GAMER with out-of-core computation

GAMER is a GPU-accelerated Adaptive-MEsh-Refinement code for astrophysical simulations. In this work, two further extensions of the code are reported. First, we have implemented the MUSCL-Hancock method with the Roe's Riemann solver for the hydrodynamic evolution, by which the accuracy, overall performance and the GPU versus CPU speed-up factor are improved. Second, we have implemented the out-of-core computation, which utilizes the large storage space of multiple hard disks as the additional run-time virtual memory and permits an extremely large problem to be solved in a relatively small-size GPU cluster. The communication overhead associated with the data transfer between the parallel hard disks and the main memory is carefully reduced by overlapping it with the CPU/GPU computations.Comment: 4 pages, 4 figures, conference proceedings of IAU Symposium 270 (eds. Alves, Elmegreen, Girart, Trimble

Graphic-Card Cluster for Astrophysics (GraCCA) -- Performance Tests

In this paper, we describe the architecture and performance of the GraCCA system, a Graphic-Card Cluster for Astrophysics simulations. It consists of 16 nodes, with each node equipped with 2 modern graphic cards, the NVIDIA GeForce 8800 GTX. This computing cluster provides a theoretical performance of 16.2 TFLOPS. To demonstrate its performance in astrophysics computation, we have implemented a parallel direct N-body simulation program with shared time-step algorithm in this system. Our system achieves a measured performance of 7.1 TFLOPS and a parallel efficiency of 90% for simulating a globular cluster of 1024K particles. In comparing with the GRAPE-6A cluster at RIT (Rochester Institute of Technology), the GraCCA system achieves a more than twice higher measured speed and an even higher performance-per-dollar ratio. Moreover, our system can handle up to 320M particles and can serve as a general-purpose computing cluster for a wide range of astrophysics problems.Comment: Accepted for publication in New Astronom

Rapid identification and application of Lactobacillus plantarum, Lactobacillus paracasei and Lactobacillus pentosus using multiplex polymerase chain reaction and species-specific primers, targeting 16S ribosomal RNA and recA genes

Background and Objective: Various products on the market contain probiotics such as lactic acid bacteria, which are promoted with a wide range of benefits. Functionality of these products is linked to the specific strains, bacterial species and viable cell counts. This study aimed to assess conformity of targeted lactic acid bacterial species and viable cell counts in commercially available probiotic products with their labeling, ensuring efficacy of the products. Material and Methods: Multiplex polymerase chain reaction technique was developed using specific primers to effectively differentiate lactic acid bacteria in probiotic products. Therefore, strains used in the products were targeted and relevant nucleotide sequence data were searched to select two sets of polymerase chain reaction primer pairs of L. pla-F/R and L. para-F/R, targeting 16S ribosomal RNA genes, and L .pen-F/R, targeting recA genes. Results and Conclusion: The individual primer sets produced the expected target products that matched the labeling for the tested strains of Lactobacillus plantarum, Lactobacillus paracasei and Lactobacillus pentosus. Then, specificity assessing was carried out using multiplex primer sets for single strains, pairwise combinations and triple combinations of lactic acid bacteria. After verifying specificity for all the three strains under similar polymerase chain reaction conditions, sensitivity of the multiplex polymerase chain reaction was investigated by assessing various dilutions of the three lactic acid bacterial strains and commercially available probiotic products. These findings demonstrated potential uses of multiplex polymerase chain reaction in lactic acid bacterial detection techniques. In conclusion, specific primer sets can be used in multiplex polymerase chain reaction to rapidly and effectively detect lactic acid bacterial strains in commercial products. Conflict of interest: The authors declare no conflict of interest. Lactic acid bacteria (LAB) are addressed for their beneficial effects on the human gastrointestinal tract, enhan-cing overall immune health. There are recent interests in development of functional LAB products. Demands for the probiotic functional foods are rapidly increasing due to the increased consumer awareness of food effects on health [1]. Researchers have assessed potential uses of probiotics in dairy and nondairy products and their viabilities during storage [2]. They have concluded that the final product should contain a minimum of 106-107 viable cells per serving to benefit consumer health [2]. Their studies have shown that mislabeling of probiotic species is common in commercial products [3]. Lack of appropriate identification of the strains and false efficacy claims have led to confusion. Probiotic products available in the market often use mixed strains. Thus, there are needs to monitor conformities of the labeled bacterial species and viable cell counts. Polymerase chain reaction (PCR) technique has success-fully been used to detect and differentiate viruses and bacteria in various foods [4]. Rapid and reliable nature of PCR provides a valuable tool for distinguishing closely related species within two groups of lactobacilli [5]. This technique has been used to rapidly identify Lactobacillus plantarum in kimchi [6]. Oligonucleotide primers have been developed from sequences between the 16S and 23S rRNA genes, enabling identification of various lactobacilli strains in dairy products and probiotics using PCR [7]. Further-more, strain-specific PCR can be used for the rapid identi-fication of lactobacilli isolated from food samples [8] and specific identification of ten common lactobacilli and bifi-dobacteria strains in fermented milks [9]. In this study, multiplex PCR method was developed to investigate applicability of molecular detection techniques for LAB using three sets of specific primers sourced from the literature. Moreover, 16S rRNA gene sequences were targeted to explore molecular LAB detection. By amplifying 16S rRNA and recA gene sequences through PCR, this study simultaneously detected three LAB strains as well as mixed LAB strains in the products. Sensitivity of detection was assessed to establish a simple, reliable rapid method appropriate for the effective identification of LAB strains in probiotic products. Materials and Methods 2.1 Bacterial strains and culture conditions The LAB strains were stored in a -80 °C freezer. Before the experiments, strains were activated twice using lactobacilli MRS broth (Difco, Detroit, MI, USA) supplemented with 0.05% (w/w) L-cysteine (Merck, Taipei, Taiwan). Strains were cultured under optimal growth conditions at 37 °C for 24 h. Reference strains were provided by the Bioresources Collection and Research Center (BCRC, Hsin-Chu, Tai-wan). The L. pentosus BCRC 17972 and 17973, L. plantar-um F7-1 and L. paracasei BCRC 12193, 12188, 12248 and 17002 were used in this study. Seven strains were used in the current study as well. The commercial probiotic product was purchased from Li-Fong, Tainan, Taiwan, for PCR detection. Each sachet of the bacterial powder contained a high level of viable probiotic cells with 5.0 × 1010 CFU.g-1. Specific strains included in the product were L. plantarum LP112, L. paracasei LPC188 and L. pentosus LPE588. ThIS study was carried out at Testing and Analysis Center for Food and Cosmetics, HungKuang University, Taichung City, Taiwan. 2.2 Genomic DNA preparation and polymerase chain reaction primers Total chromosomal DNA of the LAB cells was extracted using Blood and Tissue Genomic DNA Extraction Miniprep System (Viogene, Taipei, Taiwan) based on the manuf-acturer’s instructions. Specific primer sequences for the LAB detection are shown in Table 1. Experiments were repeated thrice [10-12]. 2.3 Polymerase chain reaction amplification Method was carried out according to [13]. For each PCR cycle, denaturation, annealing and extension were carried out at 94 °C for 60 s, 57 °C for 60 s and 72 °C for 120 s, respectively. Final extension was carried out at 72 °C for 5 min. 2.4 Sensitivity of the polymerase chain reaction assay A 24-h culture of the LAB strain was serially diluted 10-fold with sterile water. Purification of DNA was carried out as described in Section 2.2 [14]. 2.5 Polymerase chain reaction detection in the commercial probiotic product The probiotic product was purchased from Li-Fong, Tainan, Taiwan. After diluting the product to 108–106, 1 ml of the diluted sample was collected and DNA extraction was carried out. Then, 2 μl of the extracted DNA was used for multiplex PCR. Experiments were repeated thrice. Results and Discussion 3.1 Multiplex Polymerase chain reaction Figure 1 shows gel electrophoresis results of the multiplex PCR for DNA detection of individual LAB strains. Results demonstrated specificity of the three primer sets for their respective target genes in each strain. Small interferences were seen for L. plantarum F7-4 with no effects on amplification of other strains. Figure 1 shows gel electrophoresis results of multiplex PCR for DNA detection of two LAB strains. Results demonstrated that L.pla-F/R, L.pen-F/R and L.para-F/R primer sets could accurately amplify DNA from combination of two LAB strains. No nonspecific products were observed. Thus, 57°C was determined as the optimal annealing temperature for successful primer binding and DNA polymerase activity. Gel electrophoresis results validated effectiveness and specificity of the multiplex PCR for identifying and discriminating various LAB strains. These findings demonstrated applicability of the developed primer sets and verified their suitability for use in multiplex PCR. The optimized annealing temperature ensured robust amplifica-tion without nonspecific amplification products. 3.2 Sensitivity assessment of the lactic acid bacterial strains using multiplex polymerase chain reaction In Figure 2A, DNA extracted directly from the mixed cultures of three LAB strains (109, 108 and 107 cfu ml-1) are shown. At a concentration of 106 cfu ml-1, only L. paracasei (BCRC 12188) demonstrated amplifications in multiplex PCR, indicating that detection sensitivity of L. plantarum and L. pentosus was limited to 107 cfu ml-1. Figure 2B shows mixed cultures of the three LAB strains at similar concen-trations after preculture in MRS broth (37 °C, 24 h). Multi-plex PCR detected all the three strains at a sensitivity of 106 cfu ml-1, suggesting that L. plantarum and L. pentosus proliferated and could be detected. Figure 2 shows detection limits and proliferation capabilities of the three LAB strains using multiplex PCR. Results indicated that preculture of the mixed cultures in MRS broth improves detection sensitivity, enabling accurate identification of L. plantarum and L. pentosus strains at lower concentrations. 3.3 Preculture and mixed various concentrations of lactic acid bacterial strains using multiplex polymerase chain reaction Figure 3A shows gel electrophoresis results of the multiplex PCR carried out on DNA samples extracted from a mixture of L. plantarum (109 cfu ml-1) with two other LAB strains after preculture for 24 h. In Lanes 5–8, amplification products of L. pentosus and L. paracasei diluted to 106 cfu ml-1 were less expressed. The PCR amplification products of 106 cfu ml-1 DNA could be observed. The L. pentosus BCRC 17973 demonstrated a bacterial count of ~109 cfu ml-1 after 24 h of cultivation, whereas L. paracasei BCRC 12188 showed increased bacterial count, suggesting that preculture could enhance detection rate of low-concen-tration bacterial strains. Figure 3B shows gel electrophoresis results of the multiplex PCR on DNA extracted from a mixture of L. plantarum (108 cfu ml-1) with two other LAB strains after preculture for 24 h. The PCR products in Lanes 1–16 indicated that all the three sets of species-specific primer pairs yielded the expected PCR products for various concentrations of the bacterial suspensions after 24 h of preculture. Figure 3 shows effectiveness of the multiplex PCR in detecting L. plantarum at various concentrations in a mixed culture with other LAB strains. Results highlighted effects of preculture on enhancing assay detection rate and sensitivity. 3.4 Polymerase chain reaction detection of the commercial probiotic product Figure 4 demonstrates results of the multiplex PCR. Whether directly detected or precultured, the three LAB strains provided DNA amplification products from 107 to 109 cfu ml-1. It was suggested that 107 cfu ml-1 was the detection limit of the product (not detected when diluted to 106 cfu ml-1). The PCR-based species identification is a critical highly valuable tool for detecting and identifying bacteria. It offers advantages, including time efficiency and reliability in microbial identification. Compared to traditional methods such as culture-based techniques, PCR can provide results in a relatively short time. It eliminates the need of time-consuming cultivation of bacteria, allowing for further rapid identification and subsequent decision-making processes. In industrial uses, species identification is critical in selecting and developing bacterial strains appropriate for specific purposes. Whether in food, agriculture or biotechnology industries, PCR-based species identification enables researchers to screen and select the most appropriate bacterial species for desired characteristics and functions. The 16S rRNA gene in the ribosomal RNA of prokaryotes is the best molecular marker for bacterial evolutionary analysis. This is due to several gene characteristics, including its presence across various species, abundance, sufficient sequence length and presence of conserved and variable loci. The 16S rRNA gene is widely used in identifying lactobacilli and a commonly rapid technique for bacterial classification and identification in dairy products. Caro et al. reported that partial sequencing of 16S rRNA genes is often used for lactobacilli identification [15]. The RecA protein is a DNA recombinase that plays critical roles in DNA repair and recombination processes of bacteria. It is encoded by the recA gene in the genomes of various prokaryotic microorganisms. The recA gene and its corresponding protein have extensively been studied and used in various research, including evolutionary analysis, phylogenetic studies and identification of bacterial strains. Conserved nature and functional importance of the RecA protein make it a valuable molecular marker for understanding genetic relatedness and evolutionary relationships within bacteria. By comparing the recA gene sequences of various bacterial strains, researchers can have insights into their genetic diversity, evolutionary history and phylogenetic classification. Lu et al. developed a multiplex PCR method that could effectively be used in key vaginal microbiota evaluation in women with bacterial vaginosis [16]. You et al. used multiplex PCR to detect six species of L. acidophilus group [17]. Petri et al. used multiplex PCR for the rapid identification of wine-associated LAB [18]. Settanni et al. introduced a method and reported its state-of-the-art uses for microbial identification in foods and beverages [19]. Sciancalepore et al. described use of a simple, low-cost, rapid sensitive method based on droplet-based multiplex PCR directly on food matrices for the simultaneous detection of bacterial genes involved in biogenic amine synthesis [20]. Specific primers were designed based on similar sequences and multiplex PCR was optimized for the simultaneous identification of L. plantarum, L. pentosus and L. paraplantarum [21]. Sul et al. developed a multiplex PCR to detect Lactobacillus and Bifidobacterium spp. in commercial probiotic products [13]. Previously, Gram-negative broth enrichment was used in studies, followed by immunomagnetic separation multiplex PCR to enable the simultaneous detection of Salmonella spp. and enterohemorrhagic Escherichia coli in food samples, irrespective of their significant discrepancy in cell counts [22]. A PCR primer set derived from the seque-nce in 16S to 23S internal transcribed spacer (ITS) region was also developed for the specific detection of B. adoles-centis in probiotics. This primer set included potentials for inspecting dairy food and environmental samples [14]. To ensure food safety during direct vat inoculation of Paocai, a propidium monoazide-based quantitative PCR method was developed to quantify L. plantarum NCU116 fermentation starter, as well as Saccharomyces spp. and potentially present pathogenic bacteria [23]. Plate counting was carried out and demonstrated similar results to quantitative PCR analysis, indicating appropriateness and effectiveness of absolute quantitative PCR for rapidly detecting microbial composition in the Paocai system [23]. In a recent study, surveillance of Lactobacillus bacteremia was carried out using biochemical and conventional-PCR assays. However, these methods could not provide target quantification and might lead to false-positive results [24]. To address this limitation, a L. rhamnosus-specific quantitative PCR assay was developed. This assay delivers accurate and reproduci-ble results, leveraging specificity of a TaqMan probe, targ-eting unique 16S rDNA sequences of L. rhamnosus [24]. Conclusion In summary, the three sets of PCR primer combinations, targeting various LAB strains, demonstrated specificity and generated the expected amplicons during PCR amplifica-tion. Use of multiplex PCR in LAB genomic detection showed potentials and was appropriate for detecting various species in food products. Multiplex PCR decreased experimental cost and time, eliminating the need of time-consuming sequencing processes. Therefore, this method is expected to contribute to the reliability of probiotic labeling systems by facilitating strain identification. This molecular technique offers a valuable tool for quality control, product development and microbial monitoring of probiotic strains in various fields. Conflict of Interest The authors report no conflict of interest. Authors Contributions Conceptualization, TCC; methodology, LZY; data curation, LZY; writing, TCC. References Latif A, Shehzad A, Niazi S, Zahid A, Ashraf W, Iqbal MW, Rehman A, Riaz T, Aadil RM, Khan IM, Özogul F, Rocha JM, Esatbeyoglu T, Korma SA. Probiotics: mechanism of action, health benefits and their application in food industries. Front Microbiol. 2023; 14: 1216674. https://doi.org/10.3389/fmicb.2023.1216674 Jena R, Choudhury PK. Bifidobacteria in Fermented Dairy Foods: A Health Beneficial Outlook. Probiotics Antimicrob Proteins. 2023; Online ahead of print. https://doi.org/10.1007/s12602-023-10189-w Yeung PSM, Sanders ME, Kitts CL, Cano R, Tong PS. Species-specific identification of commercial probiotic strains. J Dairy Sci. 2002; 85 (5):1039-1051. https://doi.org/10.3168/jds.S0022-0302(02)74164-7  Pyar H, Liong MT, Masazurah AR, Lew LC, Peh KK. Study of genotypic characteristics of probiotics Lactobacillus using PCR. Asian Pac J Trop Dis. 2014; 4 (3): 225. https://doi.org/10.1016/S2222-1808(14)60515-6 Berthier F, Ehrlich S D. Rapid species identification within two groups of closely related lactobacilli using PCR primers that target the 16S/23S rRNA spacer region. FEMS Microbiol Lett. 1998; 161 (1): 97-106. https://doi.org/10.1111/j.1574-6968.1998.tb12934.x Kim TW, Min SG, Choi DH, Jo JS, Kim HY. Rapid identification of Lactobacillus plantarum in kimchi using polymerase chain reaction. J Microbiol Biotech. 2000;10(6): 881-884. Tilsala-Timisjaervi A, Alatossava T. Development of oligonucleotide primers from the 16S-23S rRNA intergenic sequences for identifying different dairy and probiotic lactic acid bacteria by PCR. Int J Food Microbiol. 1997; 35 (1): 49-56. https://doi.org/10.1016/S0168-1605(97)88066-X Rossetti L, Giraffa G. Rapid identification of dairy lactic acid bacteria by M13-generated, RAPD-PCR fingerprint databases. J Microbiol Methods. 2005; 63 (2): 135-144. https://doi.org/10.1016/j.mimet.2005.03.001 Lu W, Kong W, Yang P, Kong J. A one-step PCR-based method for specific identification of 10 common lactic acid bacteria and Bifidobacterium in fermented milk. Int Dairy J. 2015; 41, 7-12. https://doi.org/10.1016/j.idairyj.2014.08.020 Tajabadi N, Mardan M, Saari N, Mustafa S, Bahreini R, Manap MY. Identification of Lactobacillus plantarum, Lactobacillus pentosus and Lactobacillus fermentum from honey stomach of honeybee. Braz J Microbiol. 2014; 44(3): 717-722. https://doi.org/10.1590/s1517-83822013000300008 Sheu SJ, Hwang WZ, Chen HC, Chiang YC, Tsen HY. Development and use of tuf gene-based primers for the multiplex PCR detection of Lactobacillus acidophilus, Lactobacillus casei group, Lactobacillus delbrueckii and Bifidobacterium longum in commercial dairy products. J Food Prot. 2009; 72 (1): 93-100. https://doi.org/10.4315/0362-028x-72.1.93 Song Y, Kato N, Liu C, Matsumiya Y, Kato H, Watanabe K. Rapid identification of 11 human intestinal Lactobacillus species by multiplex PCR assays using group- and species-specific primers derived from the 16S-23S rRNA intergenic spacer region and its flanking 23S rRNA. FEMS Microbiol Lett. 2000;187(2):167-173. https://doi.org/10.1111/j.1574-6968.2000.tb09155.x Sul, YS, Kim HJ, Kim TW, Kim HY. Rapid identification of Lactobacillus and Bifidobacterium in probiotic products using multiplex PCR. J Microbiol Biotechnol. 2007; 17 (3):490-495. Tsai CC, Lai CH, Yu B, Tsen HY. Use of specific primers based on the 16S-23S internal transcribed spacer (ITS) region for the screening Bifidobacterium adolescentis in yogurt products and human stool samples. Anaerobe. 2008;14(4): 219-223. https://doi.org/10.1016/j.anaerobe.2008.05.001 Caro I, Bécares G, Fuentes L, Garcia-Armesto MR, Rúa J, Castro JM, Quinto EJ, Mateo J. Evaluation of three PCR primers based on the 16S rRNA gene for the identification of lactic acid bacteria from dairy origin. CyTA-J Food. 2015; 13 (2): 181-187. https://doi.org/10.1080/19476337.2014.934297 Lu S, Li Z, Chen X, Chen F, Yao H, Sun X, Cheng Y, Wang L, Dai P. Vaginal microbiota molecular profiling and diagnostic performance of artificial intelligence-assisted multiplex PCR testing in women with bacterial vaginosis: a single-center experience. Front Cell Infect Microbiol. 2024; 14:1377225. https://doi.org/10.3389/fcimb.2024.1377225  You I, Kim EB. Genome-based species-specific primers for rapid identification of six species of Lactobacillus acidophilus group using multiplex PCR. PLoS One. 2020; 15(3): e0230550. https://doi.org/10.1371/journal.pone.0230550  Petri A, Pfannebecker J, Fröhlich J, König H. Fast identification of wine related lactic acid bacteria by multiplex PCR. Food Microbiol. 2013; 33 (1): 48-54. https://doi.org/10.1016/j.fm.2012.08.011 Settanni L, Corsetti A. The use of multiplex PCR to detect and differentiate food- and beverage-associated micro-organisms: A review. J Microbiol Methods. 2007; 69 (1): 1-22. https://doi.org/10.1016/j.mimet.2006.12.008  Sciancalepore AG, Mele E, Arcadio V, Reddavide F, Grieco F, Spano G, Lucas P, Mita G, Pisignano D. Microdroplet-based multiplex PCR on chip to detect foodborne bacteria producing biogenic amines. 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Discovering important factors of intangible firm value by association rules

It is very important for investors to understand the critical factors affecting the value of firms before making investments. In knowledge-based economy, the method for creating firm value transfers from traditional physical assets to intangible knowledge. As intangible assets value is an important part of firm value, valuation of intangible assets becomes a widespread topic of interest in the future of economy. This paper applies association rules, one data mining technique, to discover critical factors affecting firm value in Taiwan and to provide a more flexible model than the traditional regression method. Based on collecting related factors found in literature, the results indicate that R&D intensity, family, participation in management, pyramids, profitability, and dividend are the six important factors, in which some are consistent with significant important variables in prior literature, but most of them are unique for Taiwan, one emerging economy

A peroxiredoxin cDNA from Taiwanofungus camphorata: role of Cys31 in dimerization

Peroxiredoxins (Prxs) play important roles in antioxidant defense and redox signaling pathways. A Prx isozyme cDNA (TcPrx2, 745 bp, EF552425) was cloned from Taiwanofungus camphorata and its recombinant protein was overexpressed. The purified protein was shown to exist predominantly as a dimer by sodium dodecyl sulfate-polyacrylamide gel electrolysis in the absence of a reducing agent. The protein in its dimeric form showed no detectable Prx activity. However, the protein showed increased Prx activity with increasing dithiothreitol concentration which correlates with dissociation of the dimer into monomer. The TcPrx2 contains two Cys residues. The Cys(60) located in the conserved active site is the putative active peroxidatic Cys. The role of Cys(31) was investigated by site-directed mutagenesis. The C31S mutant (C(31) → S(31)) exists predominantly as a monomer with noticeable Prx activity. The Prx activity of the mutant was higher than that of the corresponding wild-type protein by nearly twofold at 12 μg/mL. The substrate preference of the mutant was H2O2 > cumene peroxide > t-butyl peroxide. The Michaelis constant (K M) value for H2O2 of the mutant was 0.11 mM. The mutant enzyme was active under a broad pH range from 6 to 10. The results suggest a role of Cys(31) in dimerization of the TcPrx2, a role which, at least in part, may be involved in determining the activity of Prx. The C(31) residue does not function as a resolving Cys and therefore the TcPrx2 must follow the reaction mechanism of 1-Cys Prx. This TcPrx2 represents a new isoform of Prx family