DeepOrgan: Multi-level Deep Convolutional Networks for Automated Pancreas Segmentation

Automatic organ segmentation is an important yet challenging problem for medical image analysis. The pancreas is an abdominal organ with very high anatomical variability. This inhibits previous segmentation methods from achieving high accuracies, especially compared to other organs such as the liver, heart or kidneys. In this paper, we present a probabilistic bottom-up approach for pancreas segmentation in abdominal computed tomography (CT) scans, using multi-level deep convolutional networks (ConvNets). We propose and evaluate several variations of deep ConvNets in the context of hierarchical, coarse-to-fine classification on image patches and regions, i.e. superpixels. We first present a dense labeling of local image patches via $P{-}\mathrm{ConvNet}$ and nearest neighbor fusion. Then we describe a regional ConvNet ($R_1{-}\mathrm{ConvNet}$) that samples a set of bounding boxes around each image superpixel at different scales of contexts in a "zoom-out" fashion. Our ConvNets learn to assign class probabilities for each superpixel region of being pancreas. Last, we study a stacked $R_2{-}\mathrm{ConvNet}$ leveraging the joint space of CT intensities and the $P{-}\mathrm{ConvNet}$ dense probability maps. Both 3D Gaussian smoothing and 2D conditional random fields are exploited as structured predictions for post-processing. We evaluate on CT images of 82 patients in 4-fold cross-validation. We achieve a Dice Similarity Coefficient of 83.6$\pm$6.3% in training and 71.8$\pm$10.7% in testing.Comment: To be presented at MICCAI 2015 - 18th International Conference on Medical Computing and Computer Assisted Interventions, Munich, German

Polyunsaturated fatty acids inhibit k_v1.4 by interacting with positively charged extracellular pore residues

Polyunsaturated fatty acids (PUFAs) modulate voltage-gated K(+) channel inactivation by an unknown site and mechanism. The effects of ω-6 and ω-3 PUFAs were investigated on the heterologously expressed K(v)1.4 channel. PUFAs inhibited wild-type K(v)1.4 during repetitive pulsing as a result of slowing of recovery from inactivation. In a mutant K(v)1.4 channel lacking N-type inactivation, PUFAs reversibly enhanced C-type inactivation (K(d), 15–43 μM). C-type inactivation was affected by extracellular H(+) and K(+) as well as PUFAs and there was an interaction among the three: the effect of PUFAs was reversed during acidosis and abolished on raising K(+). Replacement of two positively charged residues in the extracellular pore (H508 and K532) abolished the effects of the PUFAs (and extracellular H(+) and K(+)) on C-type inactivation but had no effect on the lipoelectric modulation of voltage sensor activation, suggesting two separable interaction sites/mechanisms of action of PUFAs. Charge calculations suggest that the acidic head group of the PUFAs raises the pK(a) of H508 and this reduces the K(+) occupancy of the selectivity filter, stabilizing the C-type inactivated state

Rice Bran as an Alternative Feedstuff in Broiler Nutrition and Impact of Liposorb® and Vitamin E-Se on Sustainability of Performance, Carcass Traits, Blood Biochemistry, and Antioxidant Indices

The impact of dietary rice bran with or without feed additives on the performance, carcasses, and blood profiles of chickens was examined. A total of 245 unsexed one-week-old broiler chicks were divided into seven groups, with seven replications of five chicks each. The treatments were: (1) control, (2) 5% rice bran, (3) 5% rice bran + 0.5 g/kg of Liposorb®, (4) 5% rice bran + 1 g/kg of vitamin E-Se, (5) 10% rice bran, (6) 10% rice bran + 0.5 g/kg Liposorb®, and (7) 10% rice bran + 1 g/kg of vitamin E–selenium. Considering the entire experimental period, it did not affect the in vivo performance of the broilers. However, all the experimental diets decreased dressing % compared with the control (p < 0.01) and the worst values were obtained for the 10% RB groups (75.7, 75.9, and 75.8%, respectively, for 10%RB, 10%RB + Liposorb, and 10%RB + Vit. E-Se groups). All the experimental diets decreased (p < 0.01) the albumin/globulin ratio due to an increased level of serum globulins. Differences in lipid profiles, antioxidants, and immunity parameters in plasma were not related to dietary treatments. In conclusion, the use of rice bran up to 10% in diets had no harmful effect on the overall growth performance of the broilers from 1 to 5 weeks of age. Still, carcass characteristics were negatively affected, except for heart percentage. In addition, the supplementation of Liposorb® or vitamin E-Se to rice bran diets did not recover these harmful effects. Thus, rice bran could be utilized at 10% in broiler diets when growth performance was considered; further research is required

Observing intermediate-mass black holes and the upper--stellar-mass gap with LIGO and Virgo

Using ground-based gravitational-wave detectors, we probe the mass function of intermediate-mass black holes (IMBHs) wherein we also include BHs in the upper mass gap $\sim 60-130~M_\odot$. Employing the projected sensitivity of the upcoming LIGO and Virgo fourth observing (O4) run, we perform Bayesian analysis on quasi-circular non-precessing, spinning IMBH binaries (IMBHBs) with total masses 50\mbox{--} 500\, M_\odot, mass ratios 1.25, 4, and 10, and dimensionless spins up to 0.95, and estimate the precision with which the source-frame parameters can be measured. We find that, at $2\sigma$, the mass of the heavier component of IMBHBs can be constrained with an uncertainty of $\sim 10-40\%$ at a signal-to-noise ratio of $20$. Focusing on the stellar-mass gap with new tabulations of the $^{12}\text{C}(\alpha, \gamma)^{16} \text{O}$ reaction rate and its uncertanties, we evolve massive helium core stars using \MESA\, to establish the lower and upper edge of the mass gap as $\simeq$\,59$^{+34}_{-13}$\,$M_{\odot}$ and $\simeq$\,139$^{+30}_{-14}$\,$M_{\odot}$ respectively, where the error bars give the mass range that follows from the $\pm 3\sigma$ uncertainty in the $^{12}\text{C}(\alpha, \gamma) ^{16} \text{O}$ nuclear reaction rate. We find that high resolution of the tabulated reaction rate and fine temporal resolution are necessary to resolve the peak of the BH mass spectrum. We then study IMBHBs with components lying in the mass gap and show that the O4 run will be able to robustly identify most such systems. Finally, we re-analyse GW190521 with a state-of-the-art aligned-spin waveform model, finding that the primary mass lies in the mass gap with 90\% credibility

Condensates formed by prion-like low-complexity domains have small-world network structures and interfaces defined by expanded conformations

Biomolecular condensates form via coupled associative and segregative phase transitions of multivalent associative macromolecules. Phase separation coupled to percolation is one example of such transitions. Here, we characterize molecular and mesoscale structural descriptions of condensates formed by intrinsically disordered prion-like low complexity domains (PLCDs). These systems conform to sticker-and-spacers architectures. Stickers are cohesive motifs that drive associative interactions through reversible crosslinking and spacers affect the cooperativity of crosslinking and overall macromolecular solubility. Our computations reproduce experimentally measured sequence-specific phase behaviors of PLCDs. Within simulated condensates, networks of reversible inter-sticker crosslinks organize PLCDs into small-world topologies. The overall dimensions of PLCDs vary with spatial location, being most expanded at and preferring to be oriented perpendicular to the interface. Our results demonstrate that even simple condensates with one type of macromolecule feature inhomogeneous spatial organizations of molecules and interfacial features that likely prime them for biochemical activity

Prevent Cracking in Deposition of Carbon Steel on Inconel 625

Welding procedure of clad steel including deposition of carbon steel on nickel base alloy usually gives unaccepted mechanical properties. Cracks were formed along type II boundary in nickel base alloy pass and a martensitic layer was formed in carbon steel pass. In this paper, cracks along type II boundary were prevented by lowering the martensitic start temperature (TMs) of the martensitic layer. Decreasing of TMs was obtained by two methods: Dilution method and Grain refining method. Three levels of TMs (approximately 350, 200, and 50⁰C) are obtained. The results showed that: cracks along type II boundary were prevented at TMs lower than 200⁰C; however type II boundary itself was prevented at TMs lower than 50. Also post weld heat treatment was necessary to achieve accepted impact properties

Polymorphism of growth hormone gene and its association with wool traits in Egyptian sheep breeds

Growth hormone (GH) gene has been described as a candidate gene for marker-assisted selection in different farm animals. The present study was designed to identify the polymorphism in GH gene and its association with variation of wool traits in Egyptian sheep breeds. Wool and blood samples were collected from 42 animals including two breeds (Barki and Rahmani) and one crossbred (Rahmani x Awase). Measurements of wool traits were analyzed and involved staple strength (Str), staple length (STL), fiber diameter (FD) and clean fleece yield (CFW). DNA was extracted from blood samples and a 365-bp fragment from exon V was amplified by polymerase chain reaction (PCR). Single strand conformation polymorphisim (SSCP) analysis showed two conformational patterns. The pattern I was recorded to be more frequent (83.3, 92.86 and 90%) than pattern II (16.7, 7.14 and 10%) in Barki, Rahmani and crossbred, respectively. The sequence analysis showed one single nucleotide polymorphism (C/T). The pattern I (allele T) has been found to affect CFW and FD than pattern II (allele C). Whereas, C allele was more pronounced for Str and STL. These traits are the most important parameters determining commercial values of wool that are preferred for clothing or carpets industry. The nucleotide sequences of C and T alleles were submitted to GenBank and have the accession numbers: KT250511 and KT250512, respectively. In conclusion, the present results provide evidence that there is a single nucleotide polymorphism within GH gene in Egyptian sheep breeds. This mutation was found to have some effects on wool traits. Therefore our data show interesting prospects in future selection programs for improving wool industry.Key words: Sheep, wool, growth hormone (GH) gene, polymorphism, single strand conformation polymorphism (SSCP)