Birational geometry of the moduli space of rank 2 parabolic vector bundles on a rational curve

We investigate the birational geometry (in the sense of Mori's program) of the moduli space of rank 2 semistable parabolic vector bundles on a rational curve. We compute the effective cone of the moduli space and show that all birational models obtained by Mori's program are also moduli spaces of parabolic vector bundles with certain parabolic weights.Comment: 22 pages, Revised, Published version in International Mathematics Research Notices (2015

GPS-GLASS: Learning Nighttime Semantic Segmentation Using Daytime Video and GPS data

Semantic segmentation for autonomous driving should be robust against various in-the-wild environments. Nighttime semantic segmentation is especially challenging due to a lack of annotated nighttime images and a large domain gap from daytime images with sufficient annotation. In this paper, we propose a novel GPS-based training framework for nighttime semantic segmentation. Given GPS-aligned pairs of daytime and nighttime images, we perform cross-domain correspondence matching to obtain pixel-level pseudo supervision. Moreover, we conduct flow estimation between daytime video frames and apply GPS-based scaling to acquire another pixel-level pseudo supervision. Using these pseudo supervisions with a confidence map, we train a nighttime semantic segmentation network without any annotation from nighttime images. Experimental results demonstrate the effectiveness of the proposed method on several nighttime semantic segmentation datasets. Our source code is available at https://github.com/jimmy9704/GPS-GLASS.Comment: ICCVW 202

Transcriptome and proteome analyses of adaptive responses to methyl methanesulfonate in Escherichia coli K-12 and ada mutant strains

<p>Abstract</p> <p>Background</p> <p>The Ada-dependent adaptive response system in <it>Escherichia coli </it>is important for increasing resistance to alkylation damage. However, the global transcriptional and translational changes during this response have not been reported. Here we present time-dependent global gene and protein expression profiles following treatment with methyl methanesulfonate (MMS) in <it>E. coli </it>W3110 and its <it>ada </it>mutant strains.</p> <p>Results</p> <p>Transcriptome profiling showed that 1138 and 2177 genes were differentially expressed in response to MMS treatment in the wild-type and mutant strains, respectively. A total of 81 protein spots representing 76 nonredundant proteins differentially expressed were identified using 2-DE and LC-MS/MS. In the wild-type strain, many genes were differentially expressed upon long-exposure to MMS, due to both adaptive responses and stationary phase responses. In the <it>ada </it>mutant strain, the genes involved in DNA replication, recombination, modification and repair were up-regulated 0.5 h after MMS treatment, indicating its connection to the SOS and other DNA repair systems. Interestingly, expression of the genes involved in flagellar biosynthesis, chemotaxis, and two-component regulatory systems related to drug or antibiotic resistance, was found to be controlled by Ada.</p> <p>Conclusion</p> <p>These results show in detail the regulatory components and pathways controlling adaptive response and how the related genes including the Ada regulon are expressed with this response.</p

Proteome-Level Responses of Escherichia coli to Long-Chain Fatty Acids and Use of Fatty Acid Inducible Promoter in Protein Production

In Escherichia coli, a long-chain acyl-CoA is a regulatory signal that modulates gene expression through its binding to a transcription factor FadR. In this study, comparative proteomic analysis of E. coli in the presence of glucose and oleic acid was performed to understand cell physiology in response to oleic acid. Among total of 52 proteins showing altered expression levels with oleic acid presence, 9 proteins including AldA, Cdd, FadA, FadB, FadL, MalE, RbsB, Udp, and YccU were newly synthesized. Among the genes that were induced by oleic acid, the promoter of the aldA gene was used for the production of a green fluorescent protein (GFP). Analysis of fluorescence intensities and confocal microscopic images revealed that soluble GFP was highly expressed under the control of the aldA promoter. These results suggest that proteomics is playing an important role not only in biological research but also in various biotechnological applications

Enzymatic analysis of the effect of naturally occurring Leu138Pro mutation identified in SHV β-lactamase on hydrolysis of penicillin and ampicillin

<p>Abstract</p> <p>Background</p> <p>The aim of this study was to analyze the significance of leucine to proline substitution at position 138(Leu138Pro) on the hydrolysis of penicillin and ampicillin that we identified in the <it>bla</it>_SHVgene of clinical <it>Escherichia coli </it>swine isolate.</p> <p>Results</p> <p>Kinetic analysis of the mutant proteins showed that <it>K</it>_{<it>m </it>}value of the purified L138P mutant was comparatively higher than SHV-1, SHV-33 and SHV-33(L138P) enzyme for penicillin and ampicillin. Docking simulation of the SHV-1 and SHV-(L138P) enzymes also confirmed that β-lactamases preferred penicillin to ampicillin and the SHV-1 had a higher binding affinity for antibiotics compared to the SHV-(L138P) and other mutants.</p> <p>Conclusions</p> <p>Our result demonstrated that L138P has a reduced role in penicillin and ampicillin hydrolyzing properties of SHV β-lactamases. These naturally occurring mutations rendering reduced function of the existing protein could trigger the emergence or acquisition of more effective alternative mechanisms for β-lactam hydrolysis.</p

Clinical Characteristics and Risk Factors for Nosocomial Candidemia in Medical Intensive Care Units: Experience in a Single Hospital in Korea for 6.6 Years

The aim of this study was to determine candidemia incidence among patients in a medical intensive-care unit (MICU) and the associated mortality rate and to identify risk factors associated with candidemia. We retrospectively performed a 1:3 matched case-control study of MICU patients with candidemia. Controls were matched for sex, age, and Acute Physiology and Chronic Health Evaluation (APACHE) II score. Candidemia incidence was 9.1 per 1,000 admissions. The most common pathogen was Candida albicans. Crude mortality was 96% among candidemia patients and 52% among controls (P<0.001). Mortality differed significantly between the groups according to Kaplan-Meier survival analysis (P=0.024). Multivariate analysis identified the following independent risk factors for candidemia: central venous catheterization (odds ratio [OR] = 3.2, 95% confidence interval [CI]=1.2-9.0), previous steroid therapy (OR=4.7, 95% CI=1.8-12.1), blood transfusion during the same admission period (OR=6.3, 95% CI=2.4-16.7), and hepatic failure upon MICU admission (OR=6.9, 95% CI=1.7-28.4). In conclusion, we identify an additional independent risk factor for candidemia, the presence of hepatic failure on MICU admission. Therefore, increased awareness of risk factors, including hepatic failure, is necessary for the management of candidemia

Application and evaluation of the MLVA typing assay for the Brucella abortus strains isolated in Korea

<p>Abstract</p> <p>Background</p> <p>A Brucella eradication program has been executed in Korea. To effectively prevent and control brucellosis, a molecular method for genetic identification and epidemiological trace-back must be established. As part of that, the MLVA typing assay was evaluated and applied to <it>B. abortus </it>isolates for analyzing the characteristics of the regional distribution and relationships of foreign isolates.</p> <p>Results</p> <p>A total of 177 isolates originating from 105 cattle farms for the period 1996 to 2008 were selected as representatives for the nine provinces of South Korea. A dendrogram of strain relatedness was constructed in accordance with the number of tandem repeat units for 17 loci so that it was possible to trace back in the restricted areas. Even in a farm contaminated by one source, however, the <it>Brucella </it>isolates showed an increase or decrease in one TRs copy number at some loci with high DI values. Moreover, those 17 loci was confirmed in stability via <it>in-vitro </it>and <it>in-vivo </it>passage, and found to be sufficiently stable markers that can readily identify the inoculated strain even if minor changes were detected. In the parsimony analysis with foreign <it>Brucella </it>isolates, domestic isolates were clustered distinctively, and located near the Central and Southern American isolates.</p> <p>Conclusion</p> <p>The MLVA assay has enough discrimination power in the <it>Brucella </it>species level and can be utilized as a tool for the epidemiological trace-back of the <it>B. abortus </it>isolates. But it is important to consider that <it>Brucella </it>isolates may be capable of undergoing minor changes at some loci in the course of infection or in accordance with the changes of the host.</p

Identification of a novel human Rad51 variant that promotes DNA strand exchange

Rad51 plays a key role in the repair of DNA double-strand breaks through homologous recombination, which is the central process in the maintenance of genomic integrity. Five paralogs of the human Rad51 gene (hRad51) have been identified to date, including hRad51B, hRad51C, hRad51D, Xrcc2 and Xrcc3. In searches of additional hRad51 paralogs, we identified a novel hRad51 variant that lacked the sequence corresponding to exon 9 (hRad51-Δex9). The expected amino acid sequence of hRad51-Δex9 showed a frame-shift at codon 259, which resulted in a truncated C-terminus. RT-PCR analysis revealed that both hRad51 and hRad51-Δex9 were prominently expressed in the testis, but that there were subtle differences in tissue specificity. The hRad51-Δex9 protein was detected as a 31-kDa protein in the testis and localized at the nucleus. In addition, the hRad51-Δex9 protein showed a DNA-strand exchange activity comparable to that of hRad51. Taken together, these results indicate that hRad51-Δex9 promotes homologous pairing and DNA strand exchange in the nucleus, suggesting that alternative pathways in hRad51- or hRad51-Δex9-dependent manners exist for DNA recombination and repair