A Parzen-based distance between probability measures as an alternative of summary statistics in Approximate Bayesian Computation

Approximate Bayesian Computation (ABC) are likelihood-free Monte Carlo methods. ABC methods use a comparison between simulated data, using different parameters drew from a prior distribution, and observed data. This comparison process is based on computing a distance between the summary statistics from the simulated data and the observed data. For complex models, it is usually difficult to define a methodology for choosing or constructing the summary statistics. Recently, a nonparametric ABC has been proposed, that uses a dissimilarity measure between discrete distributions based on empirical kernel embeddings as an alternative for summary statistics. The nonparametric ABC outperforms other methods including ABC, kernel ABC or synthetic likelihood ABC. However, it assumes that the probability distributions are discrete, and it is not robust when dealing with few observations. In this paper, we propose to apply kernel embeddings using an smoother density estimator or Parzen estimator for comparing the empirical data distributions, and computing the ABC posterior. Synthetic data and real data were used to test the Bayesian inference of our method. We compare our method with respect to state-of-the-art methods, and demonstrate that our method is a robust estimator of the posterior distribution in terms of the number of observations

Tensor decomposition processes for interpolation of diffusion magnetic resonance imaging

Diffusion magnetic resonance imaging (dMRI) is an established medical technique used for describing water diffusion in an organic tissue. Typically, rank-2 or 2nd-order tensors quantify this diffusion. From this quantification, it is possible to calculate relevant scalar measures (i.e. fractional anisotropy) employed in the clinical diagnosis of neurological diseases. Nonetheless, 2nd-order tensors fail to represent complex tissue structures like crossing fibers. To overcome this limitation, several researchers proposed a diffusion representation with higher order tensors (HOT), specifically 4th and 6th orders. However, the current acquisition protocols of dMRI data allow images with a spatial resolution between 1 mm3 and 2 mm3, and this voxel size is much bigger than tissue structures. Therefore, several clinical procedures derived from dMRI may be inaccurate. Concerning this, interpolation has been used to enhance the resolution of dMRI in a tensorial space. Most interpolation methods are valid only for rank-2 tensors and a generalization for HOT data is missing. In this work, we propose a probabilistic framework for performing HOT data interpolation. In particular, we introduce two novel probabilistic models based on the Tucker and the canonical decompositions. We call our approaches: Tucker decomposition process (TDP) and canonical decomposition process (CDP). We test the TDP and CDP in rank-2, 4 and 6 HOT fields. For rank-2 tensors, we compare against direct interpolation, log-Euclidean approach, and Generalized Wishart processes. For rank-4 and 6 tensors, we compare against direct interpolation and raw dMRI interpolation. Results obtained show that TDP and CDP interpolate accurately the HOT fields in terms of Frobenius distance, anisotropy measurements, and fiber tracts. Besides, CDP and TDP can be generalized to any rank. Also, the proposed framework keeps the mandatory constraint of positive definite tensors, and preserves morphological properties such as fractional anisotropy (FA), generalized anisotropy (GA) and tractography

VFISV: Very Fast Inversion of the Stokes Vector for the Helioseismic and Magnetic Imager

In this paper we describe in detail the implementation and main properties of a new inversion code for the polarized radiative transfer equation (VFISV: Very Fast inversion of the Stokes vector). VFISV will routinely analyze pipeline data from the Helioseismic and Magnetic Imager (HMI) on-board of the Solar Dynamics Observatory (SDO). It will provide full-disk maps (4096$\times$4096 pixels) of the magnetic field vector on the Solar Photosphere every 10 minutes. For this reason VFISV is optimized to achieve an inversion speed that will allow it to invert 16 million pixels every 10 minutes with a modest number (approx. 50) of CPUs. Here we focus on describing a number of important details, simplifications and tweaks that have allowed us to significantly speed up the inversion process. We also give details on tests performed with data from the spectropolarimeter on-board of the Hinode spacecraft.Comment: 23 pages, 9 figures (2 color). Submitted for publication to Solar Physic

Solar Intranetwork Magnetic Elements: bipolar flux appearance

The current study aims to quantify characteristic features of bipolar flux appearance of solar intranetwork (IN) magnetic elements. To attack such a problem, we use the Narrow-band Filter Imager (NFI) magnetograms from the Solar Optical Telescope (SOT) on board \emph{Hinode}; these data are from quiet and an enhanced network areas. Cluster emergence of mixed polarities and IN ephemeral regions (ERs) are the most conspicuous forms of bipolar flux appearance within the network. Each of the clusters is characterized by a few well-developed ERs that are partially or fully co-aligned in magnetic axis orientation. On average, the sampled IN ERs have total maximum unsigned flux of several 10^{17} Mx, separation of 3-4 arcsec, and a lifetime of 10-15 minutes. The smallest IN ERs have a maximum unsigned flux of several 10^{16} Mx, separations less than 1 arcsec, and lifetimes as short as 5 minutes. Most IN ERs exhibit a rotation of their magnetic axis of more than 10 degrees during flux emergence. Peculiar flux appearance, e.g., bipole shrinkage followed by growth or the reverse, is not unusual. A few examples show repeated shrinkage-growth or growth-shrinkage, like magnetic floats in the dynamic photosphere. The observed bipolar behavior seems to carry rich information on magneto-convection in the sub-photospheric layer.Comment: 26 pages, 14 figure

Isolation of Salmonella enterica in opossum (Didelphis aurita and Didelphis albiventris) of the São Paulo State, Brazil

No Brasil, não há relato de estudos de Salmonella em gambás, sendo assim, este trabalho tem por objetivo determinar a frequência de isolamento de Salmonella enterica em gambás (D. aurita e D. albiventris) no Estado de São Paulo. No período de janeiro de 2005 a dezembro de 2006, foram necropsiados 106 D. aurita e 40 D. albiventris e colhidos fragmentos de intestinos delgado, grosso e suabe da cloaca. As amostras foram plaqueadas diretamente em ágar Mac Conkey, paralelamente suspendidas nos caldos Rappaport-Vassiliadis e Tetrationato e posteriormente plaqueados em ágar XLT4. As colônias sugestivas de Salmonella foram confirmadas através de provas bioquímicas e sorotipagem. Encontrou-se Salmonella enterica em 17,0% (18/106) dos D. aurita. Destes, 50% apresentaram positividade no intestino delgado (ID), 88,9% no intestino grosso (IG) e 66,7% na cloaca. Da espécie S. enterica, as subespécies encontradas foram: diarizonae (11,1%) houtenae e enterica (5,5% cada um); enquanto da subespécie S. enterica enterica os sorotipos foram Newport (83,3%), Typhimurium e Cerro (5,5% cada um). Nos D. albiventris, 17,5% (7/40) eram positivos, sendo que se encontraram 42,8% no ID, 85,7% no IG e 71,4% na cloaca. O sorotipo mais prevalente também foi Newport (71,4%), seguido por Typhimurium, Bareilly e Thompson (14,3% cada um). Através dos resultados obtidos neste estudo pode-se comprovar a presença de Salmonella enterica no trato intestinal de gambás no Brasil.In Brazil there is not report of Salmonella in opossum, so then, the objective of this study is to determine the isolation frequency of Salmonella enterica in opossum in São Paulo State, Brazil. From January 2005 to December 2006, 106 D. aurita and 40 D. albiventris were necropsied and samples from small and large intestine and cloacal swab were collected. These samples were submitted to direct plating in Mac Conkey agar and parallel suspension in Rappaport-Vassiliadis and Tetrationate broths with posterior streaking in XLT4 agar. The characterization of the isolates was done through biochemical tests and serotyping. Salmonella enterica was found in 17.0% (18/106) of the D. aurita; 50% presented the bacteria in the small intestine (SI), 88.9% in the large intestine (LI) and 66.7% in the cloaca. Of the S. enterica were found the subspecies: diarizonae (11.1%), enterica and houtenae (5.5% each); and the serotypes of the S. enterica enterica were Newport (83.3%), Typhimurium and Cerro (5.5% each). In the D. albiventris 17.5% (7/40) were positive; 42.8% in the SI, 85.7% in the LI and 71.4% in the cloaca. Newport (71.4%) was also the most frequent serotype and the second were Typhimurium, Bareilly and Thompson (14.3% each). The presence of Salmonella enterica in the intestines of opossums in Brazil was proved

Demonstrating the Potential of Using Bio-Based Sustainable Polyester Blends for Bone Tissue Engineering Applications

YesHealthcare applications are known to have a considerable environmental impact and the use of bio-based polymers has emerged as a powerful approach to reduce the carbon footprint in the sector. This research aims to explore the suitability of using a new sustainable polyester blend (Floreon™) as a scaffold directed to aid in musculoskeletal applications. Musculoskeletal problems arise from a wide range of diseases and injuries related to bones and joints. Specifically, bone injuries may result from trauma, cancer, or long-term infections and they are currently considered a major global problem in both developed and developing countries. In this work we have manufactured a series of 3D-printed constructs from a novel biopolymer blend using fused deposition modelling (FDM), and we have modified these materials using a bioceramic (wollastonite, 15% w/w). We have evaluated their performance in vitro using human dermal fibroblasts and rat mesenchymal stromal cells. The new sustainable blend is biocompatible, showing no differences in cell metabolic activity when compared to PLA controls for periods 1-18 days. FloreonTM blend has proven to be a promising material to be used in bone tissue regeneration as it shows an impact strength in the same range of that shown by native bone (just under 10 kJ/m2) and supports an improvement in osteogenic activity when modified with wollastonite.We would like to acknowledge the Medical Research Council in the UK (MRC) for funding this research throughout a MRC Proximity to Discovery award (P2D) with grant number MC_PC_16084. We would also like to acknowledge CONACYT for funding DH RamosRodriguez’s work

Small-scale solar magnetic fields

As we resolve ever smaller structures in the solar atmosphere, it has become clear that magnetism is an important component of those small structures. Small-scale magnetism holds the key to many poorly understood facets of solar magnetism on all scales, such as the existence of a local dynamo, chromospheric heating, and flux emergence, to name a few. Here, we review our knowledge of small-scale photospheric fields, with particular emphasis on quiet-sun field, and discuss the implications of several results obtained recently using new instruments, as well as future prospects in this field of research.Comment: 43 pages, 18 figure

Thermally Triggered Hydrogel Injection Into Bovine Intervertebral Disc Tissue Explants Induces Differentiation Of Mesenchymal Stem Cells And Restores Mechanical Function.

We previously reported a synthetic Laponite® crosslinked pNIPAM-co-DMAc (L-pNIPAM-co-DMAc) hydrogel which promotes differentiation of mesenchymal stem cells (MSCs) to nucleus pulposus (NP) cells without additional growth factors. The clinical success of this hydrogel is dependent on: integration with surrounding tissue; the capacity to restore mechanical function; as well as supporting the viability and differentiation of delivered MSCs. Bovine NP tissue explants were injected with media (control), human MSCs (hMSCs) alone, acellular L-pNIPAM-co-DMAc hydrogel or hMSCs incorporated within the L-pNIPAM-co-DMAc hydrogel and maintained at 5% O2 for 6 weeks. Viability of native NP cells and delivered MSCs was maintained. Furthermore hMSCs delivered via the L-pNIPAM-co-DMAc hydrogel differentiated and produced NP matrix components: aggrecan, collagen type II and chondroitin sulphate, with integration of the hydrogel with native NP tissue. In addition L-pNIPAM-co-DMAc hydrogel injected into collagenase digested bovine discs filled micro and macro fissures, were maintained within the disc during loading and restored IVD stiffness. The mechanical support of the L-pNIPAM-co-DMAc hydrogel, to restore disc height, could provide immediate symptomatic pain relief, whilst the delivery of MSCs over time regenerates the NP extracellular matrix; thus the L-pNIPAM-co-DMAc hydrogel could provide a combined cellular and mechanical repair approach

Trends and outcome of neoadjuvant treatment for rectal cancer: A retrospective analysis and critical assessment of a 10-year prospective national registry on behalf of the Spanish Rectal Cancer Project

Introduction: Preoperative treatment and adequate surgery increase local control in rectal cancer. However, modalities and indications for neoadjuvant treatment may be controversial. Aim of this study was to assess the trends of preoperative treatment and outcomes in patients with rectal cancer included in the Rectal Cancer Registry of the Spanish Associations of Surgeons. Method: This is a STROBE-compliant retrospective analysis of a prospective database. All patients operated on with curative intention included in the Rectal Cancer Registry were included. Analyses were performed to compare the use of neoadjuvant/adjuvant treatment in three timeframes: I)2006–2009; II)2010–2013; III)2014–2017. Survival analyses were run for 3-year survival in timeframes I-II. Results: Out of 14, 391 patients, 8871 (61.6%) received neoadjuvant treatment. Long-course chemo/radiotherapy was the most used approach (79.9%), followed by short-course radiotherapy ± chemotherapy (7.6%). The use of neoadjuvant treatment for cancer of the upper third (15-11 cm) increased over time (31.5%vs 34.5%vs 38.6%, p = 0.0018). The complete regression rate slightly increased over time (15.6% vs 16% vs 18.5%; p = 0.0093); the proportion of patients with involved circumferential resection margins (CRM) went down from 8.2% to 7.3%and 5.5% (p = 0.0004). Neoadjuvant treatment significantly decreased positive CRM in lower third tumors (OR 0.71, 0.59–0.87, Cochrane-Mantel-Haenszel P = 0.0008). Most ypN0 patients also received adjuvant therapy. In MR-defined stage III patients, preoperative treatment was associated with significantly longer local-recurrence-free survival (p < 0.0001), and cancer-specific survival (p < 0.0001). The survival benefit was smaller in upper third cancers. Conclusion: There was an increasing trend and a potential overuse of neoadjuvant treatment in cancer of the upper rectum. Most ypN0 patients received postoperative treatment. Involvement of CRM in lower third tumors was reduced after neoadjuvant treatment. Stage III and MRcN + benefited the most