Evaluation of test methods for self-healing concrete with macrocapsules by inter-laboratory testing

Self-healing of concrete is a promising way to increase the service life of structures. Innovative research is being performed, yet it is difficult to compare results due to a lack of standardised test methods. In the framework of the COST action SARCOS (CA15202) [1] six different interlaboratory tests are being executed, in which different test methods are being evaluated for six self-healing approaches. Here, the results of the inter-laboratory test concerning mortar and concrete with macrocapsules filled with a polyurethane healing agent will be discussed. The specimens were manufactured in one laboratory and then shipped to the other five participating laboratories. All six laboratories evaluated two test methods: a water permeability test and a capillary water absorption test. For the water permeability test, mortar specimens were cracked and afterwards their crack width was controlled using an active control technique. Due to the active crack control, the crack width of 90% of the samples deviated by less than 10 μm from the target of 300 μm. This made it more straightforward to compare the permeability test results, which indicated a similar sealing efficiency for several of the laboratories. For the capillary water absorption test, concrete specimens were cracked in a crack-width-controlled three-point bending test setup without active control after unloading. Compared to the water permeability specimens, there was a lot more variation on the crack width of the capillary water absorption specimens. The variability on the crack width and differences in quality of waterproofing resulted in diverging findings in the capillary water absorption test

Evaluation of Methodologies for Assessing Self-Healing Performance of Concrete with Mineral Expansive Agents: An Interlaboratory Study.

Self-healing concrete has the potential to optimise traditional design approaches; however, commercial uptake requires the ability to harmonize against standardized frameworks. Within EU SARCOS COST Action, different interlaboratory tests were executed on different self-healing techniques. This paper reports on the evaluation of the effectiveness of proposed experimental methodologies suited for self-healing concrete with expansive mineral additions. Concrete prisms and discs with MgO-based healing agents were produced and precracked. Water absorption and water flow tests were executed over a healing period spanning 6 months to assess the sealing efficiency, and the crack width reduction with time was monitored. High variability was reported for both reference (REF) and healing-addition (ADD) series affecting the reproducibility of cracking. However, within each lab, the crack width creation was repeatable. ADD reported larger crack widths. The latter influenced the observed healing making direct comparisons across labs prone to errors. Water absorption tests highlighted were susceptible to application errors. Concurrently, the potential of water flow tests as a facile method for assessment of healing performance was shown across all labs. Overall, the importance of repeatability and reproducibility of testing methods is highlighted in providing a sound basis for incorporation of self-healing concepts in practical applications.EPSR

Non-Invasive Mapping of the Gastrointestinal Microbiota Identifies Children with Inflammatory Bowel Disease

Background: Pediatric inflammatory bowel disease (IBD) is challenging to diagnose because of the non-specificity of symptoms; an unequivocal diagnosis can only be made using colonoscopy, which clinicians are reluctant to recommend for children. Diagnosis of pediatric IBD is therefore frequently delayed, leading to inappropriate treatment plans and poor outcomes. We investigated the use of 16S rRNA sequencing of fecal samples and new analytical methods to assess differences in the microbiota of children with IBD and other gastrointestinal disorders. Methodology/Principal Findings: We applied synthetic learning in microbial ecology (SLiME) analysis to 16S sequencing data obtained from i) published surveys of microbiota diversity in IBD and ii) fecal samples from 91 children and young adults who were treated in the gastroenterology program of Children’s Hospital (Boston, USA). The developed method accurately distinguished control samples from those of patients with IBD; the area under the receiver-operating-characteristic curve (AUC) value was 0.83 (corresponding to 80.3% sensitivity and 69.7% specificity at a set threshold). The accuracy was maintained among data sets collected by different sampling and sequencing methods. The method identified taxa associated with disease states and distinguished patients with Crohn’s disease from those with ulcerative colitis with reasonable accuracy. The findings were validated using samples from an additional group of 68 patients; the validation test identified patients with IBD with an AUC value of 0.84 (e.g. 92% sensitivity, 58.5% specificity). Conclusions/Significance: Microbiome-based diagnostics can distinguish pediatric patients with IBD from patients with similar symptoms. Although this test can not replace endoscopy and histological examination as diagnostic tools, classification based on microbial diversity is an effective complementary technique for IBD detection in pediatric patients.Natural Sciences and Engineering Research Council of Canada (Award NSERC PGS D)National Institutes of Health (U.S.) (1-R21-A1084032-01A1

Analysis of the African coelacanth genome sheds light on tetrapod evolution

It was a zoological sensation when a living specimen of the coelacanth was first discovered in 1938, as this lineage of lobe-finned fish was thought to have gone extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features . Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain, and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues demonstrate the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University

Evaluation of test methods for self-healing concrete with macrocapsules by inter-laboratory testing

Self-healing of concrete is a promising way to increase the service life of structures. Innovative research is being performed, yet it is difficult to compare results due to a lack of standardised test methods. In the framework of the COST action SARCOS (CA15202) [1] six different interlaboratory tests are being executed, in which different test methods are being evaluated for six self-healing approaches. Here, the results of the inter-laboratory test concerning mortar and concrete with macrocapsules filled with a polyurethane healing agent will be discussed. The specimens were manufactured in one laboratory and then shipped to the other five participating laboratories. All six laboratories evaluated two test methods: a water permeability test and a capillary water absorption test. For the water permeability test, mortar specimens were cracked and afterwards their crack width was controlled using an active control technique. Due to the active crack control, the crack width of 90% of the samples deviated by less than 10 μm from the target of 300 μm. This made it more straightforward to compare the permeability test results, which indicated a similar sealing efficiency for several of the laboratories. For the capillary water absorption test, concrete specimens were cracked in a crack-width-controlled three-point bending test setup without active control after unloading. Compared to the water permeability specimens, there was a lot more variation on the crack width of the capillary water absorption specimens. The variability on the crack width and differences in quality of waterproofing resulted in diverging findings in the capillary water absorption test

Addressing the need for standardization of test methods for self-healing concrete: an inter-laboratory study on concrete with macrocapsules

Development and commercialization of self-healing concrete is hampered due to a lack of standardized test methods. Six inter-laboratory testing programs are being executed by the EU COST action SARCOS, each focusing on test methods for a specific self-healing technique. This paper reports on the comparison of tests for mortar and concrete specimens with polyurethane encapsulated in glass macrocapsules. First, the pre-cracking method was analysed: mortar specimens were cracked in a three-point bending test followed by an active crack width control technique to restrain the crack width up to a predefined value, while the concrete specimens were cracked in a three-point bending setup with a displacement-controlled loading system. Microscopic measurements showed that with the application of the active control technique almost all crack widths were within a narrow predefined range. Conversely, for the concrete specimens the variation on the crack width was higher. After pre-cracking, the self-healing effect was characterized via durability tests: the mortar specimens were tested in a water permeability test and the spread of the healing agent on the crack surfaces was determined, while the concrete specimens were subjected to two capillary water absorption tests, executed with a different type of waterproofing applied on the zone around the crack. The quality of the waterproofing was found to be important, as different results were obtained in each absorption test. For the permeability test, 4 out of 6 labs obtained a comparable flow rate for the reference specimens, yet all 6 labs obtained comparable sealing efficiencies, highlighting the potential for further standardization.status: Published onlin

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

Bacterial diversity among environmental samples is commonly assessed with PCR-amplified 16S rRNA gene (16S) sequences. Perceived diversity, however, can be influenced by sample preparation, primer selection, and formation of chimeric 16S amplification products. Chimeras are hybrid products between multiple parent sequences that can be falsely interpreted as novel organisms, thus inflating apparent diversity. We developed a new chimera detection tool called Chimera Slayer (CS). CS detects chimeras with greater sensitivity than previous methods, performs well on short sequences such as those produced by the 454 Life Sciences (Roche) Genome Sequencer, and can scale to large data sets. By benchmarking CS performance against sequences derived from a controlled DNA mixture of known organisms and a simulated chimera set, we provide insights into the factors that affect chimera formation such as sequence abundance, the extent of similarity between 16S genes, and PCR conditions. Chimeras were found to reproducibly form among independent amplifications and contributed to false perceptions of sample diversity and the false identification of novel taxa, with less-abundant species exhibiting chimera rates exceeding 70%. Shotgun metagenomic sequences of our mock community appear to be devoid of 16S chimeras, supporting a role for shotgun metagenomics in validating novel organisms discovered in targeted sequence surveys

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

Bacterial diversity among environmental samples is commonly assessed with PCR-amplified 16S rRNA gene (16S) sequences. Perceived diversity, however, can be influenced by sample preparation, primer selection, and formation of chimeric 16S amplification products. Chimeras are hybrid products between multiple parent sequences that can be falsely interpreted as novel organisms, thus inflating apparent diversity. We developed a new chimera detection tool called Chimera Slayer (CS). CS detects chimeras with greater sensitivity than previous methods, performs well on short sequences such as those produced by the 454 Life Sciences (Roche) Genome Sequencer, and can scale to large data sets. By benchmarking CS performance against sequences derived from a controlled DNA mixture of known organisms and a simulated chimera set, we provide insights into the factors that affect chimera formation such as sequence abundance, the extent of similarity between 16S genes, and PCR conditions. Chimeras were found to reproducibly form among independent amplifications and contributed to false perceptions of sample diversity and the false identification of novel taxa, with less-abundant species exhibiting chimera rates exceeding 70%. Shotgun metagenomic sequences of our mock community appear to be devoid of 16S chimeras, supporting a role for shotgun metagenomics in validating novel organisms discovered in targeted sequence surveys