Parallel random number generators in Monte Carlo derivative pricing: An application-based test

Parallel pseudorandom number generators (PPRNG) that satisfy classical statistical tests may still demonstrate intra-stream and inter-stream correlations in real life applications. In order to investigate the suitability of a PPRNG for use in Monte Carlo pricing of financial derivatives, an application-based test is proposed to evaluate the bias and the standard error of the mean (SE) associated with the PPRNG as a gauge of intrastream and inter-stream correlations respectively. This test involves estimating the price of a vanilla European call option via Monte Carlo simulation, where the asset price at maturity is estimated by propagating the Black-Scholes stochastic differential equation via the Euler-Maruyama discretization scheme. The mean and SE profiles of the numerical results based on three PPRNG libraries (RNGSTREAM, TRNG and SPRNG) that implement parallel random numbers via sequence splitting strategies (RNGSTREAM and TRNG) and parameterization strategy (SPRNG) are compared. In terms of the bias and SE profiles, the best performing PPRNG constructed using the sequence splitting strategy is comparable to that constructed using parameterization, both use multiple recursive generators in their kernel. © de Gruyter 2012

Stapled hemorrhoidopexy: “mucosectomy or not only mucosectomy, this is the problem”

Introduction: Stapled hemorrhoidopexy was originally defined as a rectal mucosectomy. The aims of our retrospective, single-center study were to demonstrate if the excised specimen comprises only the mucosa or more wall rectal layers and if the latter excision should be considered a technical mistake with an increase in complications. Materials and Methods: We histopathologically analyzed surgical samples from patients who underwent stapled hemorrhoidopexy performed between 2014 and 2019. Patients were divided into three groups, according to the stapler used: Group A (single PPH®), Group B (double PPH®), and Group C (CPH34 HVTM). We evaluated the actual wall layers included in the stapled rectal ring. For every specimen, we reconstructed the history of the corresponding patient and the incidence of complications. Results: Of the 137 histological slides available, 13 were only mucosectomies (9.5%), and 124 presented also the submucosa and muscularis propria (90.5%)−50/58 patients in Group A, 28/28 in Group B, and 46/51 in Group C. No statistically significant difference in the rate of complications was found when stratifying patients according to the thickness of the resection [mucosectomy (M) or “full thickness” (FT)]. Discussion: Stapled hemorrhoidopexy is not a simple mucosectomy but a resection of the rectal wall with almost all its layers. This concept defines the entity of the surgical procedure and excludes a direct correlation with an increased rate of complications

Genome-wide analysis of LTR retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.)

Background: Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels. Results: After determining the relative genome size of each species, genomic DNA was isolated and subjected to Illumina sequencing. Then, different assembling and clustering approaches allowed exploring the repetitive component of all genomes. On average, repetitive DNA in Helianthus species represented more than 75% of the genome, being composed mostly by long terminal repeat retrotransposons. Also, the prevalence of Gypsy over Copia superfamily was observed and, among lineages, Chromovirus was by far the most represented. Although nearly all the same sublineages are present in all species, we found considerable variability in the abundance of diverse retrotransposon lineages and sublineages, especially between annual and perennial species. Conclusions: This large variability should indicate that different events of amplification or loss related to these elements occurred following species separation and should have been involved in species differentiation. Our data allowed us inferring on the extent of interspecific repetitive DNA variation related to LTR-RE abundance, investigating the relationship between changes of LTR-RE abundance and the evolution of the genus, and determining the degree of coevolution of different LTR-RE lineages or sublineages between and within species. Moreover, the data suggested that LTR-RE abundance in a species was affected by the annual or perennial habit of that species

Aflatoxin Production in Corn by Aspergillus flavus Relative to Inoculation, Planting Date, and Harvest Moisture in Louisiana (Research Report #102)

Contamination of food and feed grains by aflatoxins is a problem throughout the world. Corn produced in the southeastern United States has higher levels of aflatoxin than corn produced in the Corn Belt of the Midwest.https://digitalcommons.lsu.edu/agcenter_researchreports/1008/thumbnail.jp

Decoding the Genomic Landscape of Pomegranate: A Genome-Wide Analysis of Transposable Elements and Their Structural Proximity to Functional Genes

Transposable elements (TEs) significantly drive dynamic changes that characterize genome evolution. However, understanding the variability associated with TE insertions among different cultivars remains challenging. The pomegranate (Punica granatum L.) has yet to be extensively studied regarding the roles of TEs in the diversification of cultivars. Herein, we explored the genome distribution of TEs and its potential functional implications among four pomegranate cultivars, ‘Bhagwa’, ‘Dabenzi’, ‘Taishanhong’ and ‘Tunisia’, whose genome sequences are available. A total of 8404 full-length TEs were isolated. The content of TEs varied among the cultivars, ranging from 41.67% of ‘Taishanhong’ to 52.45% of ‘Bhagwa’. In all cultivars, the Gypsy superfamily of retrotransposons accounted for a larger genome proportion than the Copia superfamily. Seventy-three full-length TEs were found at the same genomic loci in all four cultivars. By contrast, 947, 297, 311, and 874 TEs were found exclusively in ‘Bhagwa’, ‘Dabenzi’, ‘Taishanhong’, and ‘Tunisia’ cultivars, respectively. Phylogenetic clustering based on the presence of TE insertions in specific loci reflected the geographic origins of the cultivars. The insertion time profiles of LTR-REs were studied in the four cultivars. Shared elements across the four cultivars exhibited, on average, a more ancient insertion date than those exclusive to three, two, or one cultivars. The majority of TEs were located within 1000 bp from the nearest gene. This localization was observed for 57% of DNA TEs and 55% of long-terminal repeat retrotransposons (LTR-RE). More than 10% of TEs resulted inserted within genes. Concerning DNA TEs, 3.91% of insertions occurred in introns, while 2.42% occurred in exons. As to LTR-REs, 4% of insertions occurred in exons and 1.98% in introns. Functional analysis of the genes lying close to TEs was performed to infer if differences in TE insertion can affect the fruit quality. Two TE insertions were found close to two genes encoding 4-coumarate--CoA ligase, an enzyme involved in the phenylpropanoid pathway. Moreover, a TIR/Mariner element was found within the exon of a gene encoding anthocyanidin reductase in the ‘Tunisia’ genotype, crucial in the biosynthesis of flavan-3-ols and proanthocyanidins, strictly correlated with the nutraceutical properties of pomegranate. Although functional and metabolomic studies are essential to elucidate the consequences of TE insertions, these results contribute to advancing our comprehension of the role of TEs in pomegranate genomics, providing insights for crop breeding

The application of molecular techniques for the rapid and sensitive detection of gastrointestinal pathogens directly in food

Conventional microbiological methods are slow, labour intensive and are unable to meet the demands for rapid food testing. Molecular methods, such as PCR, offer a rapid, sensitive and specific means of detecting pathogens, however loss of sensitivity and lack of robustness have been reported when PCR is applied to heterogeneous and complex food matrices. The aim of this study was to establish a rapid, reliable and sensitive molecular method to detect pathogens in food samples. Real-time PCR assays for the detection of Campylobacter jejuni and coli, Clostridium perfringens, Escherichia coli O157:H7, Listeria monocytogenes, Salmonella enterica and Staphylococcus aureus in food enrichment samples were developed. A novel organism was constructed using a gfp gene cloned into the chromosome of a non-pathogenic Escherichia coli. Viable cells of the modified strain were encapsulated in Lenticule discs and used as process control in the PCR assays. MagNA Pure™ automated extraction was shown to be robust and reliable for preparing bacterial DNA from food enrichment broths. The PCR assays and MagNA Pure™ was applied to enrichment broths inoculated with 558 naturally-contaminated food and environmental samples in a field trial. Concordance was found between PCR results and those obtained using standard culture methods. Loss of assay sensitivity or PCR inhibition was detected in 6 % (32) of the enrichment samples. To improve the sensitivity the L monocytogenes hlyA gene PCR was nested. The assay was applied for the sensitive non-cultural diagnosis of listeriosis, with L monocytogenes detected in 15 of 17 clinical samples from patients with suspected listeriosis. In conclusion, these assays provided a high throughput, robust, reliable PCR detection methods that could be used in clinical and food testing laboratories. The methods will be essential in outbreak situations and could be further developed to detecting bacterial pathogens, viruses, parasites, new and emerging pathogens

The Singular Evolution of Olea Genome Structure

The current view of plant genome evolution proposes that genome size has mainly been determined by polyploidisation and amplification/loss of transposons, with a minor role played by other repeated sequences, such as tandem repeats. In cultivated olive (Olea europaea subsp. europaea var. europaea), available data suggest a singular model of genome evolution, in which a massive expansion of tandem-repeated sequences accompanied changes in nuclear architecture. This peculiar scenario highlights the importance of focusing on Olea genus evolution, to shed light on mechanisms that led to its present genomic structure. Next-generation sequencing technologies, bioinformatics and in situ hybridisation were applied to study the genomic structure of five related Olea taxa, which originated at different times from their last common ancestor. On average, repetitive DNA in the Olea taxa ranged from ~59% to ~73% of the total genome, showing remarkable differences in terms of composition. Among repeats, we identified 11 major families of tandem repeats, with different abundances in the analysed taxa, five of which were novel discoveries. Interestingly, overall tandem repeat abundance was inversely correlated to that of retrotransposons. This trend might imply a competition in the proliferation of these repeat classes. Indeed, O. paniculata, the species closest to the Olea common ancestor, showed very few tandem-repeated sequences, while it was rich in long terminal repeat retrotransposons, suggesting that the amplification of tandem repeats occurred after its divergence from the Olea ancestor. Furthermore, some tandem repeats were physically localised in closely related O. europaea subspecies (i.e., cultivated olive and O. europaea subsp. cuspidata), which showed a significant difference in tandem repeats abundance. For 4 tandem repeats families, a similar number of hybridisation signals were observed in both subspecies, apparently indicating that, after their dissemination throughout the olive genome, these tandem repeats families differentially amplified maintaining the same positions in each genome. Overall, our research identified the temporal dynamics shaping genome structure during Olea speciation, which represented a singular model of genome evolution in higher plants

Simultaneous computer-assisted assessment of mucosal and serosal perfusion in a model of segmental colonic ischemia

BACKGROUND: Fluorescence-based enhanced reality (FLER) enables the quantification of fluorescence signal dynamics, which can be superimposed onto real-time laparoscopic images by using a virtual perfusion cartogram. The current practice of perfusion assessment relies on visualizing the bowel serosa. The aim of this experimental study was to quantify potential differences in mucosal and serosal perfusion levels in an ischemic colon segment. METHODS: An ischemic colon segment was created in 12 pigs. Simultaneous quantitative mucosal and serosal fluorescence imaging was obtained via intravenous indocyanine green injection (0.2 mg/kg), using two near-infrared camera systems, and computer-assisted FLER analysis. Lactate levels were measured in capillary blood of the colonic wall at seven regions of interest (ROIs) as determined with FLER perfusion cartography: the ischemic zone (I), the proximal and distal vascularized areas (PV, DV), and the 50% perfusion threshold proximally and distally at the mucosal and serosal side (P50M, P50S, D50M, D50S). RESULTS: The mean ischemic zone as measured (mm) for the mucosal side was significantly larger than the serosal one (56.3 ± 21.3 vs. 40.8 ± 14.9, p = 0.001) with significantly lower lactate values at the mucosal ROIs. There was a significant weak inverse correlation between lactate and slope values for the defined ROIs (r = - 0.2452, p = 0.0246). CONCLUSIONS: Mucosal ischemic zones were larger than serosal zones. These results suggest that an assessment of bowel perfusion from the serosal side only can underestimate the extent of ischemia. Further studies are required to predict the optimal resection margin and anastomotic site

HDAC inhibitor treatment of hepatoma cells induces both TRAIL-independent apoptosis and restoration of sensitivity to TRAIL

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Neuron splitting in compute-bound parallel network simulations enables runtime scaling with twice as many processors

Neuron tree topology equations can be split into two subtrees and solved on different processors with no change in accuracy, stability, or computational effort; communication costs involve only sending and receiving two double precision values by each subtree at each time step. Splitting cells is useful in attaining load balance in neural network simulations, especially when there is a wide range of cell sizes and the number of cells is about the same as the number of processors. For compute-bound simulations load balance results in almost ideal runtime scaling. Application of the cell splitting method to two published network models exhibits good runtime scaling on twice as many processors as could be effectively used with whole-cell balancing