Primary mucinous adenocarcinoma in a defunctionalized urinary bladder: a case report

<p>Abstract</p> <p>Introduction</p> <p>Malignancies are rare in defunctionalized bladders and are thought to arise from metaplasia secondary to chronic inflammation. Transitional cell and squamous cell carcinomas are the most common but there are three reported cases of mucinous adenocarcinoma.</p> <p>Case presentation</p> <p>We report a 57-year-old Caucasian man presenting with penile discharge for 30 years following ileal conduit surgery for neurogenic bladder, and who was found to have primary mucinous adenocarcinoma of his defunctionalized bladder.</p> <p>Conclusion</p> <p>Although urinary diversion without cystectomy is less common in current urologic practice, there are many patients with longstanding defunctionalized bladders. While there are no established surveillance protocols, defunctionalized bladder patients with urethral discharge should be evaluated.</p

Amino Acid Usage Is Asymmetrically Biased in AT- and GC-Rich Microbial Genomes.

INTRODUCTION: Genomic base composition ranges from less than 25% AT to more than 85% AT in prokaryotes. Since only a small fraction of prokaryotic genomes is not protein coding even a minor change in genomic base composition will induce profound protein changes. We examined how amino acid and codon frequencies were distributed in over 2000 microbial genomes and how these distributions were affected by base compositional changes. In addition, we wanted to know how genome-wide amino acid usage was biased in the different genomes and how changes to base composition and mutations affected this bias. To carry this out, we used a Generalized Additive Mixed-effects Model (GAMM) to explore non-linear associations and strong data dependences in closely related microbes; principal component analysis (PCA) was used to examine genomic amino acid- and codon frequencies, while the concept of relative entropy was used to analyze genomic mutation rates. RESULTS: We found that genomic amino acid frequencies carried a stronger phylogenetic signal than codon frequencies, but that this signal was weak compared to that of genomic %AT. Further, in contrast to codon usage bias (CUB), amino acid usage bias (AAUB) was differently distributed in AT- and GC-rich genomes in the sense that AT-rich genomes did not prefer specific amino acids over others to the same extent as GC-rich genomes. AAUB was also associated with relative entropy; genomes with low AAUB contained more random mutations as a consequence of relaxed purifying selection than genomes with higher AAUB. CONCLUSION: Genomic base composition has a substantial effect on both amino acid- and codon frequencies in bacterial genomes. While phylogeny influenced amino acid usage more in GC-rich genomes, AT-content was driving amino acid usage in AT-rich genomes. We found the GAMM model to be an excellent tool to analyze the genomic data used in this study

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter-and intraspecies genomic variation. We further predicted 17,903 carbohydrateactive enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.Peer reviewe

Establishing a robust testing approach for displacement measurement on a rotating horizontal-axis wind turbine

Health monitoring by conventional sensors like accelerometers or strain gauges becomes challenging for large rotating structures due to the issues with feasibility, sensing and data transmission. In addition, acceleration measurements have low capability of presenting very small frequencies, which happen very often for large structures (for instance, frequencies between 0.2 and 0.5 Hz in horizontal-axis wind turbines). By contrast, displacement measurement using stereo vision is rapid, non-contacting and distributed over the structure. The sensors are cheaper and more easily applied to many places on the object to be measured. Horizontal-axis wind turbines are one of the most important large rotating structures and need to be measured and monitored in time to prevent damage and failure, and the blade tip position is one of the key parameters to measure in order to prevent the blade hitting the turbine tower.This paper presents a clearly described and easily applicable procedure for measuring the displacement on the components of a rotating horizontal-axis wind turbine with stereophotogrammetry. Paper markers have been applied on the rotor and tower of a scaled-down horizontal-axis wind turbine model in the workshop and the displacement measurement method has been demonstrated by measuring displacement during operation. The method is mainly developed in two parts: (1) camera calibration and (2) tracking algorithm. We introduce an efficient camera calibration method for measurement in large fields of view, which has always been a challenge. This method is easy and practical and offers better accuracy compared with 2-D traditional camera calibration. The tracking algorithm also works successfully and is able to track the points during rotation within the measurement time. Finally, the accuracy analysis has been conducted and has shown better accuracy of the new calibration method compared with 2-D traditional camera calibration

Genomic taxonomy of vibrios

<p>Abstract</p> <p>Background</p> <p>Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (<it>i</it>.<it>e</it>. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios.</p> <p>Results</p> <p>We have generated four new genome sequences of three <it>Vibrio </it>species, <it>i</it>.<it>e</it>., <it>V. alginolyticus </it>40B, <it>V</it>. <it>harveyi</it>-like 1DA3, and <it>V</it>. <it>mimicus </it>strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced <it>Vibrio </it>species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, <it>e</it>.<it>g</it>. <it>V. cholerae </it>and <it>V. mimicus</it>. The vibrio pangenome contains around 26504 genes. The <it>V. cholerae </it>core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of <it>V. cholerae </it>to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (<it>Vibrio </it>core group, <it>V. cholerae-V. mimicus</it>, <it>Aliivibrio </it>spp., and <it>Photobacterium </it>spp.). A <it>Vibrio </it>species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree.</p> <p>Conclusion</p> <p>The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding.</p