2BAD: an application to estimate the parental contributions during two independent admixture events

Several approaches have been developed to calculate the relative contributions of parental populations in single admixture event scenarios, including Bayesian methods. In many breeds and populations, it may be more realistic to consider multiple admixture events. However, no approach has been developed to date to estimate admixture in such cases. This report describes a program application, 2BAD (for 2-event Bayesian ADmixture), which allows the consideration of up to two independent admixture events involving two or three parental populations and a single admixed population, depending on the number of populations sampled. For each of these models, it is possible to estimate several parameters (admixture, effective sizes, etc.) using an approximate Bayesian computation approach. In addition, the program allows comparing pairs of admixture models, determining which is the most likely given data. The application was tested through simulations and was found to provide good estimates for the contribution of the populations at the two admixture events. We were also able to determine whether an admixture model was more likely than a simple split model

Dirac fields in the background of a magnetic flux string and spectral boundary conditions

We study the problem of a Dirac field in the background of an Aharonov-Bohm flux string. We exclude the origin by imposing spectral boundary conditions at a finite radius then shrinked to zero. Thus, we obtain a behaviour of eigenfunctions which is compatible with the self-adjointness of the radial Hamiltonian and the invariance under integer translations of the reduced flux. After confining the theory to a finite region, we check the consistency with the index theorem, and evaluate its vacuum fermionic number and Casimir energy.Comment: 9 pages, 1 figure Two references added To be published in International Journal of Modern Physics

Liver haemangioma: common and uncommon findings and how to improve the differential diagnosis

Haemangiomas are common focal liver lesions, generally detected in the work-up of asymptomatic patients. From the pathological point of view, they can be classified as small (capillary) or large, with cavernous vascular spaces that may show thrombosis, calcifications and hyalinisation. The polymorphic imaging appearance of haemangiomas depends on their histological features and flow pattern. The widespread use of cross-sectional imaging has allowed an increased detection rate and a better characterisation of this benign tumour. Recent developments of ultrasound (US), computed tomography (CT) and magnetic resonance imaging (MRI) providing high spatial and temporal resolution, together with the use of new contrast agents and/or pulse sequences has broadened the spectrum of imaging findings, contributing to diagnostic refinement in difficult cases. The scope of the present article is to provide an overview of the range of appearances of haemangiomas, explored with recent cross-sectional imaging modalities, emphasising its atypical findings as explored by temporally resolved contrast-enhanced imaging

Oxaliplatin toxicity presenting as a liver nodule - case report

BACKGROUND: Oxaliplatin based chemotherapy is often used as adjuvant therapy in colon and rectal cancer. A reported side effect is Sinusoidal Obstruction Syndrome which is characterized by a spectrum of pathologic changes, from sinusoidal dilation, peri-sinusoidal haemorrhage, peliosis and nodular regenerative hyperplasia. Very rarely it can cause the development of liver nodules mimicking liver metastases. Herein, we report a case of Sinusoidal Obstruction Syndrome causing a liver nodule suspicious of liver metastasis on imaging. This is the third reported case of this complication of oxaliplatin toxicity, in which resection was performed and pathological diagnosis confirmed. CASE PRESENTATION: We report the case of a 59 year old man with stage III colon cancer who underwent sigmoidectomy followed by adjuvant chemotherapy with oxaliplatin. One year after surgery a liver nodule was detected and the patient underwent right hepatectomy. Pathology showed no liver nodule and diagnosed sinusoidal obstruction syndrome. CONCLUSION: We describe the third reported case of a liver lesion mimicking a liver metastasis after oxaliplatin-based chemotherapy for colon cancer. We suggest that in patients heavily treated with oxaliplatin with de novo liver nodules, this differential diagnosis should be considered. In particular, in this population of patients an intense imagiologic evaluation and even a preoperative biopsy should be pursued to confirm the diagnosis of malignancy and avoid overtreatment.info:eu-repo/semantics/publishedVersio

T-cell allorecognition of donor glutathione S-transferase T1 in plasma cell-rich rejection

AIM: To investigate the role of glutathione S-transferase T1 donor-specific T lymphocytes in plasma cell-rich rejection of liver allografts. METHODS: The study group included 22 liver transplant patients. Among them, 18 patients were mismatched for the glutathione S-transferase T1 (GSTT1) alleles (don+/rec-), and 4 were matched (don+/rec+). Seven of the mismatched patients produced anti-GSTT1 antibodies and developed plasma cell-rich rejection (former de novo immune hepatitis). For the detection of specific T lymphocytes, peripheral blood mononuclear cells were collected and stored in liquid nitrogen. The memory T cell response was studied by adding to the cell cultures to a mix of 39 custom-made, 15-mer overlapping peptides, which covered the entire GSTT1 amino acid sequence. The specific cellular response to peptides was analyzed by flow cytometry using the markers CD8, CD4, IL-4 and IFNγ. RESULTS: Activation of CD8+ T cells with different peptides was observed exclusively in the group of patients with plasma-cell rich rejection (3 out of 7), with production of IL-4 and/or IFNγ at a rate of 1%-4.92% depending on the peptides. The CD4+ response was most common and not exclusive for patients with the disease, where 5 out of 7 showed percentages of activated cells from 1.24% to 31.34%. Additionally, two patients without the disease but with the mismatch had cells that became stimulated with some peptides (1.45%-5.18%). Highly unexpected was the finding of a double positive CD4+CD8low T cell population that showed the highest degree of activation with some of the peptides in 7 patients with the mismatch, in 4 patients with plasma cell-rich rejection and in 3 patients without the disease. Unfortunately, CD4+CD8low cells represent 1% of the total number of lymphocytes, and stimulation could not be analyzed in 9 patients due to the low number of gated cells. Cells from the 4 patients included as controls did not show activation with any of the peptides. CONCLUSION: Patients with GSTT1 mismatch can develop a specific T-cell response, but the potential role of this response in the pathogenesis of plasma cell-rich rejection is unknown

IRX-2, a Novel Immunotherapeutic, Enhances Functions of Human Dendritic Cells

Background: In a recent phase II clinical trial for HNSCC patients, IRX-2, a cell-derived biologic, promoted T-cell infiltration into the tumor and prolonged overall survival. Mechanisms responsible for these IRX-2-mediated effects are unknown. We hypothesized that IRX-2 enhanced tumor antigen-(TA)-specific immunity by up-regulating functions of dendritic cells (DC). Methodology/Principal Findings: Monocyte-derived DC obtained from 18 HNSCC patients and 12 healthy donors were matured using IRX-2 or a mix of TNF-α, IL-1β and IL-6 ("conv. mix"). Multicolor flow cytometry was used to study the DC phenotype and antigen processing machinery (APM) component expression. ELISPOT and cytotoxicity assays were used to evaluate tumor-reactive cytotoxic T lymphocytes (CTL). IL-12p70 and IL-10 production by DC was measured by Luminex® and DC migration toward CCL21 was tested in transwell migration assays. IRX-2-matured DC functions were compared with those of conv. mix-matured DC. IRX-2-matured DC expressed higher levels (p<0.05) of CD11c, CD40, CCR7 as well as LMP2, TAP1, TAP2 and tapasin than conv. mix-matured DC. IRX-2-matured DC migrated significantly better towards CCL21, produced more IL-12p70 and had a higher IL12p70/IL-10 ratio than conv. mix-matured DC (p<0.05 for all). IRX-2-matured DC carried a higher density of tumor antigen-derived peptides, and CTL primed with these DC mediated higher cytotoxicity against tumor targets (p<0.05) compared to the conv. mix-matured DC. Conclusion: Excellent ability of IRX-2 to induce ex vivo DC maturation in HNSCC patients explains, in part, its clinical benefits and emphasizes its utility in ex vivo maturation of DC generated for therapy. © 2013 Schilling et al

Comparing the hierarchy of keywords in on-line news portals

The tagging of on-line content with informative keywords is a widespread phenomenon from scientific article repositories through blogs to on-line news portals. In most of the cases, the tags on a given item are free words chosen by the authors independently. Therefore, relations among keywords in a collection of news items is unknown. However, in most cases the topics and concepts described by these keywords are forming a latent hierarchy, with the more general topics and categories at the top, and more specialised ones at the bottom. Here we apply a recent, cooccurrence-based tag hierarchy extraction method to sets of keywords obtained from four different on-line news portals. The resulting hierarchies show substantial differences not just in the topics rendered as important (being at the top of the hierarchy) or of less interest (categorised low in the hierarchy), but also in the underlying network structure. This reveals discrepancies between the plausible keyword association frameworks in the studied news portals

Microfluidic systems for the analysis of the viscoelastic fluid flow phenomena in porous media

In this study, two microfluidic devices are proposed as simplified 1-D microfluidic analogues of a porous medium. The objectives are twofold: firstly to assess the usefulness of the microchannels to mimic the porous medium in a controlled and simplified manner, and secondly to obtain a better insight about the flow characteristics of viscoelastic fluids flowing through a packed bed. For these purposes, flow visualizations and pressure drop measurements are conducted with Newtonian and viscoelastic fluids. The 1-D microfluidic analogues of porous medium consisted of microchannels with a sequence of contractions/ expansions disposed in symmetric and asymmetric arrangements. The real porous medium is in reality, a complex combination of the two arrangements of particles simulated with the microchannels, which can be considered as limiting ideal configurations. The results show that both configurations are able to mimic well the pressure drop variation with flow rate for Newtonian fluids. However, due to the intrinsic differences in the deformation rate profiles associated with each microgeometry, the symmetric configuration is more suitable for studying the flow of viscoelastic fluids at low De values, while the asymmetric configuration provides better results at high De values. In this way, both microgeometries seem to be complementary and could be interesting tools to obtain a better insight about the flow of viscoelastic fluids through a porous medium. Such model systems could be very interesting to use in polymer-flood processes for enhanced oil recovery, for instance, as a tool for selecting the most suitable viscoelastic fluid to be used in a specific formation. The selection of the fluid properties of a detergent for cleaning oil contaminated soil, sand, and in general, any porous material, is another possible application

Developing serious games for cultural heritage: a state-of-the-art review

Although the widespread use of gaming for leisure purposes has been well documented, the use of games to support cultural heritage purposes, such as historical teaching and learning, or for enhancing museum visits, has been less well considered. The state-of-the-art in serious game technology is identical to that of the state-of-the-art in entertainment games technology. As a result, the field of serious heritage games concerns itself with recent advances in computer games, real-time computer graphics, virtual and augmented reality and artificial intelligence. On the other hand, the main strengths of serious gaming applications may be generalised as being in the areas of communication, visual expression of information, collaboration mechanisms, interactivity and entertainment. In this report, we will focus on the state-of-the-art with respect to the theories, methods and technologies used in serious heritage games. We provide an overview of existing literature of relevance to the domain, discuss the strengths and weaknesses of the described methods and point out unsolved problems and challenges. In addition, several case studies illustrating the application of methods and technologies used in cultural heritage are presented