A Central Partition of Molecular Conformational Space. IV. Extracting information from the graph of cells

In previous works [physics/0204035, physics/0404052, physics/0509126] a procedure was described for dividing the $3 \times N$-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the building of a combinatorial structure from data sampled in molecular dynamics trajectories: the graph of cells, that encodes the set of cells in conformational space that are visited by the system in its thermal wandering. Here we outline a set of procedures for extracting useful information from this structure: 1st) interesting regions in the volume occupied by the system in conformational space can be bounded by a polyhedral cone whose faces are determined empirically from a set of relations between the coordinates of the molecule, 2nd) it is also shown that this cone can be decomposed into a hierarchical set of smaller cones, 3rd) the set of cells in a cone can be encoded by a simple combinatorial sequence.Comment: added an intrduction and reference

A Central Partition of Molecular Conformational Space.III. Combinatorial Determination of the Volume Spanned by a Molecular System

In the first work of this series [physics/0204035] it was shown that the conformational space of a molecule could be described to a fair degree of accuracy by means of a central hyperplane arrangement. The hyperplanes divide the espace into a hierarchical set of cells that can be encoded by the face lattice poset of the arrangement. The model however, lacked explicit rotational symmetry which made impossible to distinguish rotated structures in conformational space. This problem was solved in a second work [physics/0404052] by sorting the elementary 3D components of the molecular system into a set of morphological classes that can be properly oriented in a standard 3D reference frame. This also made possible to find a solution to the problem that is being adressed in the present work: for a molecular system immersed in a heat bath we want to enumerate the subset of cells in conformational space that are visited by the molecule in its thermal wandering. If each visited cell is a vertex on a graph with edges to the adjacent cells, here it is explained how such graph can be built

Multimodal imaging of a vascularized idiopathic epiretinal membrane

PURPOSE: To report a case of vascularized idiopathic epiretinal membrane including the multimodal imaging. METHODS: Findings on clinical examination, color fundus photography, spectral-domain optical coherence tomography, optical coherence tomography angiography, and fluorescein angiography. RESULTS: Sixty-three-year-old woman with a previous rhegmatogenous retinal detachment (RRD) who presented with an asymptomatic idiopathic neovascular complex below an epiretinal membrane. It was assessed with fluorescein angiography, OCT and OCT-A. The vascularized ERM was already present previously to the retinal detachment. CONCLUSION: Our case report describes an example of idiopathic epiretinal membrane complicated by neovascularization; we hypothesized hypertension could be one of the factors in this case, as it may lead to decreased retinal perfusion and upregulation in vascular endothelial growth factor (VEGF). Multimodal imaging can help in detecting neovascularized ERM

Subsets of Inflammatory Cytokine Gene Polymorphisms are Associated with Risk of Carcinogenic Liver Fluke Opisthorchis viverrini-Associated Advanced Periductal Fibrosis and Cholangiocarcinoma.

Opisthorchis viverrini infection induces chronic inflammation, and a minor proportion of infected individuals develop advanced periductal fibrosis (APF) and cholangiocarcinoma (CCA). Inflammatory cytokines and/or their gene polymorphisms may link to these biliary pathologies. We therefore investigated associations among cytokine gene polymorphisms and cytokine production in 510 Thai cases infected with O. viverrini who presented with APF+ or APF−, as established by abdominal ultrasonography as well as in patients diagnosed with CCA. Levels of pro-inflammatory and anti-inflammatory cytokines were determined in culture supernatants after stimulation of peripheral blood mononuclear cells (PBMCs) with O. viverrini excretory-secretory (ES) products. Pro-inflammatory cytokines, IL-1β, IL-6, IFN-γ, LT-α, and TNF-α were significantly increased in CCA patients compared with non-CCA (APF− and APF+) cases. Polymorphisms in genes encoding IL-1β-511C/T, IL-6-174G/C, IFN-γ +874T/A, LT-α +252A/G, and TNF-α −308G/A were then investigated by using PCR-RFLP or allele specific-PCR (AS-PCR) analyses. In the CCA cases, LT-α +252A/G and TNF-α −308G/A heterozygous and homozygous variants showed significantly higher levels of these cytokines than the wild type. By contrast, levels of cytokines in wild type of IFN-γ +874T/A were significantly higher than the variants in CCA cases. IFN-γ +874T/A polymorphisms were associated with advanced periductal fibrosis, whereas IL-6 −174G/C polymorphisms were associated with CCA. To our knowledge, these findings provide the first demonstration that O. viverrini infected individuals carrying several specific cytokine gene polymorphisms are susceptible to develop fibrosis and CCA

3D sunken relief generation from a single image by feature line enhancement

Sunken relief is an art form whereby the depicted shapes are sunk into a given flat plane with a shallow overall depth. In this paper, we propose an efficient sunken relief generation algorithm based on a single image by the technique of feature line enhancement. Our method starts from a single image. First, we smoothen the image with morphological operations such as opening and closing operations and extract the feature lines by comparing the values of adjacent pixels. Then we apply unsharp masking to sharpen the feature lines. After that, we enhance and smoothen the local information to obtain an image with less burrs and jaggies. Differential operations are applied to produce the perceptive relief-like images. Finally, we construct the sunken relief surface by triangularization which transforms two-dimensional information into a three-dimensional model. The experimental results demonstrate that our method is simple and efficient

Nature and frequency of respiratory involvement in chronic progressive external ophthalmoplegia

Chronic progressive external ophthalmoplegia (CPEO) is a relatively common mitochondrial disorder. Weakness of the extra-ocular, limb girdle and laryngeal muscles are established clinical features. Respiratory muscle involvement however has never been studied systematically, even though respiratory complications are one of the main causes of death. We therefore determined the prevalence and nature of respiratory muscle involvement in 23 patients with genetically confirmed CPEO. The main finding was decreased respiratory muscle strength, both expiratory (76.8% of predicted, p = 0.002) and inspiratory (79.5% of predicted, p = 0.004). Although the inspiratory vital capacity (92.5% of predicted, p = 0.021) and the forced expiratory volume in 1 s (89.3% of predicted, p = 0.002) were below predicted values, both were still within the normal range in the majority of patients. Expiratory weakness was associated with a decreased vital capacity (ρ = 0.502, p = 0.015) and decreased peak expiratory flow (ρ = 0.422, p = 0.045). Moreover, expiratory muscle strength was lower in patients with limb girdle weakness (62.6 ± 26.1% of predicted vs. 98.9 ± 22.5% in patients with normal limb girdle strength, p = 0.003), but was not associated with other clinical features, subjective respiratory complaints, disease severity or disease duration. Since respiratory involvement in CPEO is associated with severe morbidity and mortality, the present data justify periodic assessment of respiratory functions in all CPEO patients

Towards sustainable agriculture: fossil-free ammonia

Citation: Pfromm, P. H. (2017). Towards sustainable agriculture: Fossil-free ammonia. Journal of Renewable and Sustainable Energy, 9(3), 034702. https://doi.org/10.1063/1.4985090About 40% of our food would not exist without synthetic ammonia (NH3) for fertilization. Yet, NH3 production is energy intensive. About 2% of the world's commercial energy is consumed as fossil fuels for NH3 synthesis based on the century-old Haber-Bosch (H.-B.) process. The state of the art and the opportunities for reducing the fossil energy footprint of industrial H.-B. NH3 synthesis are discussed. It is shown that even a hypothetical utterly revolutionary H.-B. catalyst could not significantly reduce the energy demand of H.-B. NH3 as this is governed by hydrogen production. Renewable energy-enabled, fossil-free NH3 synthesis is then evaluated based on the exceptional and continuing cost decline of renewable electricity. H.-B. syngas (H2, N2) is assumed to be produced by electrolysis and cryogenic air separation, and then supplied to an existing H.-B. synthesis loop. Fossil-free NH3 could be produced for energy costs of about $232 per tonne NH3 without claiming any economic benefits for the avoidance of about 1.5 tonnes of CO2 released per tonne NH3 compared to the most efficient H.-B. implementations. Research into alternatives to the H.-B. process might be best targeted at emerging markets with currently little NH3 synthesis capacity but significant future population growth such as Africa. Reduced capital intensity, good scale-down economics, tolerance for process upsets and contamination, and intermittent operability are some desirable characteristics of NH3 synthesis in less developed markets, and for stranded resources. Processes that are fundamentally different from H.-B. may come to the fore under these specific boundary conditions