a numerical analysis together with six reference strains using both simple matching (SsM)a nd Jaccard (S,) coefficients, and cluster analysis was carried out by the unweighted pair group method of association (UPGMA), single linkage and complete linkage. With the S, coefficient and UPGMA clustering, eight phenons were obtained at the 65% similarity level. From each phenon representative strains were chosen for the determination of DNA base composition and for electron microscopy. Bacteria belonging to phenons D, E, and F were assigned to the genus Alcaligenes. Phenon G included 27 strains assigned to Acinetobacter, but the high G + C composition (58.9 mol%) of a representative strain of this phenon suggests that it may represent a new taxon. Phenons A, B, and C were designated Flavobacterium and phenon H was Pseudomonas. The bacteria found in these environments are not related to those from hypersaline waters or normal soils

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

Background: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. Methodology/Principal Findings: We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. Conclusions/Significance: We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with different protocols are not suitable for comparative metagenomics

Present situation of the autochthonous donkey population in Spain

A study of the present census and administrative situation has been studied also the possibilities of conservation has been analysed During the last 5 years the donkey census has increased because the consideration like a breed in danger of extinction. There are several initiatives looking for the consolidation of the autochthonous breeds of donkeys in Spain but most of them are less important and very isolated. Except for these conservation initiatives, the donkey breeds be considered in a serious danger of extinction.Se realiza un estudio de la situación actual censal y administrativa de las razas asnales españolas y se analizan sus posibilidades y perspectivas de conservación Queda reflejado cómo en los últimos 5 años se ha producido un aumento en los efectivos asnales como respuesta a las diferentes acciones de sensibilización con respecto a las razas en peligro de extinción. No faltan iniciativas que adaptándose a los nuevos tipos de demanda busquen soluciones para la consolidación de nuestras razas autóctonas asnales aunque aún muchas de ellas son discretas y localizadas. Fuera del ámbito esas actuaciones el panorama no se muestra muy alentador

A synthetic-lethality RNAi screen reveals an ERK-mTOR co-targeting pro-apoptotic switch in PIK3CA+ oral cancers.

mTOR inhibition has emerged as a promising strategy for head and neck squamous cell carcinomas (HNSCC) treatment. However, most targeted therapies ultimately develop resistance due to the activation of adaptive survival signaling mechanisms limiting the activity of targeted agents. Thus, co-targeting key adaptive mechanisms may enable more effective cancer cell killing. Here, we performed a synthetic lethality screen using shRNA libraries to identify druggable candidates for combinatorial signal inhibition. We found that the ERK pathway was the most highly represented. Combination of rapamycin with trametinib, a MEK1/2 inhibitor, demonstrated strong synergism in HNSCC-derived cells in vitro and in vivo, including HNSCC cells expressing the HRAS and PIK3CA oncogenes. Interestingly, cleaved caspase-3 was potently induced by the combination therapy in PIK3CA+ cells in vitro and tumor xenografts. Moreover, ectopic expression of PIK3CA mutations into PIK3CA- HNSCC cells sensitized them to the pro-apoptotic activity of the combination therapy. These findings indicate that co-targeting the mTOR/ERK pathways may provide a suitable precision strategy for HNSCC treatment. Moreover, PIK3CA+ HNSCC are particularly prone to undergo apoptosis after mTOR and ERK inhibition, thereby providing a potential biomarker of predictive value for the selection of patients that may benefit from this combination therapy