Local Entropy Characterization of Correlated Random Microstructures

A rigorous connection is established between the local porosity entropy introduced by Boger et al. (Physica A 187, 55 (1992)) and the configurational entropy of Andraud et al. (Physica A 207, 208 (1994)). These entropies were introduced as morphological descriptors derived from local volume fluctuations in arbitrary correlated microstructures occuring in porous media, composites or other heterogeneous systems. It is found that the entropy lengths at which the entropies assume an extremum become identical for high enough resolution of the underlying configurations. Several examples of porous and heterogeneous media are given which demonstrate the usefulness and importance of this morphological local entropy concept.Comment: 15 pages. please contact [email protected] and have a look at http://www.ica1.uni-stuttgart.de/ . To appear in Physica

Diverse Stress-Inducing Treatments cause Distinct Aberrant Body Morphologies in the Chlamydia-Related Bacterium, Waddlia chondrophila.

Chlamydiae, such as Chlamydia trachomatis and Chlamydia pneumoniae, can cause chronic infections. It is believed that persistent forms called aberrant bodies (ABs) might be involved in this process. AB formation seems to be a common trait of all members of the Chlamydiales order and is caused by distinct stress stimuli, such as β-lactam antibiotics or nutrient starvation. While the diverse stimuli inducing ABs are well described, no comprehensive morphological characterization has been performed in Chlamydiales up to now. We thus infected mammalian cells with the Chlamydia-related bacterium Waddlia chondrophila and induced AB formation using different stimuli. Their morphology, differences in DNA content and in gene expression were assessed by immunofluorescence, quantitative PCR, and reverse transcription PCR, respectively. All stimuli induced AB formation. Interestingly, we show here for the first time that the DNA gyrase inhibitor novobiocin also caused appearance of ABs. Two distinct patterns of ABs could be defined, according to their morphology and number: (i) small and multiple ABs versus (ii) large and rare ABs. DNA replication of W. chondrophila was generally not affected by the different treatments. Finally, no correlation could be observed between specific types of ABs and expression patterns of mreB and rodZ genes

Multiplexed nanoplasmonic biosensor for one-step simultaneous detection of Chlamydia trachomatis and Neisseria gonorrhoeae in urine.

Development of rapid and multiplexed diagnostic tools is a top priority to address the current epidemic problem of sexually transmitted diseases. Here we introduce a novel nanoplasmonic biosensor for simultaneous detection of the two most common bacterial infections: Chlamydia trachomatis and Neisseria gonorrhoeae. Our plasmonic microarray is composed of gold nanohole sensor arrays that exhibit the extraordinary optical transmission (EOT), providing highly sensitive analysis in a label-free configuration. The integration in a microfluidic system and the precise immobilization of specific antibodies on the individual sensor arrays allow for selective detection and quantification of the bacteria in real-time. We achieved outstanding sensitivities for direct immunoassay of urine samples, with a limit of detection of 300 colony forming units (CFU)/mL for C. trachomatis and 1500CFU/mL for N. gonorrhoeae. The multiplexing capability of our biosensor was demonstrated by analyzing different urine samples spiked with either C. trachomatis or N. gonorrhoeae, and also containing both bacteria. We could successfully detect, identify and quantify the levels of the two bacteria in a one-step assay, without the need for DNA extraction or amplification techniques. This work opens up new possibilities for the implementation of point-of-care biosensors that enable fast, simple and efficient diagnosis of sexually transmitted infections

Undressing of Waddlia chondrophila to enrich its outer membrane proteins to develop a new species-specific ELISA.

Waddlia chondrophila, an obligate intracellular bacterium of the Chlamydiales order, is considered as an agent of bovine abortion and a likely cause of miscarriage in humans. Its role in respiratory diseases was questioned after the detection of its DNA in clinical samples taken from patients suffering from pneumonia or bronchiolitis. To better define the role of Waddlia in both miscarriage and pneumonia, a tool allowing large-scale serological investigations of Waddlia seropositivity is needed. Therefore, enriched outer membrane proteins of W. chondrophila were used as antigens to develop a specific ELISA. After thorough analytical optimization, the ELISA was validated by comparison with micro-immunofluorescence and it showed a sensitivity above 85% with 100% specificity. The ELISA was subsequently applied to human sera to specify the role of W. chondrophila in pneumonia. Overall, 3.6% of children showed antibody reactivity against W. chondrophila but no significant difference was observed between children with and without pneumonia. Proteomic analyses were then performed using mass spectrometry, highlighting members of the outer membrane protein family as the dominant proteins. The major Waddlia putative immunogenic proteins were identified by immunoblot using positive and negative human sera. The new ELISA represents an efficient tool with high throughput applications. Although no association with pneumonia and Waddlia seropositivity was observed, this ELISA could be used to specify the role of W. chondrophila in miscarriage and in other diseases

A predation assay using amoebae to screen for virulence factors unearthed the first W. chondrophila inclusion membrane protein.

Waddlia chondrophila is an intracellular bacterium phylogenetically related to the well-studied human and animal pathogens of the Chlamydiaceae family. In the last decade, W. chondrophila was convincingly demonstrated to be associated with adverse pregnancy outcomes in humans and abortions in animals. All members of the phylum Chlamydiae possess a Type Three Secretion System that they use for delivering virulence proteins into the host cell cytosol to modulate their environment and create optimal conditions to complete their life cycle. To identify W. chondrophila virulence proteins, we used an original screening approach that combines a cosmid library with an assay monitoring resistance to predation by phagocytic amoebae. This technique combined with bioinformatic data allowed the identification of 28 candidate virulence proteins, including Wimp1, the first identified inclusion membrane protein of W. chondrophila

CRISPR System Acquisition and Evolution of an Obligate Intracellular Chlamydia-Related Bacterium.

Recently, a new Chlamydia-related organism, Protochlamydia naegleriophila KNic, was discovered within a Naegleria amoeba. To decipher the mechanisms at play in the modeling of genomes from the Protochlamydia genus, we sequenced the full genome of Pr. naegleriophila, which includes a 2,885,090 bp chromosome and a 145,285 bp megaplasmid. For the first time within the Chlamydiales order, we describe the presence of a clustered regularly interspaced short palindromic repeats (CRISPR) system, the immune system of bacteria, located on the chromosome. It is composed of a small CRISPR locus comprising eight repeats and associated cas-cse genes of the subtype I-E. A CRISPR locus is also present within Chlamydia sp. Diamant, another Pr. naegleriophila strain, suggesting that the CRISPR system was acquired by a common ancestor of Pr. naegleriophila, after its divergence from Pr. amoebophila. Both nucleotide bias and comparative genomics approaches identified probable horizontal gene acquisitions within two and four genomic islands in Pr. naegleriophila KNic and Diamant genomes, respectively. The plasmid encodes an F-type conjugative system highly similar to 1) that found in the Pam100G genomic island of Pr. amoebophila UWE25 chromosome, as well as on the plasmid of Rubidus massiliensis and 2) to the three genes remaining in the chromosome of Parachlamydia acanthamoebae strains. Therefore, this conjugative system was likely acquired on an ancestral plasmid before the divergence of Parachlamydiaceae Overall, this new complete Pr. naegleriophila genome sequence enables further investigation of the dynamic processes shaping the genomes of the family Parachlamydiaceae and the genus Protochlamydia

Multi-resolution Mean-Shift Algorithm for Vector Quantization

The generation of stratified codebooks, providing a subset of vectors at different scale levels, has become necessary with the emergence of embedded coder/decoder for scalable image and video formats. We propose an approach based on mean-shift, invoking the multi-resolution framework to generate codebook vectors. Applied to the entire image, mean-shift is slow because it requires each sample to converge to a mode of the distribution. The procedure can be sped up with three simple assumptions: kernel truncation, code attraction and trajectory attraction. Here we propose to apply the mean-shift algorithm to the four image subbands generated by a DWT, namely the LL, LH, HL and HH subbands. It can be concluded from experimental results that the proposed MR-MS achieves similar PSNR to the LBG algorithm but outperforms it in terms of computation time

Multi-descriptor random sampling for patch-based face recognition

While there has been a massive increase in research into face recognition, it remains a challenging problem due to conditions present in real life. This paper focuses on the inherently present issue of partial occlusion distortions in real face recognition applications. We propose an approach to tackle this problem. First, face images are divided into multiple patches before local descriptors of Local Binary Patterns and Histograms of Oriented Gradients are applied on each patch. Next, the resulting histograms are concatenated, and their dimensionality is then reduced using Kernel Principle Component Analysis. Once completed, patches are randomly selected using the concept of random sampling to finally construct several sub-Support Vector Machine classifiers. The results obtained from these sub-classifiers are combined to generate the final recognition outcome. Experimental results based on the AR face database and the Extended Yale B database show the effectiveness of our proposed technique

Predictors of mortality following emergency open colectomy for ischemic colitis: A single-center experience

Background: Ischemic colitis (IC) is a severe emergency in gastrointestinal surgery. The aim of the present study was to identify the predictors of postoperative mortality after emergent open colectomy for IC treatment. Additionally, we compared postoperative outcomes of patients undergoing emergent colectomy due to aortic surgery-related IC (AS-IC group) vs. other IC etiologies (Other-IC group). Methods: We analyzed records of consecutive patients who underwent emergency open colectomy for IC between 2008 and 2019. Logistic regression analysis was performed to identify clinical and operative parameters associated with postoperative mortality. The AS-IC and Other-IC groups were compared for mortality, morbidity, ICU stay, hospital stay, and survival. Results: During the study period, 94 patients (mean age, 67.4 ± 13.7 years) underwent emergent open colectomy for IC. In the majority of cases, IC involved the entire colon (53.2%) and vasopressor agents were required preoperatively (63.8%) and/or intraoperatively (78.8%). Thirty-four patients underwent surgery due to AS-IC, whereas 60 due to Other-IC causes. In the AS-IC group, 9 patients had undergone endovascular aortic repair and 25 open aortic surgery; 61.8% of patients needed aortic surgery for ruptured abdominal aortic aneurism (AAA). Overall, 66 patients (70.2%) died within 90 days from surgery. The AS-IC and Other-IC groups showed similar operative outcomes and postoperative complication rates. However, the duration of the ICU stay (19 days vs. 11 days; p = 0.003) and of the total hospital stay (22 days vs. 16 days; p = 0.016) was significantly longer for the AS-IC group than for the Other-IC group. The rate of intestinal continuity restoration at 1 year after surgery was higher for the Other-IC group than for the AS-IC group (58.8% vs. 22.2%; p = 0.05). In the multivariate model, preoperative increased lactate levels, a delay between signs/symptoms' onset and surgery > 12 h, and the occurrence of postoperative acute kidney injury were statistically associated with postoperative mortality. Neither IC etiology (aortic surgery vs. other etiology) nor ruptured AAA was associated with postoperative mortality. Conclusion: Emergency open colectomy for IC is associated with high postoperative mortality, which appears to be unrelated to the IC etiology. Preoperative lactate levels, > 12-h delay to surgery, and postoperative acute kidney injury are independent predictors of postoperative mortality

OmpA family proteins and Pmp-like autotransporter: new adhesins of Waddlia chondrophila.

Waddlia chondrophila is a obligate intracellular bacterium belonging to the Chlamydiales order, a clade that also includes the well-known classical Chlamydia responsible for a number of severe human and animal diseases. Waddlia is an emerging pathogen associated with adverse pregnancy outcomes in humans and abortion in ruminants. Adhesion to the host cell is an essential prerequisite for survival of every strict intracellular bacteria and, in classical Chlamydia, this step is partially mediated by polymorphic outer membrane proteins (Pmps), a family of highly diverse autotransporters that represent about 15% of the bacterial coding capacity. Waddlia chondrophila genome however only encodes one putative Pmp-like protein. Using a proteomic approach, we identified several bacterial proteins potentially implicated in the adhesion process and we characterized their expression during the replication cycle of the bacteria. In addition, we demonstrated that the Waddlia Pmp-like autotransporter as well as OmpA2 and OmpA3, two members of the extended Waddlia OmpA protein family, exhibit adhesive properties on epithelial cells. We hypothesize that the large diversity of the OmpA protein family is linked to the wide host range of these bacteria that are able to enter and multiply in various host cells ranging from protozoa to mammalian and fish cells