Impact of Mild Paravalvular Regurgitation on Long- Term Clinical Outcomes After Transcatheter Aortic Valve Implantation

The impact of mild paravalvular regurgitation (PVR) after transcatheter aortic valve implantation (TAVI) remains controversial. We evaluated the impact of mild PVR after TAVI on long-term clinical outcomes. We included patients who underwent TAVI for severe symptomatic aortic stenosis between December 2008 and June 2019 at 2 interna-tional centers and compared all-cause death between the group with mild PVR (group 1) and the group with none or trace PVR (group 2). PVR was categorized using a 3-class grading scheme, and patients with PVR >= moderate and those who were lost to follow-up were excluded. This retrospective analysis included 1,404 patients (mean age 81.7 +/- 6.5 years, 58.0% women). Three hundred fifty eight patients (25.5%) were classified into group 1 and 1,046 patients (74.5%) into group 2. At baseline, group 1 was older and had a lower body mass index, worse co-morbidities, and more severe aortic stenosis. To account for these differences, propensity score matching was performed, resulting in 332 matched pairs. Within these matched groups, during a mean follow-up of 3.2 years, group 1 had a significantly lower survival rate at 5 years (group 1: 62.0% vs group 2: 68.0%, log-rank p = 0.029, hazard ratio: 1.41 [95% confidence interval: 1.04 to 1.91]). In the matched cohort, patients with mild PVR had a significant 1.4-fold increased risk of mortality at 5 years after TAVI compared with those with none or trace PVR. Further studies with more patients are needed to evaluate the impact of longer-term outcomes.(c) 2022 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/) (Am J Cardiol 2023;191:14-22)Peer reviewe

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

Background: Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another. Results: The PXO99 A genome is a single circular chromosome of 5,240,075 bp, considerably longer than the genomes of the other strains (4,941,439 bp and 4,940,217 bp, respectively), and it contains 5083 protein-coding genes, including 87 not found in KACC10331 or MAFF311018. PXO99A contains a greater number of virulence-associated transcription activator-like effector genes and has at least ten major chromosomal rearrangements relative to KACC10331 and MAFF311018. PXO99 A contains numerous copies of diverse insertion sequence elements, members of which are associated with 7 out of 10 of the major rearrangements. A rapidly-evolving CRISPR (clustered regularly interspersed short palindromic repeats) region contains evidence of dozens of phage infections unique to the PXO99A lineage. PXO99A also contains a unique, near-perfect tandem repeat of 212 kilobases close to the replication terminus. Conclusion: Our results provide striking evidence of genome plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The comparisons point to sources of genomic variation and candidates for strain-specific adaptations of this pathogen that help to explain the extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and races that have been isolated from around the world. © 2008 Salzberg et al; licensee BioMed Central Ltd

Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae

<p>Abstract</p> <p>Background</p> <p>Small non-coding RNAs (sRNAs) are regarded as important regulators in prokaryotes and play essential roles in diverse cellular processes. <it>Xanthomonas oryzae </it>pathovar <it>oryzae </it>(<it>Xoo</it>) is an important plant pathogenic bacterium which causes serious bacterial blight of rice. However, little is known about the number, genomic distribution and biological functions of sRNAs in <it>Xoo</it>.</p> <p>Results</p> <p>Here, we performed a systematic screen to identify sRNAs in the <it>Xoo </it>strain PXO99. A total of 850 putative non-coding RNA sequences originated from intergenic and gene antisense regions were identified by cloning, of which 63 were also identified as sRNA candidates by computational prediction, thus were considered as <it>Xoo </it>sRNA candidates. Northern blot hybridization confirmed the size and expression of 6 sRNA candidates and other 2 cloned small RNA sequences, which were then added to the sRNA candidate list. We further examined the expression profiles of the eight sRNAs in an <it>hfq </it>deletion mutant and found that two of them showed drastically decreased expression levels, and another exhibited an Hfq-dependent transcript processing pattern. Deletion mutants were obtained for seven of the Northern confirmed sRNAs, but none of them exhibited obvious phenotypes. Comparison of the proteomic differences between three of the ΔsRNA mutants and the wild-type strain by two-dimensional gel electrophoresis (2-DE) analysis showed that these sRNAs are involved in multiple physiological and biochemical processes.</p> <p>Conclusions</p> <p>We experimentally verified eight sRNAs in a genome-wide screen and uncovered three Hfq-dependent sRNAs in <it>Xoo</it>. Proteomics analysis revealed <it>Xoo </it>sRNAs may take part in various metabolic processes. Taken together, this work represents the first comprehensive screen and functional analysis of sRNAs in rice pathogenic bacteria and facilitates future studies on sRNA-mediated regulatory networks in this important phytopathogen.</p

Explicit beat structure modeling for non-negative matrix factorization-based multipitch analysis

This paper proposes model-based non-negative matrix factorization (NMF) for estimating basis spectra and activations, detecting note onsets and offsets, and determining beat locations, simultaneously. Multipitch analysis is a process of detecting the pitch and onset of each note from a musical signal. Conventional NMF-based approaches often lead to unsatisfactory results very possibly due to the lack of musically meaningful constraints. As music is highly structured in terms of the temporal regularity underlying the onset occurrences of notes, we use this rhythmic structure to constrain NMF by parametrically modeling each note activation with a Gaussian mixture and derive an algorithm for iteratively updating model parameters. It is experimentally shown that the proposed model outperforms the standard NMF algorithms as regards onset detection rate. Index Terms — Polyphonic pitch transcription, Non-negative matrix factorization, Rhythmic/Beat structure, Onset detectio

Interactions between two <i>Arabidopsis</i> ecotypes vs. 16 <i>X. campestris</i> pv. <i>campestris</i> isolates.

<p>All strains are shown by their MAFF collection number except for ATCC33913 type strain (ATCC33913^T), and the distribution of genes coding for type III secreted proteins is indicated. The pathogenicity (mean disease index at 7 dpi) of these <i>X. campestris</i> pv. <i>campestris</i> strains on Arabidopsis ecotypes Col-0 and Sf-2 is indicated by color coding (0 to 1 indicates no symptoms, 1 to 2 indicates weak chlorosis, 2 to 3 indicates strong chlorosis, and 3 to 4 indicates necrosis as shown in the upper panel). Bacteria were inoculated by piercing the central leaf vein three times with a D200 pipette tip that had been dipped in a bacterial suspension (10⁹cfu mL⁻¹). The presence or absence of a homologous T3SP gene sequence was determined by PCR. Strains were also inoculated on nonhost tomato (momotaro) and <i>N. benthamiana</i>. HR, hypersensitive response; -, no HR. Dark-gray squares and+represent the presence of the corresponding genes with both primer combinations at the expected sizes, whereas white squares and - represent the absence of PCR amplification or PCR with a different amplicon size.</p

An AcGFP-expressing <i>Xcc</i>MAFF106712 bacteria colonized distal to the inoculated site at 6 days post inoculation.

<p>An inoculated leaf was detached from the plant and observed by a CLSM. Shown is the merged image of green fluorescence (green) and bright field. (A) Image shown around the inoculation site (I) in a low magnification. The red circles indicates the approximate location of the images taken in this manuscript. i, around (I); ii, central vein around (I); iii, distal to (I); iv, central vein distal to (I). White square showed the image shown in B Bar, 500 μm. (B) Image shown at the white square part of panel A in a higher magnification. Bar, 100 μm.</p

AcGFP-expressing <i>Xcc</i>MAFF106712Δ<i>hrcC</i> do not colonize a Col-0 plant.

<p>Localization of AcGFP-expressing <i>Xcc</i>MAFF106712Δ<i>hrcC</i> (A to F) in an Arabidopsis Col-0 plant. Leaf surface (A, C and E), central vein 100 μm away from the inoculation site (B) and the xylem vessel of the central vein (D, F) were observed by CLSM. Photographs were taken at 2 days (A, B), 6 days (C, D) and 9 days (E, F) after inoculation. Bacteria only proliferated inside cells adjacent to the inoculation site (I in panel C-d and E-d). Location indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094386#pone-0094386-g002" target="_blank">Figure 2</a>; i, (A, C and E); ii, (B, D and F). a, green fluorescence; b, chlorophyll autofluorescence; c, bright field; d, merged image. Bars, 10 μM (A, C, D and F); 20 μM (E); 50 μM (B).</p

AcGFP-expressing <i>Xcc</i>MAFF106712 do not colonize a Sf-2 plant.

<p>Localization of AcGFP-expressing <i>Xcc</i>MAFF106712 in the incompatible Sf-2 plant was determined by green fluorescence 6 days after inoculation of epidermal cells at the central vein (A), xylem vessel (B) epidermal cells (C). Location indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094386#pone-0094386-g002" target="_blank">Figure 2</a>; i, (C); ii, (A, B). Bacteria did not proliferate in the xylem vessel (B). Epidermal cell shrinkage was observed where bacteria localized (C). a, green fluorescence; b, chlorophyll autofluorescence; c, bright field; d, merged image. Bars, 5 μM (AB); 100 μM(C).</p