Numerical studies of different mixed phase-field fracture models for simulating crack propagation in punctured EPDM strips

We consider a monolithic phase-field description for fractures in nearly incompressible materials, i.e., carbon black filled ethylene propylene diene monomer rubber (EPDM). A quasi-static phase-field fracture problem is formulated in mixed form based on three different energy functionals (AT2, AT1 and Wu’s model) combined with two different stress splitting approaches (according to Miehe and Amor). It leads to six different phase-field fracture formulations in mixed form. The coupled variational inequality systems are solved in a quasi-monolithic manner with the help of a primal-dual active set method handling the inequality constraint. Further, adaptive mesh refinement is used to get a sharper crack zone. Numerical results based on the six different problem setups are validated on crack propagation experiments of punctured EPDM strips with five different test configurations. As a quantity of interest, the crack paths of experiments and numerical computations are discussed

Genetic diversity of Mycobacterium tuberculosis isolated from tuberculosis patients in the Serengeti ecosystem in Tanzania

SummaryThis study was part of a larger cross-sectional survey that was evaluating tuberculosis (TB) infection in humans, livestock and wildlife in the Serengeti ecosystem in Tanzania. The study aimed at evaluating the genetic diversity of Mycobacterium tuberculosis isolates from TB patients attending health facilities in the Serengeti ecosystem. DNA was extracted from 214 sputum cultures obtained from consecutively enrolled newly diagnosed untreated TB patients aged ≥18 years. Spacer oligonucleotide typing (spoligotyping) and Mycobacterium Interspersed Repetitive Units and Variable Number Tandem Repeat (MIRU-VNTR) were used to genotype M. tuberculosis to establish the circulating lineages. Of the214 M. tuberculosis isolates genotyped, 55 (25.7%) belonged to the Central Asian (CAS) family, 52 (24.3%) were T family (an ill-defined family), 38 (17.8%) belonged to the Latin American Mediterranean (LAM) family, 25 (11.7%) to the East-African Indian (EAI) family, 25 (11.7%) comprised of different unassigned (‘Serengeti’) strain families, while 8 (3.7%) belonged to the Beijing family. A minority group that included Haarlem, X, U and S altogether accounted for 11 (5.2%) of all genotypes. MIRU-VNTR typing produced diverse patterns within and between families indicative of unlinked transmission chains. We conclude that, in the Serengeti ecosystem only a few successful families predominate namely CAS, T, LAM and EAI families. Other types found in lower prevalence are Beijing, Haarlem, X, S and MANU. The Haarlem, EAI_Somalia, LAM3 and S/convergent and X2 subfamilies found in this study were not reported in previous studies in Tanzania

The Forest behind the Tree: Phylogenetic Exploration of a Dominant Mycobacterium tuberculosis Strain Lineage from a High Tuberculosis Burden Country

BACKGROUND: Genotyping of Mycobacterium tuberculosis isolates is a powerful tool for epidemiological control of tuberculosis (TB) and phylogenetic exploration of the pathogen. Standardized PCR-based typing, based on 15 to 24 mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) loci combined with spoligotyping, has been shown to have adequate resolution power for tracing TB transmission and to be useful for predicting diverse strain lineages in European settings. Its informative value needs to be tested in high TB-burden countries, where the use of genotyping is often complicated by dominance of geographically specific, genetically homogeneous strain lineages. METHODOLOGY/PRINCIPAL FINDINGS: We tested this genotyping system for molecular epidemiological analysis of 369 M. tuberculosis isolates from 3 regions of Brazil, a high TB-burden country. Deligotyping, targeting 43 large sequence polymorphisms (LSPs), and the MIRU-VNTRplus identification database were used to assess phylogenetic predictions. High congruence between the different typing results consistently revealed the countrywide supremacy of the Latin-American-Mediterranean (LAM) lineage, comprised of three main branches. In addition to an already known RDRio branch, at least one other branch characterized by a phylogenetically informative LAM3 spoligo-signature seems to be globally distributed beyond Brazil. Nevertheless, by distinguishing 321 genotypes in this strain population, combined MIRU-VNTR typing and spoligotyping demonstrated the presence of multiple distinct clones. The use of 15 to 24 loci discriminated 21 to 25% more strains within the LAM lineage, compared to a restricted lineage-specific locus set suggested to be used after SNP analysis. Noteworthy, 23 of the 28 molecular clusters identified were exclusively composed of patient isolates from a same region, consistent with expected patterns of mostly local TB transmission. CONCLUSIONS/SIGNIFICANCE: Standard MIRU-VNTR typing combined with spoligotyping can reveal epidemiologically meaningful clonal diversity behind a dominant M. tuberculosis strain lineage in a high TB-burden country and is useful to explore international phylogenetical ramifications

Observation of a maternal transmission of scrapie in sheep

A pregnant ewe with suspected scrapie was referred to the Regional Veterinary Laboratory in Limoges on 11 January 2002, in compliance with the French scrapie eradication program. Western Blot confirmed the diagnosis of scrapie. Ten days later, the ewe gave birth. As we had to help the ewe, we were able to isolate the ewe lamb before she had any contact with her mother, and especially no colostrum. The ewe lamb was fed with milk replacers and isolated to prevent all possibility of horizontal transmission of scrapie. In August 2002, the first symptoms of scrapie appeared in the ewe lamb. Euthanasia was decided on 18 December 2002, as the animal was no longer able to stand. Western Blot and immunohistochemistry tests confirmed natural scrapie in the ewe lamb. PrP genotyping of this lamb was ARQ/VRQ. This first confirmed case of maternal transmission of scrapie in sheep is associated with a particularly short incubation time (6 months) in natural conditions.Dans le cadre du programme d'éradication de la tremblante en France, nous avons reçu une brebis gestante suspecte de tremblante le 11 janvier 2002, au laboratoire vétérinaire départemental de Limoges (confirmée ultérieurement par un Western Blot). Dix jours plus tard, la brebis agnela avec difficulté et nous avons dû intervenir pour l'aider. Cette assistance à l'agnelage nous permit d'isoler immédiatement le nouveau-né, en évitant tout contact ultérieur avec sa mère, en particulier sans la possibilité d'absorber le colostrum. L'agnelle fut placée dans un endroit isolé sans qu'il n'y ait de possibilité de transmission horizontale de la tremblante et fut nourrie avec des lactoremplaceurs. En août 2002, les premiers symptômes de la tremblante sont apparus chez l'agnelle née de cette brebis. Du fait d'une évolution vers le décubitus, l'euthanasie de l'agnelle fut décidée le 18 décembre 2002. La confirmation d'une tremblante naturelle chez l'agnelle a été obtenue par le Western-Blot et les examens immunohistochimiques. Le génotype de l'agnelle était ARQ/VRQ. Cette première confirmation d'une transmission maternelle de la tremblante chez le mouton s'accompagne aussi d'un temps d'incubation particulièrement court (6 mois) dans les conditions naturelles

Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages

There is increasing evidence that strain variation in Mycobacterium tuberculosis complex (MTBC) might influence the outcome of tuberculosis infection and disease. To assess genotype-phenotype associations, phylogenetically robust molecular markers and appropriate genotyping tools are required. Most current genotyping methods for MTBC are based on mobile or repetitive DNA elements. Because these elements are prone to convergent evolution, the corresponding genotyping techniques are suboptimal for phylogenetic studies and strain classification. By contrast, single nucleotide polymorphisms (SNP) are ideal markers for classifying MTBC into phylogenetic lineages, as they exhibit very low degrees of homoplasy. In this study, we developed two complementary SNP-based genotyping methods to classify strains into the six main human-associated lineages of MTBC, the 'Beijing' sublineage, and the clade comprising Mycobacterium bovis and Mycobacterium caprae. Phylogenetically informative SNPs were obtained from 22 MTBC whole-genome sequences. The first assay, referred to as MOL-PCR, is a ligation-dependent PCR with signal detection by fluorescent microspheres and a Luminex flow cytometer, which simultaneously interrogates eight SNPs. The second assay is based on six individual TaqMan real-time PCR assays for singleplex SNP-typing. We compared MOL-PCR and TaqMan results in two panels of clinical MTBC isolates. Both methods agreed fully when assigning 36 well-characterized strains into the main phylogenetic lineages. The sensitivity in allele-calling was 98.6% and 98.8% for MOL-PCR and TaqMan, respectively. Typing of an additional panel of 78 unknown clinical isolates revealed 99.2% and 100% sensitivity in allele-calling, respectively, and 100% agreement in lineage assignment between both methods. While MOL-PCR and TaqMan are both highly sensitive and specific, MOL-PCR is ideal for classification of isolates with no previous information, whereas TaqMan is faster for confirmation. Furthermore, both methods are rapid, flexible and comparably inexpensive

Mycobacterium tuberculosis ecology in Venezuela: epidemiologic correlates of common spoligotypes and a large clonal cluster defined by MIRU-VNTR-24

<p>Abstract</p> <p>Background</p> <p>Tuberculosis remains an endemic public health problem, but the ecology of the TB strains prevalent, and their transmission, can vary by country and by region. We sought to investigate the prevalence of <it>Mycobacterium tuberculosis </it>strains in different regions of Venezuela. A previous study identified the most prevalent strains in Venezuela but did not show geographical distribution nor identify clonal genotypes. To better understand local strain ecology, we used spoligotyping to analyze 1298 <it>M. tuberculosis </it>strains isolated in Venezuela from 1997 to 2006, predominantly from two large urban centers and two geographically distinct indigenous areas, and then studied a subgroup with MIRU-VNTR 24 loci.</p> <p>Results</p> <p>The distribution of spoligotype families is similar to that previously reported for Venezuela and other South American countries: LAM 53%, T 10%, Haarlem 5%, S 1.9%, X 1.2%, Beijing 0.4%, and EAI 0.2%. The six most common shared types (SIT's 17, 93, 605, 42, 53, 20) accounted for 49% of the isolates and were the most common in almost all regions, but only a minority were clustered by MIRU-VNTR 24. One exception was the third most frequent overall, SIT 605, which is the most common spoligotype in the state of Carabobo but infrequent in other regions. MIRU-VNTR homogeneity suggests it is a clonal group of strains and was named the "Carabobo" genotype. Epidemiologic comparisons showed that patients with SIT 17 were younger and more likely to have had specimens positive for Acid Fast Bacilli on microscopy, and patients with SIT 53 were older and more commonly smear negative. Female TB patients tended to be younger than male patients. Patients from the high incidence, indigenous population in Delta Amacuro state were younger and had a nearly equal male:female distribution.</p> <p>Conclusion</p> <p>Six SIT's cause nearly half of the cases of tuberculosis in Venezuela and dominate in nearly all regions. Strains with SIT 17, the most common pattern overall may be more actively transmitted and SIT 53 strains may be less virulent and associated with reactivation of past infections in older patients. In contrast to other common spoligotypes, strains with SIT 605 form a clonal group centered in the state of Carabobo.</p

Clonal Population of Mycobacterium tuberculosis Strains Reside within Multiple Lung Cavities

(MTB) are localized within lung cavities of patients suffering from chronic progressive TB.Multiple cavity isolates from lung of 5 patients who had undergone pulmonary resection surgery were analyzed on the basis of their drug susceptibility profile, and genotyped by spoligotyping and 24-loci MIRU-VNTR. The patients past history including treatment was studied. Three of the 5 patients had extensive drug resistant TB. Heteroresistance was also reported within different cavity isolates of the lung. Both genotyping methods reported the presence of clonal population of MTB strain within different cavities of the each patient, even those reporting heteroresistance. Four of the 5 patients were infected with a population of the Beijing genotype. Post-surgery they were prescribed a drug regimen consisting of cycloserine, a fluoroquinolone and an injectable drug. A 6 month post-surgery follow-up reported only 2 patients with positive clinical outcome, showing sputum conversion.Identical spoligotype patterns and MIRU-VNTR profiles between multiple cavities of each patient, characterize the presence of clonal population of MTB strains (and absence of multiple MTB infection)

Polymorphs of Rb3ScF6: X-ray and Neutron Diffraction, Solid-State NMR, and Density Functional Theory Calculations Study

The crystal structures of three polymorphs of Rb3ScF6 have been determined through a combination of synchrotron, laboratory X-ray, and neutron powder diffraction, electron diffraction, and multinuclear high-field solid-state NMR studies. The room temperature (RT; α) and medium-temperature (β) structures are tetragonal, with space groups I41/a (Z = 80) and I4/m (Z = 10) and lattice parameters a = 20.2561(4) Å, c = 36.5160(0) Å and a = 14.4093(2) Å, c = 9.2015(1) Å at RT and 187 °C, respectively. The high-temperature (γ) structure is cubic space group Fm3¯ m (Z = 4) with a = 9.1944(1) Å at 250 °C. The temperatures of the phase transitions were measured at 141 and 201 °C. The three α, β, and γRb3ScF6 phases are isostructural with the α, β, and δforms of the potassium cryolite. Detailed structural characterizations were performed by density functional theory as well as NMR. In the case of the β polymorph, the dynamic rotations of the ScF6 octahedra of both Sc crystallographic sites have been detailed. © 2021 American Chemical Society.For DFT calculations, we thank the “Centre de Calcul Scientifique en region Centre” (Orléans, France). We acknowledge the Interface, Confinement, Materials and Nanostructures (Orléans, France) for access to their transmission electron microscope. Financial support from the IR-RMN-THC Fr3050 CNRS for conducting the research is gratefully acknowledged. This study was also financially supported by VEGA-2/0060/18 and ITMS project (code 313021T081, Research & Innovation Operational Programme funded by the ERDF). We thank also Dr. F. Vivet, Dr. F. Fayon, and Dr. D. Massiot for useful discussions