402 research outputs found

    High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements

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    Approximately 80 long interspersed element (LINE-1 or L1) copies are able to retrotranspose actively in the human genome, and these are termed retrotransposition-competent L1s. The 5′ untranslated region (UTR) of the human-specific L1 contains an internal promoter and several transcription factor binding sites. To better understand the effect of the L1 5′ UTR on the evolution of human-specific L1s, we examined this population of elements, focusing on the sequence diversity and accumulated substitutions within their 5′ UTRs. Using network analysis, we estimated the age of each L1 component (the 5′ UTR, ORF1, ORF2, and 3′ UTR). Through the comparison of the L1 components based on their estimated ages, we found that the 5′ UTR of human-specific L1s accumulates mutations at a faster rate than the other components. To further investigate the L1 5′ UTR, we examined the substitution frequency per nucleotide position among them. The results showed that the L1 5′ UTRs shared relatively conserved transcription factor binding sites, despite their high sequence diversity. Thus, we suggest that the high level of sequence diversity in the 5′ UTRs could be one of the factors controlling the number of retrotransposition-competent L1s in the human genome during the evolutionary battle between L1s and their host genomes

    The Connection between the Intracluster Light and its Host Halo: Formation Time and Contribution from Different Channels

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    We extend the analysis presented in \cite{contini2023a} to higher redshifts, up to z=2z=2, by focusing on the relation between the intracluster light (ICL) fraction and the halo mass, its dependence with redshift, role played by the halo concentration and formation time, in a large sample of simulated galaxy groups/clusters with 13logMhalo1513\lesssim \log M_{halo} \lesssim 15. Moreover, a key focus is to isolate the relative contributions provided by the main channels for the ICL formation to the total amount. The ICL fraction at higher redshift is weakly dependent on halo mass, and comparable with that at the present time, in agreement with recent observations. Stellar stripping, mergers and pre-processing are the major responsible channels of the ICL formation, with stellar stripping that accounts for 90%\sim 90\% of the total ICL, regardless of halo mass and redshift. Pre-processing is an important process for clusters to accrete already formed ICL. The diffuse component forms very early, z0.6z\sim 0.6, and its formation depends on both concentration and formation time of the halo, with more concentrated and earlier formed haloes that assemble their ICL earlier than later formed ones. The efficiency of this process is independent of halo mass, but increases with decreasing redshift, which implies that stellar stripping becomes more important with time as the concentration increases. This highlights the link between the ICL and the dynamical state of a halo: groups/clusters that have a higher fraction of diffuse light are more concentrated, relaxed and in an advanced stage of growth.Comment: Corrected for several bugs and typos. Clean no

    Equivalent acceleration assessment of JEDEC moisture sensitivity levels using peridynamics

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    The moisture inside the IC packages induces the several deformation failures, such as popcorn crack and swelling during the solder reflowing process. In semiconductor industry, over the past few years, the equivalent acceleration time for JEDEC moisture sensitivity level has been updated based on the weight gain measurements when the package structure and materials were modified. It costs long test times which may induce the significant delay of new product development and reliability evaluation. Additionally, the weight gain equivalency may not be sufficient to determine the equivalent accelerated time. In this paper, the new approach for evaluating the equivalent acceleration test time for preconditioning is proposed using the numerical calculation by peridynamics (PD) theory. The essential of proposed method is analyzing a moisture concentration and a vapor pressure which can cause the moisture induced failure in IC packages without facing the discontinuity problems of moisture concentration along the interfaces

    Tributyrin and anise mixture supplementation improves growth performance, nutrient digestibility, jejunal villus height, and fecal microbiota in weaned pigs

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    IntroductionThe objective of this study was to investigate the effects of dietary supplementation of tributyrin and anise mixture (TA) on growth performance, apparent nutrient digestibility, fecal noxious gas emission, fecal score, jejunal villus height, hematology parameters, and fecal microbiota of weaned pigs.MethodsA total of 150 21-day-old crossbred weaned pigs [(Landrace × Yorkshire) × Duroc] were used in a randomized complete block design experiment. All pigs were randomly assigned to 3 groups based on the initial body weight (6.19 ± 0.29 kg). Each group had 10 replicate pens with 5 pigs (three barrows and two gilts) per pen. The experimental period was 42 days and consisted of 3 phases (phase 1, days 1–7; phase 2, days 8–21; phase 3, days 22–42). Dietary treatments were based on a corn-soybean meal-basal diet and supplemented with 0.000, 0.075, or 0.150% TA.Results and discussionWe found that dietary supplementation of graded levels of TA linearly improved body weight, body weight gain, average daily feed intake, and feed efficiency (P < 0.05). TA supplementation also had positive effects on apparent dry matter, crude protein, and energy digestibility (P < 0.05) and jejunal villus height (P < 0.05). The emission of ammonia from feces decreased linearly with the dose of TA increased (P < 0.05). Moreover, TA supplementation was capable to regulate the fecal microbiota diversity, manifesting in a linearly increased Chao1 index and observed species and a linearly decreased Pielou's index (P < 0.05). The abundance of Lactobacillus reuteri, Lactobacillus amylovorus, Clostridium butyricum were increased, while the abundance of Prevotella copri was decreased, by treatment (P < 0.05). Therefore, we speculated that TA supplementation would improve growth performance and reduce fecal ammonia emission through improving nutrient digestibility, which was attributed to the increase of jejunal villus height and the regulation of fecal microbiota

    Star formation history and transition epoch of cluster galaxies based on the Horizon-AGN simulation

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    Cluster galaxies exhibit substantially lower star formation rates than field galaxies today, but it is conceivable that clusters were sites of more active star formation in the early universe. Herein, we present an interpretation of the star formation history (SFH) of group/cluster galaxies based on the large-scale cosmological hydrodynamic simulation, Horizon-AGN. We find that massive galaxies in general have small values of e-folding timescales of star formation decay (i.e., ``mass quenching'') regardless of their environment, whilst low-mass galaxies exhibit prominent environmental dependence. In massive host halos (i.e., clusters), the e-folding timescales of low-mass galaxies are further decreased if they reside in such halos for a longer period of time. This ``environmental quenching'' trend is consistent with the theoretical expectation from ram pressure stripping. Furthermore, we define a ``transition epoch'' as where cluster galaxies become less star-forming than field galaxies. The transition epoch of group/cluster galaxies varies according to their stellar and host cluster halo masses. Low-mass galaxies in massive clusters show the earliest transition epoch of 7.6\sim 7.6 Gyr ago in lookback time. However, it decreases to 5.2\sim 5.2 Gyr for massive galaxies in low-mass clusters. Based on our findings, we can describe cluster galaxy's SFH with regard to the cluster halo-to-stellar mass ratio.Comment: 17 pages, 10 figures, resubmitted to ApJ following first referee repor

    Delineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cells at the early stage of infection via dual RNA-seq analysis

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    Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease, a chronic debilitating disease in ruminants. To control this disease, it is crucial to understand immune evasion and the mechanism of persistence by analyzing the early phase interplays of the intracellular pathogens and their hosts. In the present study, host-pathogen interactions at the transcriptomic level were investigated in an in vitro macrophage infection model. When differentiated human THP-1 cells were infected with MAP, the expression of various genes associated with stress responses and metabolism was altered in both host and MAP at 3 h post-infection. MAP upregulates stress-responsive global gene regulators, such as two-component systems and sigma factors, in response to oxidative and cell wall stress. Downstream genes involved in type VII secretion systems, cell wall synthesis (polyketide biosynthesis proteins), and iron uptake were changed in response to the intracellular environment of macrophages. On the host side, upregulation of inflammatory cytokine genes was observed along with pattern recognition receptor genes. Notably, alterations in gene sets involved in arginine metabolism were observed in both the host and MAP, along with significant downregulation of NOS2 expression. These observations suggest that the utilization of metabolites such as arginine by intracellular MAP might affect host NO production. Our dual RNA-seq data can provide novel insights by capturing the global transcriptome with higher resolution, especially in MAP, thus enabling a more systematic understanding of host-pathogen interactions

    Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

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    Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne's disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits

    Large expert-curated database for benchmarking document similarity detection in biomedical literature search

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    Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

    System size, collision energy, and rapidity dependence of collective dynamics measured by the PHENIX experiment at RHIC

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    In high energy collisions, partons produced in the initial stage undergo multiple interactions and yield a collective motion as a whole. Recently, several questions have risen including how small the system can be for producing the collectivity, and how far in rapidity the collectivity extends. PHENIX has measured the particle flow in p + Au, d + Au, and 3He + Au collisions over several energies as well as over wider rapidity range. In this work, we summarize our results on the particle flow and discuss the implications for collectivity in small collision systems