Fracture of bio-cemented sands

Bio-chemical reactions enable the production of biomimetic materials such as sandstones. In the present study, microbiologically-induced calcium carbonate precipitation (MICP) is used to manufacture laboratory-scale specimens for fracture toughness measurement. The mode I and mixed-mode fracture toughnesses are measured as a function of cementation, and are correlated with strength, permeability and porosity. A micromechanical model is developed to predict the dependence of mode I fracture toughness upon the degree of cementation. In addition, the role of the crack tip $T$-stress in dictating kink angle and toughness is determined for mixed mode loading. At a sufficiently low degree of cementation, the zone of microcracking in the vicinity of the crack tip is sufficiently large for a crack tip $K$-field to cease to exist and for crack kinking theory to not apply. The interplay between cementation and fracture properties of sedimentary rocks is explained; this understanding underpins a wide range of rock fracture phenomena including hydraulic fracture

The Use of Sodium Pyrophosphate to Improve a Translucent Clay Simulate

In the ever expanding quest to understand the nature and behavior of soil, translucent and even transparent media have been developed to serve as soil simulates. These artificial soils can be used in experimental models to make visual measurement of phenomena such as geosystem kinematics, soil mass movement, soil particle motion, and pore fluid flow that would be nearly impossible to obtain in natural opaque soils without expensive equipment or boundary effects. One successful type of translucent clay simulate is lithium sodium magnesium silicate (LNM silicate); however, it’s low density/high void ratio results in higher than typical permeability, low undrained shear strength, and extremely long consolidation times. Until now, translucent soil simulates of only 4.5% by mass LNM silicate to total mass have been possible. This paper provides a method for creating mixtures of translucent LNM silicate gel/glass as high as 15% by mass with the additions of an emulsifier, sodium pyrophosphate decahydrate (SPP), which impedes gelation so additional silicate powder can be added. Further, digital image processing techniques are used to present a relationship between LNM silicate, SPP, and translucency and an analysis of the modified simulate’s permeability and consolidation properties, with comparisons to natural clays, is also included.The lead author would like to acknowledge the excellent work of the undergraduate researchers on this project: Elliese Shaughnessy for the laboratory work and MATLAB programming necessary to create the Laponite-SPP curve, Kristen Ewert for conducting and interpreting the consolidation experiments, Nicholas Boardman for mixing the testing specimens and conducting the permeability experiments, and Tom Anderson for assisting with the permeability experiments. We would also like to thank Dr. Cassandra Rutherford for her assistance on the project. This research was funded through the National Science Foundation, Award Number: 1041604.This is the author accepted manuscript. The final version is available from American Society of Civil Engineers via http://dx.doi.org/10.1061/9780784480151.00

Water retention and characteristic curves representing tropical clay soils from Africa

Soil water retention curves (SWRCs) form an essential component of frameworks coupling the hydromechanical behaviour of unsaturated soils. The curves describe how suction changes with variables such as degree of saturation, void ratio and volumetric/gravimetric water content. SWRCs can be determined from incrementally drying initially saturated reconstituted samples to a final residual state, thus developing the primary drying curve (PDC). The primary wetting curve (PWC) is established from subsequent incremental wetting from residual state and is hysteretic compared with the PDC. SWRCs for reconstituted, high-plasticity, tropical clays from Africa (Sudan, Tanzania and South Africa) will be produced using suction measuring instruments, a tensiometer, filter paper and a dew point potentiometer. The development of SWRCs under various subsequent cycles of drying will be presented and discussed along with details concerning volumetric changes and cracking during drying. In order to investigate the uniqueness of the PDC and PWC and the effect of initial void ratio, SWRCs will be determined for samples formed by reconstituted from slurry under different applied energy levels.</jats:p

Seismological and geotechnical aspects of the Mw=6.3 l’Aquila earthquake in central Italy on 6 April 2009

The L’Aquila earthquake occurred on April 6 2009 at 03:32:39 local time. The earthquake (Mw=6.3) was located in the central Italy region of Abruzzo. Much of the damage occurred in the capital city of L’Aquila, a city of approximate population 73000, although many small villages in the surrounding region of the middle Aterno river valley were also significantly damaged. In the weeks following the earthquake, the Geo-Engineering Extreme Events Reconnaissance (GEER) international team, comprised of members from different European countries and the U.S., was assembled to provide post-earthquake field reconnaissance. The GEER team focused on the geological, seismological, and geotechnical engineering aspects of the event. We describe the principal seismological findings related to this earthquake including moment tensors of the main shock and two triggered events, the aftershock pattern and its variation with time, tectonic deformations associated with the main shock, surface fault rupture, and the inferred fault rupture plane. We describe damage patterns on a village-to-village scale and on a more local scale within the city of L’Aquila. In many cases the damage patterns imply site effects, as neighbouring villages on rock and soil had significantly different damage intensities (damage more pronounced on softer sediments). The April 6 mainshock was the best-recorded event to date in Italy. We present metadata related to the recording sites and then present preliminary comparisons of the data to GMPEs. Those comparisons support the notion of faster distance attenuation in Italy relative to the average for active regions as reflected in NGA GMPEs. Several incidents of ground failure are then discussed, including a number of rockfalls and minor landslides. Perhaps the most significant incidents of ground failure occurred at Lake Sinizzo, for which we describe a number of slumps and spreads around the lake perimeter. This is documented using field observations as well as LIDAR and bathymetric data

Dysmetabolic circulating tumor cells are prognostic in metastatic breast cancer

Circulating tumor cells (CTCs) belong to a heterogeneous pool of rare cells, and a unequivocal phenotypic definition of CTC is lacking. Here, we present a definition of metabolically-altered CTC (MBA-CTCs) as CD45-negative cells with an increased extracellular acidification rate, detected with a single-cell droplet microfluidic technique. We tested the prognostic value of MBA-CTCs in 31 metastatic breast cancer patients before starting a new systemic therapy (T0) and 3\u20134 weeks after (T1), comparing results with a parallel FDA-approved CellSearch (CS) approach. An increased level of MBA-CTCs was associated with: I) a shorter median PFS pre-therapy (123 days vs. 306; p < 0.0001) and during therapy (139 vs. 266 days; p = 0.0009); ii) a worse OS pre-therapy (p = 0.0003, 82% survival vs. 20%) and during therapy (p = 0.0301, 67% survival vs. 38%); iii) good agreement with therapy response (kappa = 0.685). The trend of MBA-CTCs over time (combining data at T0 and T1) added information with respect to separate evaluation of T0 and T1. The combined results of the two assays (MBA and CS) increased stratification accuracy, while correlation between MBA and CS was not significant, suggesting that the two assays are detecting different CTC subsets. In conclusion, this study suggests that MBA allows detection of both EpCAM-negative and EpCAM-positive, viable and label-free CTCs, which provide clinical information apparently equivalent and complementary to CS. A further validation of proposed method and cut-offs is needed in a larger, separate study

KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)

© 2017 Sales et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Antarctic krill (Euphausia superba) is a key species in the Southern Ocean with an estimated biomass between 100 and 500 million tonnes. Changes in krill population viability would have catastrophic effect on the Antarctic ecosystem. One looming threat due to elevated levels of anthropogenic atmospheric carbon dioxide (CO2) is ocean acidification (lowering of sea water pH by CO2 dissolving into the oceans). The genetics of Antarctic krill has long been of scientific interest for both for the analysis of population structure and analysis of functional genetics. However, the genetic resources available for the species are relatively modest. We have developed the most advanced genetic database on Euphausia superba, KrillDB, which includes comprehensive data sets of former and present transcriptome projects. In particular, we have built a de novo transcriptome assembly using more than 360 million Illumina sequence reads generated from larval krill including individuals subjected to different CO2levels. The database gives access to: 1) the full list of assembled genes and transcripts; 2) their level of similarity to transcripts and proteins from other species; 3) the predicted protein domains contained within each transcript; 4) their predicted GO terms; 5) the level of expression of each transcript in the different larval stages and CO2treatments. All references to external entities (sequences, domains, GO terms) are equipped with a link to the appropriate source database. Moreover, the software implements a full-text search engine that makes it possible to submit free-form queries. KrillDB represents the first largescale attempt at classifying and annotating the full krill transcriptome. For this reason, we believe it will constitute a cornerstone of future approaches devoted to physiological and molecular study of this key species in the Southern Ocean food web

The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights

Antarctic krill (Euphausia superba) is Earth’smost abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research

Population genomics of marine zooplankton

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here for personal use, not for redistribution. The definitive version was published in Bucklin, Ann et al. "Population Genomics of Marine Zooplankton." Population Genomics: Marine Organisms. Ed. Om P. Rajora and Marjorie Oleksiak. Springer, 2018. doi:10.1007/13836_2017_9.The exceptionally large population size and cosmopolitan biogeographic distribution that distinguish many – but not all – marine zooplankton species generate similarly exceptional patterns of population genetic and genomic diversity and structure. The phylogenetic diversity of zooplankton has slowed the application of population genomic approaches, due to lack of genomic resources for closelyrelated species and diversity of genomic architecture, including highly-replicated genomes of many crustaceans. Use of numerous genomic markers, especially single nucleotide polymorphisms (SNPs), is transforming our ability to analyze population genetics and connectivity of marine zooplankton, and providing new understanding and different answers than earlier analyses, which typically used mitochondrial DNA and microsatellite markers. Population genomic approaches have confirmed that, despite high dispersal potential, many zooplankton species exhibit genetic structuring among geographic populations, especially at large ocean-basin scales, and have revealed patterns and pathways of population connectivity that do not always track ocean circulation. Genomic and transcriptomic resources are critically needed to allow further examination of micro-evolution and local adaptation, including identification of genes that show evidence of selection. These new tools will also enable further examination of the significance of small-scale genetic heterogeneity of marine zooplankton, to discriminate genetic “noise” in large and patchy populations from local adaptation to environmental conditions and change.Support was provided by the US National Science Foundation to AB and RJO (PLR-1044982) and to RJO (MCB-1613856); support to IS and MC was provided by Nord University (Norway)

Principal stress rotation under bidirectional simple shear loadings

Previous researches have indicated the non-coaxiality of sand in unidirectional simple shear tests, in which the direction of the principal axes of stresses does not coincide with the corresponding principal axes of strain rate tensors. Due to the limitation of apparatus that most of testing facilities can only add shear stress in one direction, the influence of stress history on the noncoaxiality of sand is not fully considered in previous tests. In this study, the effect of stress history on the non-coaxiality of sand is systematically studied by using the first commercially available Variable Direction Dynamic Cyclic Simple Shear system (VDDCSS). Samples of Leighton Buzzard sand (Fraction B) are first consolidated under a vertical confining stress and consolidation shear stress, and then sheared by a drained monotonic shear stress. Angle (θ) between the consolidation shear stress and the drained monotonic shear stress is varied from 0° to 180°, with an interval of 30°. The change of principal axes of stresses is predicted by well-established equations, and the principal axe of strain rate is calculated using recorded data. Results show that the level of non-coaxiality is increased by the increasing θ, especially at the initial stage of drained shearing