ブリから分離した魚病原細菌Photobacterium damsela subsp. piscicidaの薬剤耐性の伝達性

長崎大学学位論文　学位記番号:博(海)甲第237号 学位授与年月日:平成14年3月31

Evaluating dimensionality reduction for genomic prediction

The development of genomic selection (GS) methods has allowed plant breeding programs to select favorable lines using genomic data before performing field trials. Improvements in genotyping technology have yielded high-dimensional genomic marker data which can be difficult to incorporate into statistical models. In this paper, we investigated the utility of applying dimensionality reduction (DR) methods as a pre-processing step for GS methods. We compared five DR methods and studied the trend in the prediction accuracies of each method as a function of the number of features retained. The effect of DR methods was studied using three models that involved the main effects of line, environment, marker, and the genotype by environment interactions. The methods were applied on a real data set containing 315 lines phenotyped in nine environments with 26,817 markers each. Regardless of the DR method and prediction model used, only a fraction of features was sufficient to achieve maximum correlation. Our results underline the usefulness of DR methods as a key pre-processing step in GS models to improve computational efficiency in the face of ever-increasing size of genomic data

IgG4 related pleural disease : recurrent pleural effusion after COVID-19 vaccination

IgG4-related disease is characterized by a systemic fibroinflammatory process associated with substantial infiltration by plasma cells with IgG4 in the organs. Our patient presented with pleural effusion, and was diagnosed with IgG4-related lung disease (IgG4-RLD) after he received two doses of the Pfizer COVID-19 vaccine. The patient developed dyspnea and hypoxia 2 weeks after receiving the second dose of the Pfizer COVID-19 vaccine. CT scan revealed left pleural effusion which was drained. However, the effusion recurred requiring thoracoscopic drainage, placement of an indwelling catheter, and decortication with biopsy. IgG4 serum level was 268 mg/dl and pathology revealed pleural fibrosis, lymphoplasmacytic infiltrates, and increased IgG4-positive plasma cells with no malignant cells leading to a diagnosis of IgG4-RLD. Although COVID vaccine-related IgG4-RLD is a novel finding, having a high degree of suspicion following vaccination is always important for early diagnosis and effective treatment

Community Engagement in Smart Cities: A Social Network Analysis and Community Engagement Test

This study, carried out in the ever-changing context of Smart Cities, reveals the complex interactions of digital social networks, digital community involvement, and the Community involvement Test (CET) framework. The examination of data obtained from certain Smart Cities indicates a thriving milieu of community engagement, characterized by a markedly elevated rate of active participation. The identification of urgent issues, particularly those related to environmental sustainability, safety, traffic management, and educational quality, is consistent with the larger urban difficulties that these creative urban centers are facing. Additionally, the CET framework's integration of SNA data and survey results produces very high ratings, indicating the engagement programs' outstanding performance in promoting resident satisfaction and active involvement. These results highlight how digital technologies can help Smart Cities foster vibrant, engaged communities. They also highlight the continued need for smart urban policies to address urgent issues and maintain residents' quality of life while adhering to the Smart City paradigm

Extensions of DBS and Hybrid Internet

There has been a large amount of research dedicated to extending the asymmetric networks provided by receive-only Direct Broadcast Satellite systems like Hughes Network Systems' DirecPC product. One way to further develop Direct Broadcast Satellite services and to offset the high initial cost of these systems is to implement techniques that will allow one satellite receiver to act as a gateway for many clients to receive information. This would also help broaden the range of services provided by DBS systems. Besides providing direct-to-home traffic, DBS can be used to distribute bulk traffic to the local-loop distributors (direct-to-curb). We describe some experiments which extend the DBS system, in particular, the DirecPC and DirecTV DBS, by using the PC with the satellite receiver as a gateway to connect networks together. We also discuss simple methods of receiving multimedia traffic from the multicast backbone (MBONE) [Cas94] over the satellite link, and distributing it, through this gateway, to end users. The research and scientific content in this material will be presented at the 2nd ACM International Workshop on Satellite-Based Information Services (WOSBIS), October 1, 1997, Budapest, Hungary.</Center

Genomic-enabled prediction models using multi-environment trials to estimate the effect of genotype × environment interaction on prediction accuracy in chickpea

Genomic selection (GS) by selecting lines prior to field phenotyping using genotyping data has the potential to enhance the rate of genetic gains. Genotype × environment (G × E) interaction inclusion in GS models can improve prediction accuracy hence aid in selection of lines across target environments. Phenotypic data on 320 chickpea breeding lines for eight traits for three seasons at two locations were recorded. These lines were genotyped using DArTseq (1.6 K SNPs) and Genotyping-by-Sequencing (GBS; 89 K SNPs). Thirteen models were fitted including main effects of environment and lines, markers, and/or naïve and informed interactions to estimate prediction accuracies. Three cross-validation schemes mimicking real scenarios that breeders might encounter in the fields were considered to assess prediction accuracy of the models (CV2: incomplete field trials or sparse testing; CV1: newly developed lines; and CV0: untested environments). Maximum prediction accuracies for different traits and different models were observed with CV2. DArTseq performed better than GBS and the combined genotyping set (DArTseq and GBS) regardless of the cross validation scheme with most of the main effect marker and interaction models. Improvement of GS models and application of various genotyping platforms are key factors for obtaining accurate and precise prediction accuracies, leading to more precise selection of candidates

A cross-sectional study on the nasopharyngeal microbiota of individuals with SARS-CoV-2 infection across three COVID-19 waves in India

BackgroundMultiple variants of the SARS-CoV-2 virus have plagued the world through successive waves of infection over the past three years. Independent research groups across geographies have shown that the microbiome composition in COVID-19 positive patients (CP) differs from that of COVID-19 negative individuals (CN). However, these observations were based on limited-sized sample-sets collected primarily from the early days of the pandemic. Here, we study the nasopharyngeal microbiota in COVID-19 patients, wherein the samples have been collected across the three COVID-19 waves witnessed in India, which were driven by different variants of concern.MethodsThe nasopharyngeal swabs were collected from 589 subjects providing samples for diagnostics purposes at the Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India and subjected to 16s rRNA gene amplicon - based sequencing.FindingsWe found variations in the microbiota of symptomatic vs. asymptomatic COVID-19 patients. CP showed a marked shift in the microbial diversity and composition compared to CN, in a wave-dependent manner. Rickettsiaceae was the only family that was noted to be consistently depleted in CP samples across the waves. The genera Staphylococcus, Anhydrobacter, Thermus, and Aerococcus were observed to be highly abundant in the symptomatic CP patients when compared to the asymptomatic group. In general, we observed a decrease in the burden of opportunistic pathogens in the host microbiota during the later waves of infection.InterpretationTo our knowledge, this is the first analytical cross-sectional study of this scale, which was designed to understand the relation between the evolving nature of the virus and the changes in the human nasopharyngeal microbiota. Although no clear signatures were observed, this study shall pave the way for a better understanding of the disease pathophysiology and help gather preliminary evidence on whether interventions to the host microbiota can help in better protection or faster recovery