Quantification of the spatial gradient of local volume fraction from tomography images

Asphalt concrete has three constituents: aggregate, asphalt binder and air voids. In the mixture, aggregates serve as a skeleton of the mixture; asphalt serves as a binder to hold the aggregates together; and air voids prevent asphalt concrete from bleeding to avoid plastic mixes. The properties of asphalt concrete are controlled by the interaction of these three components. In asphalt concrete, asphalt binder, voids and aggregates are not uniformly distributed. The local volume fractions of these constituents vary with spatial locations. As a result, there exist a spatial gradient of the local volume fractions between two locations. Due to the inhomogeneous distribution of the volumes of the constituents, the effective properties such as the modulus also vary with spatial locations, resulting in the stress concentration or strain localization. The purpose of this study is to make a preparation for modeling asphalt concrete in the continuum scheme by developing methods to quantify the local volume fractions of voids and the spatial gradients of the local volume fractions. X-ray tomography images were used to characterize the local volume fractions of voids and their gradients. By using Image-Pro Plus software as a platform, automated macros were developed to obtain the distribution of local volume fractions of voids as well as the gradients of local volume fractions. Statistical analysis of the experimental results shows that the field performance of the mixture is related to the mean local volume fractions of voids and their gradients. It may be concluded that local volume fraction and its gradient might be good field variables to characterize the internal structure of asphalt concrete. The experimental results are consistent with the predictions of several theories that use local volume fraction and the gradient of local volume fraction as field variables, and the field performance of the three mixes studied

ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval

<p>Abstract</p> <p>Background</p> <p>The need to retrieve or classify protein molecules using structure or sequence-based similarity measures underlies a wide range of biomedical applications. Traditional protein search methods rely on a pairwise dissimilarity/similarity measure for comparing a pair of proteins. This kind of pairwise measures suffer from the limitation of neglecting the distribution of other proteins and thus cannot satisfy the need for high accuracy of the retrieval systems. Recent work in the machine learning community has shown that exploiting the global structure of the database and learning the contextual dissimilarity/similarity measures can improve the retrieval performance significantly. However, most existing contextual dissimilarity/similarity learning algorithms work in an unsupervised manner, which does not utilize the information of the known class labels of proteins in the database.</p> <p>Results</p> <p>In this paper, we propose a novel protein-protein dissimilarity learning algorithm, ProDis-ContSHC. ProDis-ContSHC regularizes an existing dissimilarity measure <it>d_ij</it>by considering the contextual information of the proteins. The context of a protein is defined by its neighboring proteins. The basic idea is, for a pair of proteins (<it>i</it>, <it>j</it>), if their context <inline-formula><m:math xmlns:m="http://www.w3.org/1998/Math/MathML" name="1471-2105-13-S7-S2-i1"><m:mi mathvariant="script">N</m:mi><m:mrow><m:mo class="MathClass-open">(</m:mo><m:mrow><m:mi>i</m:mi></m:mrow><m:mo class="MathClass-close">)</m:mo></m:mrow></m:math></inline-formula> and <inline-formula><m:math xmlns:m="http://www.w3.org/1998/Math/MathML" name="1471-2105-13-S7-S2-i2"><m:mi mathvariant="script">N</m:mi><m:mrow><m:mo class="MathClass-open">(</m:mo><m:mrow><m:mi>j</m:mi></m:mrow><m:mo class="MathClass-close">)</m:mo></m:mrow></m:math></inline-formula> is similar to each other, the two proteins should also have a high similarity. We implement this idea by regularizing <it>d_ij</it>by a factor learned from the context <inline-formula><m:math xmlns:m="http://www.w3.org/1998/Math/MathML" name="1471-2105-13-S7-S2-i3"><m:mi mathvariant="script">N</m:mi><m:mrow><m:mo class="MathClass-open">(</m:mo><m:mrow><m:mi>i</m:mi></m:mrow><m:mo class="MathClass-close">)</m:mo></m:mrow></m:math></inline-formula> and <inline-formula><m:math xmlns:m="http://www.w3.org/1998/Math/MathML" name="1471-2105-13-S7-S2-i4"><m:mi mathvariant="script">N</m:mi><m:mrow><m:mo class="MathClass-open">(</m:mo><m:mrow><m:mi>j</m:mi></m:mrow><m:mo class="MathClass-close">)</m:mo></m:mrow></m:math></inline-formula>.</p> <p>Moreover, we divide the context to hierarchial sub-context and get the contextual dissimilarity vector for each protein pair. Using the class label information of the proteins, we select the relevant (a pair of proteins that has the same class labels) and irrelevant (with different labels) protein pairs, and train an SVM model to distinguish between their contextual dissimilarity vectors. The SVM model is further used to learn a supervised regularizing factor. Finally, with the new <b>S</b>upervised learned <b>Dis</b>similarity measure, we update the <b>Pro</b>tein <b>H</b>ierarchial <b>Cont</b>ext <b>C</b>oherently in an iterative algorithm--<b>ProDis-ContSHC</b>.</p> <p>We test the performance of ProDis-ContSHC on two benchmark sets, i.e., the ASTRAL 1.73 database and the FSSP/DALI database. Experimental results demonstrate that plugging our supervised contextual dissimilarity measures into the retrieval systems significantly outperforms the context-free dissimilarity/similarity measures and other unsupervised contextual dissimilarity measures that do not use the class label information.</p> <p>Conclusions</p> <p>Using the contextual proteins with their class labels in the database, we can improve the accuracy of the pairwise dissimilarity/similarity measures dramatically for the protein retrieval tasks. In this work, for the first time, we propose the idea of supervised contextual dissimilarity learning, resulting in the ProDis-ContSHC algorithm. Among different contextual dissimilarity learning approaches that can be used to compare a pair of proteins, ProDis-ContSHC provides the highest accuracy. Finally, ProDis-ContSHC compares favorably with other methods reported in the recent literature.</p

Effects of receptor dimerization on the interaction between the class I major histocompatibility complex-related Fc receptor and IgG

The neonatal Fc receptor (FcRn) transports maternal IgG from ingested milk in the gut to the bloodstream of newborn mammals. An FcRn dimer was observed in crystals of the receptor alone and of an FcRn-Fc complex, but its biological relevance was unknown. Here we use surface plasmon resonance-based biosensor assays to assess the role of FcRn dimerization in IgG binding. We find high-affinity IgG binding when FcRn is immobilized on a biosensor chip in an orientation facilitating dimerization but not when its orientation disrupts dimerization. This result supports a model in which IgG-induced dimerization of FcRn is relevant for signaling the cell to initiate endocytosis of the IgG-FcRn complex

High adsorption rate is detrimental to bacteriophage fitness in a biofilm-like environment.

BACKGROUND: Bacterial biofilm is ubiquitous in nature. However, it is not clear how this crowded habitat would impact the evolution of bacteriophage (phage) life history traits. In this study, we constructed isogenic lambda phage strains that only differed in their adsorption rates, because of the presence/absence of extra side tail fibers or improved tail fiber J, and maker states. The high cell density and viscosity of the biofilm environment was approximated by the standard double-layer agar plate. The phage infection cycle in the biofilm environment was decomposed into three stages: settlement on to the biofilm surface, production of phage progeny inside the biofilm, and emigration of phage progeny out of the current focus of infection. RESULTS: We found that in all cases high adsorption rate is beneficial for phage settlement, but detrimental to phage production (in terms of plaque size and productivity) and emigration out of the current plaque. Overall, the advantage of high adsorption accrued during settlement is more than offset by the disadvantages experienced during the production and emigration stages. The advantage of low adsorption rate was further demonstrated by the rapid emergence of low-adsorption mutant from a high-adsorption phage strain with the side tail fibers. DNA sequencing showed that 19 out of the 21 independent mutant clones have mutations in the stf gene, with the majority of them being single-nucleotide insertion/deletion mutations occurring in regions with homonucleotide runs. CONCLUSION: We conclude that high mutation rate of the stf gene would ensure the existence of side tail fiber polymorphism, thus contributing to rapid adaptation of the phage population between diametrically different habitats of benthic biofilm and planktonic liquid culture. Such adaptability would also help to explain the maintenance of the stf gene in phage lambda\u27s genome

Quantum Transport and Band Structure Evolution under High Magnetic Field in Few-Layer Tellurene

Quantum Hall effect (QHE) is a macroscopic manifestation of quantized states which only occurs in confined two-dimensional electron gas (2DEG) systems. Experimentally, QHE is hosted in high mobility 2DEG with large external magnetic field at low temperature. Two-dimensional van der Waals materials, such as graphene and black phosphorus, are considered interesting material systems to study quantum transport, because it could unveil unique host material properties due to its easy accessibility of monolayer or few-layer thin films at 2D quantum limit. Here for the first time, we report direct observation of QHE in a novel low-dimensional material system: tellurene.High-quality 2D tellurene thin films were acquired from recently reported hydrothermal method with high hole mobility of nearly 3,000 cm2/Vs at low temperatures, which allows the observation of well-developed Shubnikov-de-Haas (SdH) oscillations and QHE. A four-fold degeneracy of Landau levels in SdH oscillations and QHE was revealed. Quantum oscillations were investigated under different gate biases, tilted magnetic fields and various temperatures, and the results manifest the inherent information of the electronic structure of Te. Anomalies in both temperature-dependent oscillation amplitudes and transport characteristics were observed which are ascribed to the interplay between Zeeman effect and spin-orbit coupling as depicted by the density functional theory (DFT) calculations

Differential effects of sulforaphane in regulation of angiogenesis in a co-culture model of endothelial cells and pericytes

Aberrant neovascularization supports nutrients and the oxygen microenvironment in tumour growth, invasion and metastasis. Recapitulation of functional microvascular structures in vitro could provide a platform for the study of vascular conditions. Sulforaphane (SFN), an isothiocyanate, has been reported to possess chemopreventive properties. In the present study, the effects of SFN on cell proliferation and tubular formation have been investigated using endothelial cells (ECs) and pericytes in coculture. SFN showed a dose-dependent inhibition on the growth of ECs and pericytes with IC50 values 46.7 and 32.4 µM, respectively. SFN (5-20 µM) inhibited tube formation in a 3D coculture although a lower dose (1.25 µM) promoted 30% more endothelial tube formation than control. Moreover, SFN affected intercellular communication between ECs and pericytes via inhibition of angiogenic factor such as vascular endothelial growth factor (VEGF) expression in pericytes. However, the expression of its receptor (VEGFR-2) was found significantly increased in ECs. These effects were associated with down-regulation of prolyl hydroxylase domain-containing protein 1 and 2 (PHD1/2) and activation of hypoxia-inducible factor-1 (HIF) pathway by SFN. Furthermore, thioredoxin reductase-1 was also up-regulated by SFN treatment, suggesting that anti-oxidant and redox regulation are involved in angiogenesis. Taken together, the results of this study suggest that SFN differentially regulates endothelial cells and pericytes, and disrupting their interplay through the VEGF-VEGFR signalling pathway. Anti-angiogenesis property of SFN indicates it has potential role as anticancer agent

Wannier solitons in spin-orbit-coupled Bose-Einstein condensates in optical lattices with a flat-band

We investigate families of soliton solutions in a spin-orbit coupled Bose-Einstein condensate embedded in an optical lattice, which bifurcate from the nearly flat lowest band. Unlike the conventional gap solitons the obtained solutions have the shape well approximated by a Wannier function (or a few Wannier functions) of the underlying linear Hamiltonian with amplitudes varying along the family and with nearly constant widths. The Wannier solitons (WSs) sharing all symmetries of the system Hamiltonian are found to be stable. Such solutions allow for the construction of Wannier breathers, that can be viewed as nonlinearly coupled one-hump solitons. The breathers are well described by a few-mode model and manifest stable behavior either in an oscillatory regime with balanced average populations or in a self-trapping regime characterized by unbalanced atomic populations of the local potential minima (similarly to the conventional boson Josephson junction), with the frequencies controlled by the inter-atomic interactions.Comment: Accepted for publication in Physical Review