Enhancing Biodiversity through Self-Regulation in Large Ecosystems

The competitive exclusion principle (CEP) is a fundamental concept in the niche theory, which posits that the number of available resources constrains the coexistence of species. While the CEP offers an intuitive explanation for coexistence, it has been challenged by counterexamples observed in nature. One prominent counterexample is the phytoplankton community, known as the paradox of the plankton. Diverse phytoplankton species coexist in the ocean even though they demand a limited number of resources. To shed light on this remarkable biodiversity in large ecosystems quantitatively, we consider self-regulation into the generalized MacArthur's consumer-resource model and study the relative diversity, the number ratio between coexisting consumers and resource kinds. By employing the cavity method and generating functional analysis, we analytically show how the bounds of the relative diversity can exceed unity and its dependency on the strength of the self-regulation. We confirm the analysis with numerical simulations and reveal that the self-regulation suppresses the emergence of dominant species, thereby fostering high biodiversity. Furthermore, we study the effect of the self-regulation on different environments and show that the effect relies on the environmental condition. Our work presents a comprehensive framework within the niche theory that encompasses the CEP and its counterexamples by introducing the role of self-regulation.Comment: 34 pages (including supplementary material), 24 figures (4 figures in main, 20 figures in SM

Generalized gravity model for human migration

The gravity model (GM) analogous to Newton's law of universal gravitation has successfully described the flow between different spatial regions, such as human migration, traffic flows, international economic trades, etc. This simple but powerful approach relies only on the 'mass' factor represented by the scale of the regions and the 'geometrical' factor represented by the geographical distance. However, when the population has a subpopulation structure distinguished by different attributes, the estimation of the flow solely from the coarse-grained geographical factors in the GM causes the loss of differential geographical information for each attribute. To exploit the full information contained in the geographical information of subpopulation structure, we generalize the GM for population flow by explicitly harnessing the subpopulation properties characterized by both attributes and geography. As a concrete example, we examine the marriage patterns between the bride and the groom clans of Korea in the past. By exploiting more refined geographical and clan information, our generalized GM properly describes the real data, a part of which could not be explained by the conventional GM. Therefore, we would like to emphasize the necessity of using our generalized version of the GM, when the information on such nongeographical subpopulation structures is available.Comment: 14 pages, 6 figures, 2 table

The Extraction of Knowledge Factors of Teachers for Physical Computing Education

In informatics, physical computing focuses on interactions to realize the real world as a computing system. From 2018, how to teach the physical computing in informatics as a mandatory subject is important. The purpose of this study is to analyze the problems in the physical computing education recognized by secondary school informatics teachers and to provide implications for effective programming education. First, we extracted related keywords of physical computing in the 2015 revised informatics curriculum and science curriculum. Second, extracted keywords are classified into hardware and programming. Third, we developed a questionnaire item suitable for classification keywords. Finally, web surveys were conducted and analyzed for in-service and pre-service secondary school informatics teachers. As a result of the research, it was confirmed that the informatics teachers recognized that physical computing education was helpful for programming education. However, a large proportion of the member's lack of training time and receive appropriate education and training programs, hardware, reduced the level of knowledge about the physical computing element content

NKT cells promote antibody-induced joint inflammation by suppressing transforming growth factor β1 production

Although NKT cells has been known to exert protective roles in the development of autoimmune diseases, the functional roles of NKT cells in the downstream events of antibody-induced joint inflammation remain unknown. Thus, we explored the functional roles of NKT cells in antibody-induced arthritis using the K/BxN serum transfer model. NKT cell–deficient mice were resistant to the development of arthritis, and wild-type mice administrated with α-galactosyl ceramide, a potent NKT cell activator, aggravated arthritis. In CD1d−/− mice, transforming growth factor (TGF)-β1 was found to be elevated in joint tissues, and the blockade of TGF-β1 using neutralizing monoclonal antibodies restored arthritis. The administration of recombinant TGF-β1 into C57BL/6 mice reduced joint inflammation. Moreover, the adoptive transfer of NKT cells into CD1d−/− mice restored arthritis and reduced TGF-β1 production. In vitro assay demonstrated that interleukin (IL)-4 and interferon (IFN)-γ were involved in suppressing TGF-β1 production in joint cells. The adoptive transfer of NKT cells from IL-4−/− or IFN-γ−/− mice did not reverse arthritis and TGF-β1 production in CD1d−/− mice. In conclusion, NKT cells producing IL-4 and IFN-γ play a role in immune complex–induced joint inflammation by regulating TGF-β1

Prevalent Multidrug-resistant Nonvaccine Serotypes in Pneumococcal Carriage of Healthy Korean Children Associated with the Low Coverage of the Seven-valent Pneumococcal Conjugate Vaccine

AbstractObjectivesOur previous longitudinal multicenter-based carriage study showed that the average carriage rate of Streptococcus pneumoniae was 16.8% in 582 healthy children attending kindergarten or elementary school in Seoul, Korea. We assessed serotype-specific prevalence and antimicrobial resistance among colonizing pneumococcal isolates from young children in the era of low use of the seven-valent pneumococcal conjugate vaccine (PCV7).MethodsSerotypes were determined by an agglutination test with specific antisera or by a multiplex polymerase chain reaction (PCR) assay. An antimicrobial susceptibility test was performed with broth microdilution in Korean 96-well panels from Dade-MicroScan (Sacramento, CA, USA).ResultsPneumococcal colonization patterns were dynamic and longterm persistent carriage was rare, which indicated a sequential turnover of pneumococcal strains. Of the 369 pneumococci (except for 23 killed isolates), 129 (34.9%) isolates were PCV7 vaccine serotypes (VTs); 213 (57.8%) isolates were nonvaccine serotypes (NVTs); and the remaining 27 (7.2%) isolates were nontypable (NT). The highest rates of multidrug resistance (MDR) were observed in VTs (86.0%; 111/129 isolates) and NVTs (70.0%; 149/213 isolates).ConclusionThis study overall showed the frequent carriage of VTs and NVTs with MDR in healthy children attending kindergarten or elementary school. Efforts should be directed toward reducing the extensive prescription of antibiotics and using new broader vaccines to reduce the expansion of MDR strains of NVTs in our community

Functional elements demarcated by histone modifications in breast cancer cells

AbstractHistone modifications are regarded as one of markers to identify regulatory elements which are DNA segments modulating gene transcription. Aberrant changes of histone modification levels are frequently observed in cancer. We have employed ChIP-Seq to identify regulatory elements in human breast cancer cell line, MCF-7 by comparing histone modification patterns of H3K4me1, H3K4me3, and H3K9/14ac to those in normal mammary epithelial cell line, MCF-10A. The genome-wide analysis shows that H3K4me3 and H3K9/14ac are highly enriched at promoter regions and H3K4me1 has a relatively broad distribution over proximity of TSSs as well as other genomic regions. We identified that many differentially expressed genes in MCF-7 have divergent histone modification patterns. To understand the functional roles of distinctively histone-modified regions, we selected 35 genomic regions marked by at least one histone modification and located from 3 to 10kb upstream of TSS in both MCF-7 and MCF-10A and assessed their transcriptional activities. About 66% and 60% of selected regions in MCF-7 and MCF-10A, respectively, enhanced the transcriptional activity. Interestingly, most regions marked by H3K4me1 exhibited an enhancer activity. Regions with two or more kinds of histone modifications did show varying activities. In conclusion, our data reflects that comprehensive analysis of histone modification profiles under cell type-specific chromatin environment should provide a better chance for defining functional regulatory elements in the genome

Correlation of the Rates of Solvolysis of i-Butyl Fluoroformate and a Consideration of Leaving-Group Effects

The specific rates of solvolysis of isobutyl fluoroformate (1) have been measured at 40.0 °C in 22 pure and binary solvents. These results correlated well with the extended Grunwald-Winstein (G-W) equation, which incorporated the NT solvent nucleophilicity scale and the YCl solvent ionizing power scale. The sensitivities (l and m-values) to changes in solvent nucleophilicity and solvent ionizing power, and the kF/kCl values are very similar to those observed previously for solvolyses of n-octyl fluoroformate, consistent with the additional step of an addition-elimination pathway being rate-determining. The solvent deuterium isotope effect value (kMeOH/kMeOD) for methanolysis of 1 was determined, and for solvolyses in ethanol, methanol, 80% ethanol, and 70% TFE, the values of the enthalpy and the entropy of activation for the solvolysis of 1 were also determined. The results are compared with those reported earlier for isobutyl chloroformate (2) and other alkyl haloformate esters and mechanistic conclusions are drawn

Genotypic Characterization of Vibrio vulnificus Clinical Isolates in Korea

AbstractObjectivesVibrio vunificus is known to cause septicemia and severe wound infections in patients with chronic liver diseases or an immuno-compromised condition. We carried out the molecular characterization of V. vulnificus isolates from human Vibrio septicemia cases based on pulsed-field gel electrophoresis (PFGE) using NotI and SfiI.Methods and ResultsPFGE was used to characterize a total of 78 strains from clinical cases after NotI or SfiI digestion. The geographical distribution of PFGE patterns for the strains from the southern part of Korea, a high-risk region for Vibrio septicemia, indicated that the isolates from southeastern Korea showed a comparatively higher degree of homology than those from southwestern Korea.ConclusionsWe report the genetic distribution of V. vulnficus isolated from Vibrio septicemia cases during 2000–2004 in Korea. This method has potential use as a subspecies-typing tool for V. vulnificus strains isolated from distant geographic regions