Recommendation of RILEM TC 261-CCF: test method to determine the flexural creep of fibre reinforced concrete in the cracked state

[EN] To date there is no clear consensus about how creep of cracked FRC structural elements should be considered. In recent years, different methodologies have been developed for multiple stress cases. The absence of a standardised methodology to evaluate flexural creep in the cracked state has hindered general comparisons and conclusions that could lead to significant advances in this topic. Since 2014, the study of the creep behaviour of cracked FRC has been coordinated by the RILEM TC 261-CCF. All the available creep methodologies were analysed in terms of procedure, equipment and results. A comprehensive Round-Robin Test (RRT) on the creep behaviour of cracked sections of FRC was proposed and undertaken by a total of 19 participant laboratories from 14 countries all over the world. The analysis and conclusions of the RRT results and the different methodologies provided the basis for this recommendation. This recommendation focuses on the test method to evaluate the flexural creep of FRC specimens in the cracked state. Guidelines on specimen production, detailed test equipment, experimental setup and test procedure as well as the definitions of the most relevant parameters are provided.Llano-Torre, A.; Serna Ros, P. (2021). Recommendation of RILEM TC 261-CCF: test method to determine the flexural creep of fibre reinforced concrete in the cracked state. Materials and Structures. 54(3):1-20. https://doi.org/10.1617/s11527-021-01675-0S120543Theodorakopoulos D (1995) Creep characteristics of glass reinforced cement under flexural loading. Cement Concr Compos 17:267–279Chanvillard G, Roque O (1999) Behaviour of fibre reinforced concrete cracked section under sustained load. High Performance Fiber Reinforced Cement Composites (HPFRCC 3) Mainz, Germany, pp 239–250, RILEM PRO 06Kurt S, Balaguru P (2000) Post crack creep of polymeric fibre-reinforced concrete in flexure. Cem Concr Res 30(2):183–190Mackay J, Trottier JF (2004) Post-crack behavior of steel and synthetic FRC under flexural creep. In: Shotcrete, Proc. 2nd Intnl. Conf. on Engineering, Cairns, Australia (2004), pp 183–192Kusterle W (2009) Viscous material behaviour of solids- creep of polymer fibre reinforced concrete. In: Proc. 5th Central European Congress on Concrete Engineering. obv, Baden, pp 95–100Arango S, Serna P, Martí-Vargas JR, García-Taengua E (2012) A test method to characterize flexural creep behaviour of pre-cracked FRC specimens. Exp Mech 52(8):1067–1078Zerbino RL, Barragan BE (2012) Long-term behaviour of cracked steel fibre-reinforced concrete beams under sustained loading. ACI Mater J 109(2):215–224Abrishambaf A, Barros JAO, Cunha VMCF (2015) Time-dependent flexural behaviour of cracked steel fibre reinforced self-compacting concrete panels. Cem Concr Res 72:21–36Buratti N, Mazzotti C (2016) Experimental tests on the long-term behaviour of SFRC and MSFRC in bending and direct tension. In: Proceedings of the BEFIB 2016, 9th RILEM international symposium on fiber reinforced concrete, pp. 163–174, Vancouver, Canada, 19–21 Sept 2016Babafemi AJ, Boshoff WP (2015) Tensile creep of macro-synthetic fibre reinforced concrete (MSFRC) under uni-axial tensile loading. Cement Concr Compos 55:62–69Vrijdaghs R, di Prisco M, Vandewalle L (2018) Uniaxial tensile creep of a cracked polypropylene fiber reinforced concrete. Mater Struct 51:5. https://doi.org/10.1617/s11527-017-1132-5Vasanelli E, Micelli F, Aiello MA, Plizzari G (2013) Long term behaviour of FRC flexural beams under sustained load. Eng Struct 56:1858–1867Bernard ES (2010) Influence of fibre type on creep deformation of cracked fibre-reinforced shotcrete panels. ACI Mater J 107(5):474–480EFNARC (2012) Testing sprayed concrete—Creep test on square panelLarive C, Rogat D, Chamoley D, Regnard A, Pannetier T, Thuaud C (2016) Influence of fibres on the creep behaviour of reinforced sprayed concrete. In: Proceedings of ITA World Tunnel Congress WTC 2016, April 22‐28, San Francisco, United StatesMonetti DH, Llano-Torre A, Torrijos MC, Giaccio G, Zerbino R, Martí-Vargas JR, Serna P (2019) Long-term behavior of cracked fiber reinforced concrete under service conditions. Construct Build Mater; 196:649–658. https://doi.org/10.1016/j.conbuildmat.2018.10.230Llano-Torre A., Martí-Vargas JR, Serna P (2020) Flexural and compressive creep behavior of UHPFRC specimens. Construct Build Mater; 244:118254. https://doi.org/10.1016/j.conbuildmat.2020.118254Serna P, Llano-Torre A and Cavalaro S H P (ed) (2017) Creep behaviour in cracked sections of fibre reinforced concrete: proceedings of the international RILEM Workshop FRC-CREEP 2016. RILEM bookseries 14 (Dordrecht: Springer)Llano-Torre A, Serna P, Cavalaro SHP (2016) International round robin test on creep behavior of FRC supported by the RILEM TC 261-CCF. In: Proceedings of the BEFIB 2016, 9th RILEM international symposium on fiber reinforced concrete, pp 127–140, Vancouver, Canada, 19–21 Sept 2016Serna P, Llano-Torre A, García-Taengua E, Martí-Vargas JR (2015) Database on the long-term behaviour of FRC: a useful tool to achieve overall conclusions. In: Proceedings of the 10th international conference on mechanics and physics of Creep, Shrinkage, and Durability of Concrete and Concrete Structures, Vienna, September 2015, pp 1544–1553Llano-Torre A., Serna P. (eds) Round-Robin test on creep behaviour in cracked sections of FRC: experimental program, results and database analysis. RILEM State-of-the-Art Reports. Springer. https://doi.org/10.1007/978-3-030-72736-9ASTM International (2015) C1812/C1812M-15e1 Standard Practice for Design of Journal Bearing Supports to be Used in Fiber Reinforced Concrete Beam Tests. West Conshohocken, PA; ASTM International. https://doi.org/10.1520/C1812_C1812M-15E0

Influence of Fibre Reinforcement on the Long-Term Behaviour of Cracked Concrete

The influence of fibre reinforcement on the long-term behaviour of cracked concrete is analysed in this work by means of a creep test. Nine concrete mixes were prepared (7 SFRCs and 2 conventional RCs) based on two basic mix designs. Concretes type I were conceived for structural precast applications and concretes type II reproduce a general purpose. Fibre dosages and conventional reinforcements were varied to represent a wide spectrum of post-peak flexural responses. In all cases with fibre reinforcement steel fibres were used. Conventional RC specimens were reinforced with two steel rebars. In addition to the variables of mix design of concrete, there are two significant variables related to the creep test: the pre-crack opening level (CMODpn) and the stress level (Ic) sustained during the test. Creep tests were performed by applying a constant flexural load on notched pre-cracked specimens and controlling crack opening evolution. Some of the specimens developed a sudden increase of crack opening deformations during the creep test. Creep coefficients and Crack Opening Rates were calculated and analysed. Creep coefficients show significant dependence on the analysed variables. The results of this experimental campaign show that creep of SFRC specimens may be similar to a traditional RC

Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patients.

Naturally acquired blood-stage infections of the malaria parasite Plasmodium falciparum typically harbour multiple haploid clones. The apparent number of clones observed in any single infection depends on the diversity of the polymorphic markers used for the analysis, and the relative abundance of rare clones, which frequently fail to be detected among PCR products derived from numerically dominant clones. However, minority clones are of clinical interest as they may harbour genes conferring drug resistance, leading to enhanced survival after treatment and the possibility of subsequent therapeutic failure. We deployed new generation sequencing to derive genome data for five non-propagated parasite isolates taken directly from 4 different patients treated for clinical malaria in a UK hospital. Analysis of depth of coverage and length of sequence intervals between paired reads identified both previously described and novel gene deletions and amplifications. Full-length sequence data was extracted for 6 loci considered to be under selection by antimalarial drugs, and both known and previously unknown amino acid substitutions were identified. Full mitochondrial genomes were extracted from the sequencing data for each isolate, and these are compared against a panel of polymorphic sites derived from published or unpublished but publicly available data. Finally, genome-wide analysis of clone multiplicity was performed, and the number of infecting parasite clones estimated for each isolate. Each patient harboured at least 3 clones of P. falciparum by this analysis, consistent with results obtained with conventional PCR analysis of polymorphic merozoite antigen loci. We conclude that genome sequencing of peripheral blood P. falciparum taken directly from malaria patients provides high quality data useful for drug resistance studies, genomic structural analyses and population genetics, and also robustly represents clonal multiplicity

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer than 269 kilobases. Incorporating fosmid ends recovers entire chromosomes. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. A novel memory-efficient hashing scheme is introduced. The resulting contigs are ordered and oriented using paired reads separated by ∼280 bp or ∼3.2 kbp, and many gaps between contigs can be closed using paired-end placements. Practical issues with the dataset are described, and prospects for assembling larger genomes are discussed

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

<p>Abstract</p> <p>Background</p> <p>Next-generation sequencing technologies have led to the high-throughput production of sequence data (reads) at low cost. However, these reads are significantly shorter and more error-prone than conventional Sanger shotgun reads. This poses a challenge for the <it>de novo </it>assembly in terms of assembly quality and scalability for large-scale short read datasets.</p> <p>Results</p> <p>We present DecGPU, the first parallel and distributed error correction algorithm for high-throughput short reads (HTSRs) using a hybrid combination of CUDA and MPI parallel programming models. DecGPU provides CPU-based and GPU-based versions, where the CPU-based version employs coarse-grained and fine-grained parallelism using the MPI and OpenMP parallel programming models, and the GPU-based version takes advantage of the CUDA and MPI parallel programming models and employs a hybrid CPU+GPU computing model to maximize the performance by overlapping the CPU and GPU computation. The distributed feature of our algorithm makes it feasible and flexible for the error correction of large-scale HTSR datasets. Using simulated and real datasets, our algorithm demonstrates superior performance, in terms of error correction quality and execution speed, to the existing error correction algorithms. Furthermore, when combined with Velvet and ABySS, the resulting DecGPU-Velvet and DecGPU-ABySS assemblers demonstrate the potential of our algorithm to improve <it>de novo </it>assembly quality for <it>de</it>-<it>Bruijn</it>-graph-based assemblers.</p> <p>Conclusions</p> <p>DecGPU is publicly available open-source software, written in CUDA C++ and MPI. The experimental results suggest that DecGPU is an effective and feasible error correction algorithm to tackle the flood of short reads produced by next-generation sequencing technologies.</p

Comparing De Novo Genome Assembly: The Long and Short of It

Recent advances in DNA sequencing technology and their focal role in Genome Wide Association Studies (GWAS) have rekindled a growing interest in the whole-genome sequence assembly (WGSA) problem, thereby, inundating the field with a plethora of new formalizations, algorithms, heuristics and implementations. And yet, scant attention has been paid to comparative assessments of these assemblers' quality and accuracy. No commonly accepted and standardized method for comparison exists yet. Even worse, widely used metrics to compare the assembled sequences emphasize only size, poorly capturing the contig quality and accuracy. This paper addresses these concerns: it highlights common anomalies in assembly accuracy through a rigorous study of several assemblers, compared under both standard metrics (N50, coverage, contig sizes, etc.) as well as a more comprehensive metric (Feature-Response Curves, FRC) that is introduced here; FRC transparently captures the trade-offs between contigs' quality against their sizes. For this purpose, most of the publicly available major sequence assemblers – both for low-coverage long (Sanger) and high-coverage short (Illumina) reads technologies – are compared. These assemblers are applied to microbial (Escherichia coli, Brucella, Wolbachia, Staphylococcus, Helicobacter) and partial human genome sequences (Chr. Y), using sequence reads of various read-lengths, coverages, accuracies, and with and without mate-pairs. It is hoped that, based on these evaluations, computational biologists will identify innovative sequence assembly paradigms, bioinformaticists will determine promising approaches for developing “next-generation” assemblers, and biotechnologists will formulate more meaningful design desiderata for sequencing technology platforms. A new software tool for computing the FRC metric has been developed and is available through the AMOS open-source consortium

Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants

The goal of human genome re-sequencing is obtaining an accurate assembly of an individual's genome. Recently, there has been great excitement in the development of many technologies for this (e.g. medium and short read sequencing from companies such as 454 and SOLiD, and high-density oligo-arrays from Affymetrix and NimbelGen), with even more expected to appear. The costs and sensitivities of these technologies differ considerably from each other. As an important goal of personal genomics is to reduce the cost of re-sequencing to an affordable point, it is worthwhile to consider optimally integrating technologies. Here, we build a simulation toolbox that will help us optimally combine different technologies for genome re-sequencing, especially in reconstructing large structural variants (SVs). SV reconstruction is considered the most challenging step in human genome re-sequencing. (It is sometimes even harder than de novo assembly of small genomes because of the duplications and repetitive sequences in the human genome.) To this end, we formulate canonical problems that are representative of issues in reconstruction and are of small enough scale to be computationally tractable and simulatable. Using semi-realistic simulations, we show how we can combine different technologies to optimally solve the assembly at low cost. With mapability maps, our simulations efficiently handle the inhomogeneous repeat-containing structure of the human genome and the computational complexity of practical assembly algorithms. They quantitatively show how combining different read lengths is more cost-effective than using one length, how an optimal mixed sequencing strategy for reconstructing large novel SVs usually also gives accurate detection of SNPs/indels, how paired-end reads can improve reconstruction efficiency, and how adding in arrays is more efficient than just sequencing for disentangling some complex SVs. Our strategy should facilitate the sequencing of human genomes at maximum accuracy and low cost

Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads

Recent improvements in technology have made DNA sequencing dramatically faster and more efficient than ever before. The new technologies produce highly accurate sequences, but one drawback is that the most efficient technology produces the shortest read lengths. Short-read sequencing has been applied successfully to resequence the human genome and those of other species but not to whole-genome sequencing of novel organisms. Here we describe the sequencing and assembly of a novel clinical isolate of Pseudomonas aeruginosa, strain PAb1, using very short read technology. From 8,627,900 reads, each 33 nucleotides in length, we assembled the genome into one scaffold of 76 ordered contiguous sequences containing 6,290,005 nucleotides, including one contig spanning 512,638 nucleotides, plus an additional 436 unordered contigs containing 416,897 nucleotides. Our method includes a novel gene-boosting algorithm that uses amino acid sequences from predicted proteins to build a better assembly. This study demonstrates the feasibility of very short read sequencing for the sequencing of bacterial genomes, particularly those for which a related species has been sequenced previously, and expands the potential application of this new technology to most known prokaryotic species